Contacts of the strand formed by residues 261 - 275 (chain B) in PDB entry 1VQM


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLN 261 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28080    U      2.7    41.8    +      -       -      +
   28090    G      3.8    27.1    +      -       -      +
     19B  SER*     4.2    14.9    +      -       -      +
     21B  SER      5.4     1.6    -      -       -      +
     23B  THR      4.6     0.7    -      -       -      +
     24B  PRO*     3.4    14.1    -      -       +      +
     25B  ARG*     2.8    52.1    +      -       -      +
     27B  ASN*     5.9     0.2    -      -       -      +
    203B  ALA*     5.2     1.3    -      -       +      +
    204B  GLY      3.6     8.5    -      -       -      +
    205B  VAL*     4.2     6.5    -      -       +      +
    260B  HIS*     1.3    73.3    -      -       -      +
    262B  ARG*     1.3    86.5    +      -       -      +
    263B  THR*     4.1     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27150    G      2.9    38.4    +      -       -      +
   27160    G      3.2    21.5    +      -       -      -
   28070    U      5.6     0.2    -      -       -      -
   28080    U      3.8     9.9    +      -       -      -
     13B  PHE*     3.3    51.9    +      -       -      +
     16B  ARG*     4.5     8.5    -      -       -      +
    202B  VAL      3.9     1.0    -      -       -      +
    203B  ALA*     3.2     3.6    -      -       -      +
    204B  GLY      2.9    34.8    +      -       -      +
    206B  THR*     3.5    24.5    -      -       +      -
    260B  HIS*     3.6    26.5    +      -       -      +
    261B  GLN*     1.3    94.1    +      -       -      +
    263B  THR*     1.3    63.8    +      -       -      +
    264B  GLU*     3.9     3.6    -      -       +      +
    302B  PRO*     4.2    11.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28070    U      3.5    28.5    +      -       -      +
   28080    U      2.8    23.9    +      -       -      -
     26B  PHE*     4.4    10.9    -      -       +      -
    201B  ASP*     4.4     6.7    -      -       +      -
    202B  VAL      3.5     7.4    -      -       -      +
    203B  ALA*     3.8    11.4    -      -       -      +
    261B  GLN*     4.1     2.9    +      -       -      -
    262B  ARG*     1.3    74.5    -      -       -      +
    264B  GLU*     1.3    60.1    +      -       -      +
    265B  LEU*     3.5    27.0    -      -       +      +
    312B  ARG*     4.1    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27150    G      2.7    32.4    +      -       -      +
   27160    G      3.6    23.0    +      -       -      +
   27650    C      3.3     2.8    -      -       -      +
   27660    A      4.1    12.6    -      -       -      +
    201B  ASP*     3.4     1.9    -      -       -      -
    202B  VAL*     2.7    42.7    +      -       +      +
    262B  ARG*     3.9     3.9    -      -       +      +
    263B  THR*     1.3    72.3    -      -       -      +
    265B  LEU*     1.3    62.8    +      -       -      +
    267B  LYS*     2.8    45.2    +      -       +      +
    300B  SER*     4.1     4.6    +      -       -      -
    302B  PRO*     3.8    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27660    A      2.7    34.3    +      -       -      +
   27670    C      4.5    11.4    -      -       -      -
   28060    C      3.9    12.1    -      -       -      +
   28070    U      4.4    10.1    -      -       -      -
    201B  ASP*     3.3    18.6    -      -       -      +
    263B  THR*     3.5    33.4    -      -       +      +
    264B  GLU*     1.3    79.3    -      -       -      +
    266B  ASN*     1.3    76.3    +      -       -      +
    267B  LYS*     3.5     2.8    +      -       -      +
    312B  ARG*     4.7     2.2    -      -       -      +
    316B  ARG*     3.3    44.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27660    A      3.7    23.1    -      -       -      +
   27670    C      2.8    30.3    +      -       -      +
    199B  TYR*     3.7    24.8    -      -       +      -
    200B  ALA      3.7     2.7    -      -       -      -
    201B  ASP*     3.0    10.0    +      -       -      +
    265B  LEU*     1.3    78.3    -      -       -      +
    267B  LYS*     1.3    61.3    +      -       -      +
    268B  ARG      3.6     2.8    +      -       -      -
    314B  ALA*     3.6    10.9    -      -       -      +
    316B  ARG*     3.1    28.8    +      -       -      +
    317B  PRO*     3.4    13.5    -      -       -      +
    318B  ASN*     3.5    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27650    C      2.7    29.0    +      -       -      +
   27660    A      3.3    10.9    +      -       -      +
    199B  TYR*     4.0     0.4    -      -       -      -
    200B  ALA*     2.6    44.2    +      -       -      +
    202B  VAL*     3.9    21.5    -      -       +      -
    264B  GLU*     2.8    53.3    +      -       -      +
    265B  LEU      4.2     3.1    -      -       -      +
    266B  ASN*     1.3    71.6    -      -       -      +
    268B  ARG*     1.3    62.7    +      -       -      +
    269B  LEU*     3.5     2.5    +      -       +      +
    297B  VAL*     3.6    18.6    -      -       +      -
    298B  LYS      3.9    12.1    -      -       -      +
    300B  SER*     3.1    25.3    +      -       -      +
    301B  VAL*     5.3     0.7    -      -       -      +
    302B  PRO*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LEU*     4.5     5.9    -      -       -      +
     56B  ASP*     3.6    16.6    +      -       -      +
    197B  GLY      3.8    19.0    +      -       -      +
    198B  GLU      3.6     4.0    -      -       -      +
    199B  TYR*     3.3    31.7    +      -       +      -
    266B  ASN      3.6     4.8    +      -       -      -
    267B  LYS*     1.3    71.9    -      -       -      +
    269B  LEU*     1.3    67.6    +      -       -      +
    270B  ILE*     3.4    17.4    +      -       -      +
    297B  VAL*     3.8     0.5    -      -       -      -
    298B  LYS*     2.8    56.9    +      -       +      +
    322B  ARG*     2.9    56.8    +      -       -      +
    325B  PRO*     3.0    29.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 269 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  MET*     5.7     2.0    -      -       -      -
    194B  PHE*     3.5    45.1    -      -       +      -
    195B  ARG      4.5     5.6    -      -       -      +
    196B  ALA*     4.6     4.9    -      -       -      -
    197B  GLY*     2.6    37.5    +      -       -      +
    198B  GLU*     2.9    21.0    +      -       +      +
    200B  ALA*     4.2    15.9    -      -       +      -
    267B  LYS      4.4     1.8    -      -       -      +
    268B  ARG*     1.3    72.1    -      -       -      +
    270B  ILE*     1.3    60.6    +      -       -      +
    271B  ASP      3.5     1.8    -      -       -      +
    272B  ILE*     4.6     7.6    -      -       +      -
    295B  THR*     3.9    24.7    -      -       +      -
    296B  LEU      3.8     3.1    -      -       -      +
    297B  VAL*     3.9    17.3    -      -       +      -
    311B  PHE*     4.2    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 270 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     4.4     9.0    -      -       +      -
     53B  LEU*     3.5    33.9    -      -       +      -
     69B  VAL*     4.9     4.3    -      -       +      -
     71B  VAL*     4.0    16.2    -      -       +      -
    196B  ALA*     3.9     3.4    -      -       -      +
    268B  ARG*     4.1    26.5    -      -       -      +
    269B  LEU*     1.3    74.3    -      -       -      +
    271B  ASP*     1.3    63.9    +      -       +      +
    296B  LEU*     2.7    25.8    +      -       +      +
    298B  LYS*     4.1    23.6    -      -       +      -
    325B  PRO*     3.9    21.3    -      -       +      +
    327B  VAL*     3.9    25.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  ALA*     4.0    10.8    -      -       -      +
    269B  LEU      3.5     2.2    -      -       -      -
    270B  ILE*     1.3    86.6    -      -       +      +
    272B  ILE*     1.3    75.1    +      -       -      +
    273B  GLY*     4.8     0.7    -      -       -      -
    294B  TYR*     3.3    27.4    +      -       -      +
    295B  THR*     3.4     4.2    -      -       -      +
    296B  LEU*     2.8    47.5    +      -       +      +
    327B  VAL*     4.8    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  THR*     5.1     0.2    -      -       -      +
    190B  MET*     3.7    37.2    -      -       +      +
    191B  ASN*     3.9    25.3    -      -       -      +
    194B  PHE*     3.5    34.1    -      -       +      +
    195B  ARG*     4.1     1.3    -      -       -      -
    196B  ALA*     3.8    25.9    -      -       +      +
    269B  LEU*     4.6     6.5    -      -       +      -
    271B  ASP*     1.3    86.4    +      -       -      +
    273B  GLY*     1.3    62.5    +      -       -      +
    294B  TYR      3.5     9.9    -      -       -      +
    295B  THR*     4.5     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271B  ASP*     4.8     1.6    -      -       -      -
    272B  ILE*     1.3    78.3    -      -       -      +
    274B  GLU*     1.3    63.5    +      -       -      +
    293B  PRO*     3.4     4.5    -      -       -      +
    294B  TYR*     2.9    47.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273B  GLY*     1.3    75.9    -      -       -      +
    275B  GLY*     1.3    64.8    +      -       -      +
    277B  GLU*     3.8    12.3    -      -       -      +
    292B  GLY*     3.1    21.7    -      -       -      +
    293B  PRO*     3.9    21.7    -      -       +      +
    294B  TYR*     3.5     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274B  GLU*     1.3    81.2    -      -       -      +
    276B  ASP*     1.3    57.8    +      -       -      -
    277B  GLU*     3.7     5.6    -      -       -      -
    290B  VAL*     3.8     5.2    -      -       -      +
    291B  ASP*     2.8    35.8    +      -       -      -
    292B  GLY      2.9    12.7    +      -       -      +
    294B  TYR*     4.1     3.5    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il