Contacts of the strand formed by residues 319 - 330 (chain B) in PDB entry 3VZC


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 LEU 319 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  PHE*     4.2    11.4    -      -       +      -
    289B  TYR      3.6     5.2    -      -       -      +
    290B  VAL*     3.9    22.6    -      -       +      +
    302B  LEU*     4.2    19.5    -      -       +      -
    311B  HIS*     3.9    37.0    -      -       +      +
    312B  MET*     4.4    13.2    -      -       -      -
    315B  GLU*     5.0     9.7    -      -       -      +
    316B  CYS*     3.0    29.4    +      -       +      +
    317B  PRO      4.4     0.2    -      -       -      +
    318B  TYR*     1.3    77.3    -      -       -      +
    320B  VAL*     1.3    65.3    +      -       -      +
    321B  TYR*     4.4     0.4    +      -       +      -
   1001B  UUL      4.0    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     5.8     0.4    -      -       -      +
    287B  LEU      3.9     0.2    -      -       -      +
    288B  PHE*     3.3     9.9    -      -       -      +
    289B  TYR*     2.8    80.2    +      -       +      +
    291B  ARG*     4.5     5.8    -      -       -      +
    317B  PRO      4.0    15.5    -      -       -      +
    318B  TYR      4.1     3.4    -      -       -      +
    319B  LEU*     1.3    80.5    -      -       -      +
    321B  TYR*     1.3    67.4    +      -       -      +
    322B  VAL*     4.2    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277B  MET*     3.4    34.7    -      -       +      +
    286B  HIS*     2.9    45.7    +      +       +      -
    287B  LEU      3.4     9.9    -      -       -      -
    288B  PHE*     3.6    21.8    -      +       +      -
    312B  MET*     4.0    15.7    -      -       +      -
    319B  LEU*     4.4     0.6    +      -       +      -
    320B  VAL*     1.3    77.9    -      -       -      +
    322B  VAL*     1.3    76.9    +      -       -      +
    323B  PRO*     3.7    35.3    -      -       +      +
    149D  PRO*     5.6     2.5    -      -       +      -
    357D  ASN*     5.2     4.5    +      -       -      -
    360D  TRP*     4.1    24.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     3.8    44.4    -      -       +      +
    214B  PRO*     4.2     8.5    -      -       +      -
    287B  LEU*     2.8    41.9    +      -       +      +
    289B  TYR*     4.9     3.4    -      -       +      -
    320B  VAL*     4.2    15.0    -      -       +      -
    321B  TYR*     1.3    85.1    -      -       -      +
    323B  PRO*     1.3    83.7    -      -       +      +
    324B  VAL*     4.0     8.5    -      -       +      -
    102D  GLN*     6.2     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  PRO*     3.5     4.2    -      -       -      +
    215B  VAL*     3.1    38.6    +      -       +      -
    284B  VAL*     4.1    10.3    -      -       +      -
    285B  MET      3.6     6.7    -      -       -      +
    321B  TYR*     3.7    28.5    -      -       +      +
    322B  VAL*     1.3    90.8    -      -       +      +
    324B  VAL*     1.3    62.4    +      -       -      +
    102D  GLN*     6.1     2.2    -      -       -      +
    357D  ASN*     5.2    15.3    -      -       +      +
    360D  TRP*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     3.8    35.9    -      -       +      -
    213B  LEU      3.4    10.1    -      -       -      +
    214B  PRO*     4.1     1.6    -      -       +      -
    215B  VAL*     4.1     2.2    -      -       -      +
    284B  VAL*     3.7     4.2    -      -       -      -
    285B  MET*     2.9    62.2    +      -       +      +
    287B  LEU*     3.9    22.0    -      -       +      -
    322B  VAL*     4.0    12.1    -      -       +      +
    323B  PRO*     1.3    79.7    -      -       -      +
    325B  VAL*     1.3    64.1    +      -       -      +
    326B  ALA      3.8    13.5    -      -       -      +
    327B  PHE*     5.1     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  LEU*     2.9    41.5    +      -       +      +
    214B  PRO      4.6     2.5    -      -       -      +
    215B  VAL*     4.5    21.1    -      -       +      +
    218B  VAL      5.4     4.7    -      -       -      +
    237B  HIS*     4.3    19.5    -      -       +      +
    283B  GLY      3.3    20.2    -      -       -      +
    284B  VAL*     4.9     2.0    -      -       +      -
    285B  MET*     5.3     0.2    -      -       -      -
    324B  VAL*     1.3    76.3    -      -       -      +
    326B  ALA*     1.3    60.1    +      -       +      +
    353B  GLN*     3.3     5.9    -      -       -      +
    354B  VAL*     2.8    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     3.5     3.6    -      -       -      +
    213B  LEU*     2.9    29.6    +      -       +      +
    237B  HIS*     4.2    14.6    -      -       +      -
    238B  LEU*     4.0     6.7    -      -       +      -
    249B  TRP*     3.9    22.9    -      -       +      -
    285B  MET*     5.8     0.9    -      -       -      -
    324B  VAL*     3.7     6.5    -      -       -      +
    325B  VAL*     1.3    80.5    -      -       +      +
    327B  PHE*     1.3    67.6    +      -       -      +
    352B  GLY      3.1    15.0    -      -       -      +
    353B  GLN*     4.2     1.8    -      -       -      -
    354B  VAL*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  LEU*     4.1    11.7    -      -       +      -
    155B  LEU*     4.0    12.8    -      -       +      -
    169B  LEU*     3.4    35.0    -      -       +      -
    210B  LEU*     4.9     9.0    -      -       +      -
    211B  ALA      3.3    12.3    -      -       -      +
    212B  TYR*     4.2     6.7    -      -       +      -
    249B  TRP*     3.8    10.1    -      -       -      -
    260B  VAL*     5.7     2.7    -      -       +      -
    262B  ALA*     4.3     7.2    -      -       +      -
    285B  MET*     3.8    30.3    -      -       +      -
    287B  LEU*     5.0    10.5    -      -       +      -
    324B  VAL*     5.1     3.1    -      -       +      -
    326B  ALA*     1.3    78.3    -      -       -      +
    328B  ARG*     1.3    69.6    +      -       -      +
    329B  LEU*     4.6    15.0    -      -       +      -
    350B  VAL*     4.7     6.5    -      -       +      -
    351B  GLN*     3.2     6.4    -      -       -      +
    352B  GLY*     2.9    47.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  ARG      3.5     1.4    -      -       -      +
    210B  LEU*     3.5     3.8    -      -       -      +
    211B  ALA*     2.7    44.1    +      -       +      +
    239B  VAL*     3.5    13.3    +      -       -      +
    240B  PRO      3.4    14.8    +      -       -      -
    241B  LEU*     3.4    25.0    +      -       +      +
    243B  GLU      3.1    27.5    +      -       -      -
    244B  PRO*     4.4     1.8    -      -       -      +
    245B  VAL*     3.7    28.1    -      -       +      +
    249B  TRP*     4.2     9.0    -      -       +      -
    327B  PHE*     1.3    79.1    -      -       -      +
    329B  LEU*     1.3    63.9    -      -       -      +
    330B  GLU*     3.6    36.7    +      -       +      -
    350B  VAL      3.5    13.2    -      -       -      +
    351B  GLN*     3.1    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  LEU*     4.8     8.1    -      -       +      -
    171B  TRP*     3.5    61.2    -      -       +      -
    208B  GLY      5.1     0.2    -      -       -      -
    209B  ARG      3.4    18.6    -      -       -      +
    210B  LEU*     4.2     9.6    -      -       +      -
    260B  VAL*     4.0    25.8    -      -       +      -
    327B  PHE*     4.4    10.3    -      -       +      -
    328B  ARG*     1.3    75.1    -      -       -      +
    330B  GLU*     1.3    64.5    +      -       -      +
    331B  PRO*     4.2     4.2    -      -       +      +
    338B  PHE*     3.8    16.1    -      -       +      -
    349B  ALA*     3.5     1.6    -      -       -      -
    350B  VAL*     2.9    36.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  GLY*     4.2     0.2    -      -       -      -
    209B  ARG*     2.8    59.5    +      -       +      +
    241B  LEU*     5.6     2.2    -      -       -      -
    328B  ARG*     3.6    37.8    +      -       +      -
    329B  LEU*     1.3    76.3    -      -       -      +
    331B  PRO*     1.3    64.3    -      -       -      +
    332B  LYS*     3.2     8.4    +      -       -      +
    348B  GLU      3.8     4.3    -      -       -      +
    349B  ALA*     3.8    17.3    -      -       +      +
----------------------------------------------------------
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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