Contacts of the strand formed by residues 315 - 324 (chain B) in PDB entry 3R2W


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 ILE 315 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  PRO*     4.3     6.7    -      -       +      -
     75B  ILE*     4.0    40.4    -      -       +      -
    271B  VAL*     3.4    19.3    -      -       +      -
    272B  THR      3.2     2.2    -      -       -      -
    274B  LYS*     5.0     0.9    -      -       -      +
    283B  THR*     2.9    33.1    -      -       -      +
    284B  LEU*     3.1    51.4    -      -       +      +
    285B  THR*     6.0     0.2    -      -       +      -
    313B  PHE*     2.4    27.8    +      -       +      +
    314B  LYS*     1.3    75.6    -      -       -      +
    316B  PHE*     1.3    63.9    +      -       -      +
    375B  ASN*     4.2    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271B  VAL*     3.3     7.6    -      -       -      +
    272B  THR*     2.9    41.3    +      -       -      +
    273B  ASN      3.7    18.2    -      -       -      -
    274B  LYS*     4.5    12.3    -      -       +      -
    278B  ASP*     3.4    36.3    -      -       +      +
    281B  GLY*     4.1    24.2    -      -       -      -
    282B  GLY      3.7     8.3    -      -       -      +
    283B  THR*     4.8     2.2    -      -       +      +
    315B  ILE*     1.3    75.7    -      -       -      +
    317B  ASN*     1.3    82.2    +      -       +      +
    318B  THR*     5.8     0.4    -      -       -      -
    378B  ARG*     3.4    20.4    -      -       -      -
    381B  PHE*     3.7    26.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with ASN 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  MET*     3.1    38.9    -      -       +      +
    270B  GLU      4.6     1.1    -      -       -      -
    282B  GLY*     3.0    25.5    +      -       -      +
    293B  LEU*     4.0    19.7    -      -       +      +
    295B  GLU*     5.5     3.0    +      -       -      +
    316B  PHE*     1.3    99.6    -      -       +      +
    318B  THR*     1.3    76.7    +      -       -      +
    319B  ASN*     2.5    34.7    +      -       -      +
    321B  LEU*     6.0     0.2    -      -       -      +
    362B  GLY*     4.8     3.6    -      -       -      -
    381B  PHE*     4.7     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ASN*     5.1     3.3    +      -       -      -
    243B  ASN*     4.4     2.4    +      -       -      +
    270B  GLU*     3.1    32.7    +      -       +      +
    271B  VAL*     3.3    12.8    +      -       -      -
    272B  THR*     3.8     7.3    +      -       -      +
    316B  PHE*     5.6     0.7    -      -       -      -
    317B  ASN*     1.3    79.2    +      -       -      +
    319B  ASN*     1.3    67.2    +      -       -      +
    320B  ASN*     3.3    32.7    +      -       +      +
    376B  VAL*     4.5     2.1    -      -       +      +
    380B  ARG      4.0     7.0    -      -       -      +
    381B  PHE*     3.6    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  LEU*     4.0    23.8    -      -       -      +
    212B  HIS*     3.8    29.3    +      -       -      -
    238B  VAL*     3.9     5.8    -      -       -      +
    239B  SER*     4.0     7.3    -      -       -      -
    240B  ASN*     4.2    19.1    +      -       -      +
    317B  ASN*     2.5    34.3    +      -       -      +
    318B  THR*     1.3    74.4    -      -       -      +
    320B  ASN*     1.3    64.6    +      -       -      +
    321B  LEU*     3.5    22.7    -      -       -      +
    361B  VAL*     4.6     2.4    -      -       -      +
    362B  GLY      4.5     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  PHE*     4.2     6.7    -      -       +      -
    238B  VAL      3.5     3.4    -      -       -      -
    239B  SER*     3.7     9.1    -      -       -      -
    240B  ASN      4.8     1.2    -      -       -      +
    243B  ASN*     3.8     7.3    -      -       -      +
    246B  ALA*     3.5    30.2    -      -       -      +
    268B  VAL      4.2     0.2    -      -       -      +
    269B  MET*     3.6     0.5    -      -       -      +
    270B  GLU*     3.0    59.1    +      -       +      +
    318B  THR*     3.0    20.7    +      -       +      +
    319B  ASN*     1.3    81.0    +      -       -      +
    321B  LEU*     1.3    63.7    +      -       -      +
    380B  ARG*     3.3    15.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  PHE*     3.0     8.9    -      -       -      -
    238B  VAL*     2.9    43.6    +      -       +      -
    267B  PHE*     3.3    37.5    -      -       +      -
    268B  VAL      3.4     5.2    -      -       -      +
    269B  MET*     3.9    14.1    -      -       +      -
    317B  ASN*     5.4     0.2    -      -       -      +
    319B  ASN*     3.5    26.7    -      -       -      +
    320B  ASN*     1.3    81.8    -      -       -      +
    322B  TRP*     1.3    61.3    +      -       -      +
    323B  ILE*     4.1    16.2    -      -       +      -
    361B  VAL*     3.5    30.3    -      -       +      -
    362B  GLY*     4.3     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  LEU*     3.4    21.5    -      -       +      -
    235B  TYR*     4.6     6.4    -      -       +      -
    236B  ILE      3.3     6.7    -      -       -      -
    237B  PHE*     3.6    39.6    -      +       +      -
    248B  VAL*     4.1    20.2    -      -       +      -
    249B  ASP      4.2    10.1    -      -       -      -
    252B  ILE*     3.5    37.0    -      -       +      +
    253B  LEU*     3.4    25.6    -      -       +      -
    256B  LEU*     3.6    31.6    -      -       +      -
    267B  PHE*     3.4     4.3    +      -       -      -
    268B  VAL*     2.7    60.4    +      -       +      +
    270B  GLU*     3.8    16.4    +      -       +      -
    321B  LEU*     1.3    74.5    -      -       -      +
    323B  ILE*     1.3    63.8    +      -       -      +
    380B  ARG*     4.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  ILE*     5.9     0.7    -      -       +      -
    216B  TYR*     4.0    30.5    -      -       +      +
    235B  TYR*     3.3     7.3    -      -       -      -
    236B  ILE*     2.7    62.3    +      -       +      +
    238B  VAL*     5.0    12.1    -      -       +      -
    266B  GLU      3.5    11.9    -      -       -      +
    267B  PHE*     3.6    17.7    -      -       +      -
    321B  LEU*     4.2    16.8    -      -       +      -
    322B  TRP*     1.3    79.9    -      -       -      +
    324B  SER*     1.3    65.7    +      -       -      +
    328B  VAL*     4.5     7.6    -      -       +      -
    361B  VAL*     5.2     3.4    -      -       +      -
    368B  PHE*     3.5    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  GLU      3.5     8.8    +      -       -      -
    235B  TYR*     3.6    24.2    -      -       -      -
    266B  GLU*     3.0    25.6    +      -       -      +
    323B  ILE*     1.3    70.7    -      -       -      +
    325B  LEU*     1.3    54.2    +      -       -      +
    326B  ALA*     3.4    13.0    -      -       -      +
    327B  ALA*     2.5    44.0    +      -       -      +
    328B  VAL*     3.1    11.8    +      -       -      +
----------------------------------------------------------
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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