Contacts of the strand formed by residues 319 - 330 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288C  PHE*     4.0    19.5    -      -       +      -
    289C  TYR      3.4    11.0    -      -       -      +
    290C  VAL*     4.0    18.3    -      -       +      +
    302C  LEU*     4.2    27.6    -      -       +      -
    311C  HIS*     4.3    23.1    -      -       +      +
    312C  MET*     4.4    16.1    -      -       +      +
    315C  GLU*     6.0     0.2    -      -       -      -
    316C  CYS*     3.1    31.4    +      -       +      +
    317C  PRO      4.6     1.1    -      -       -      +
    318C  TYR*     1.3    75.1    -      -       -      +
    320C  VAL*     1.3    76.9    +      -       -      +
    321C  TYR      4.2     0.7    +      -       -      -
   1001C  UUL      4.4     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 320 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  TYR*     5.5     0.2    -      -       -      +
    287C  LEU      4.5     0.2    -      -       -      -
    288C  PHE*     3.4     5.0    -      -       -      -
    289C  TYR*     2.8    82.8    +      -       +      +
    291C  ARG*     3.6    23.8    -      -       -      +
    317C  PRO      4.6     1.1    -      -       -      +
    318C  TYR      4.3     0.9    -      -       -      +
    319C  LEU*     1.3    83.0    -      -       -      +
    321C  TYR*     1.3    63.1    +      -       -      +
    322C  VAL*     3.9    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 321 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277C  MET*     3.7    31.8    -      -       +      +
    286C  HIS*     2.9    50.1    -      +       +      -
    287C  LEU      3.4    10.8    -      -       -      -
    288C  PHE*     3.6    20.4    -      +       +      -
    312C  MET*     3.7    23.1    -      -       +      -
    319C  LEU      4.2     1.2    +      -       -      -
    320C  VAL*     1.3    76.7    -      -       -      +
    322C  VAL*     1.3    74.9    +      -       -      +
    323C  PRO*     3.3    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 322 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  TYR*     3.5    43.5    -      -       +      +
    214C  PRO*     3.8    11.4    -      -       +      -
    287C  LEU*     3.0    38.7    +      -       +      +
    289C  TYR*     5.3     1.8    -      -       +      -
    320C  VAL*     3.9    17.3    -      -       +      -
    321C  TYR*     1.3    84.1    -      -       -      +
    323C  PRO*     1.4    82.0    -      -       +      +
    324C  VAL*     3.4     3.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 323 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214C  PRO*     3.4     6.1    -      -       -      +
    215C  VAL*     3.1    38.1    +      -       +      +
    284C  VAL*     3.9    11.7    -      -       +      -
    285C  MET      3.6     7.0    -      -       -      +
    321C  TYR*     3.3    33.4    -      -       +      +
    322C  VAL*     1.4    87.5    -      -       +      +
    324C  VAL*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 324 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  TYR*     3.6    29.6    -      -       +      -
    213C  LEU      3.5    10.3    -      -       -      +
    214C  PRO*     4.1     0.7    -      -       -      -
    215C  VAL*     3.8     2.0    -      -       -      +
    284C  VAL*     3.6     6.1    -      -       -      -
    285C  MET*     2.8    58.6    +      -       +      +
    287C  LEU*     3.7    22.7    -      -       +      -
    322C  VAL*     3.4    15.0    -      -       +      +
    323C  PRO*     1.3    79.0    -      -       -      +
    325C  VAL*     1.3    65.8    +      -       -      +
    326C  ALA      3.8    18.8    -      -       -      +
    327C  PHE*     5.0     1.1    -      -       +      -
    354C  VAL*     4.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 325 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213C  LEU*     3.0    41.4    +      -       +      +
    214C  PRO      4.8     1.1    -      -       -      +
    215C  VAL*     4.5    23.1    -      -       +      +
    237C  HIS*     4.2    19.3    -      -       +      +
    283C  GLY      3.6    18.4    -      -       -      +
    284C  VAL*     5.4     1.3    -      -       +      -
    324C  VAL*     1.3    75.7    -      -       -      +
    326C  ALA*     1.3    65.1    +      -       +      +
    353C  GLN*     3.4     5.9    -      -       +      +
    354C  VAL*     3.0    38.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 326 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  TYR*     3.4     3.5    -      -       -      +
    213C  LEU*     3.0    24.9    +      -       +      -
    237C  HIS*     4.3     8.7    -      -       +      -
    238C  LEU*     4.0     6.7    -      -       +      -
    249C  TRP*     3.7    26.0    -      -       +      -
    285C  MET*     5.6     0.4    -      -       -      -
    324C  VAL*     3.6     8.2    -      -       -      +
    325C  VAL*     1.3    91.5    -      -       +      +
    327C  PHE*     1.3    67.2    +      -       -      +
    352C  GLY      3.1    14.8    -      -       -      +
    353C  GLN*     4.4     1.1    -      -       -      -
    354C  VAL*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 327 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153C  LEU*     4.1     6.1    -      -       +      -
    155C  LEU*     3.9    17.5    -      -       +      -
    169C  LEU*     3.8    32.8    -      -       +      -
    210C  LEU*     4.7     5.2    -      -       +      -
    211C  ALA      3.3    13.0    -      -       -      +
    212C  TYR*     3.9     9.0    -      -       +      +
    249C  TRP*     3.7     7.6    -      -       -      -
    260C  VAL*     5.8     2.0    -      -       +      -
    262C  ALA*     3.9     8.3    -      -       +      -
    285C  MET*     3.3    35.2    -      -       +      -
    287C  LEU*     4.6    15.7    -      -       +      -
    324C  VAL*     5.0     0.7    -      -       +      -
    326C  ALA*     1.3    75.6    -      -       -      +
    328C  ARG*     1.3    71.0    +      -       -      +
    329C  LEU*     4.2     9.9    -      -       +      -
    350C  VAL*     4.1    14.4    -      -       +      -
    351C  GLN*     3.1     7.9    -      -       -      +
    352C  GLY*     3.0    45.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 328 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  ARG      3.5     3.3    -      -       -      +
    210C  LEU*     3.5     2.3    -      -       -      +
    211C  ALA*     2.7    42.0    +      -       +      +
    239C  VAL*     2.8    37.0    +      -       -      +
    240C  PRO      3.0    12.5    +      -       -      -
    241C  LEU*     3.7    27.6    +      -       +      +
    243C  GLU      2.9    21.4    +      -       -      -
    244C  PRO*     3.9    10.5    -      -       -      +
    245C  VAL*     3.7    21.6    -      -       +      +
    249C  TRP*     4.1     9.0    -      -       +      -
    327C  PHE*     1.3    78.2    -      -       -      +
    329C  LEU*     1.3    63.7    +      -       -      +
    330C  GLU*     3.6    27.6    +      -       +      +
    350C  VAL      3.5     5.4    -      -       -      +
    351C  GLN*     2.9    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 329 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169C  LEU*     4.8     6.7    -      -       +      -
    171C  TRP*     3.8    45.8    -      -       +      -
    208C  GLY      4.9     1.1    -      -       -      -
    209C  ARG      3.7    14.4    -      -       -      +
    210C  LEU*     4.2    13.2    -      -       +      -
    257C  PHE*     5.3     0.7    -      -       +      -
    260C  VAL*     3.6    38.6    -      -       +      -
    327C  PHE*     4.2    10.7    -      -       +      -
    328C  ARG*     1.3    74.5    -      -       -      +
    330C  GLU*     1.3    68.1    +      -       -      +
    331C  PRO*     4.1     3.5    -      -       +      +
    338C  PHE*     4.1    16.5    -      -       +      -
    349C  ALA*     3.7     1.7    -      -       -      -
    350C  VAL      2.7    37.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 330 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208C  GLY*     3.2     2.8    -      -       -      -
    209C  ARG*     2.8    74.7    +      -       -      +
    241C  LEU*     5.2     4.5    -      -       -      +
    328C  ARG*     3.6    33.9    +      -       +      -
    329C  LEU*     1.3    78.0    -      -       -      +
    331C  PRO*     1.3    64.7    -      -       -      +
    348C  GLU      3.8     9.4    -      -       -      +
    349C  ALA*     4.3    12.0    -      -       +      +
----------------------------------------------------------
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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