Contacts of the strand formed by residues 317 - 327 (chain D) in PDB entry 4G7Z


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 VAL 317 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238D  PRO*     3.6    16.8    -      -       -      +
    264D  LEU*     4.0    17.7    -      -       +      -
    269D  PHE*     5.8     0.9    -      -       +      -
    283D  PHE*     4.9     8.5    -      -       +      -
    313D  MET*     3.1    16.3    -      -       +      +
    314D  PRO*     3.5    42.6    +      -       +      +
    315D  ARG      3.3     0.6    -      -       -      +
    316D  GLN*     1.3    79.6    -      -       -      +
    318D  ARG*     1.3    68.1    +      -       -      +
    337D  LEU*     4.2    16.4    -      -       +      -
    338D  GLU      3.6     6.7    -      -       -      +
    339D  TRP*     3.6    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 318 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235D  ALA*     4.8     9.5    -      -       -      +
    236D  TYR      3.7     6.7    -      -       -      +
    237D  LYS*     4.2    23.0    -      -       -      +
    238D  PRO*     3.5    25.2    -      -       +      +
    313D  MET*     3.5     4.7    -      -       -      -
    317D  VAL*     1.3    72.9    -      -       -      +
    319D  ALA*     1.3    85.1    +      -       -      +
    320D  ALA*     4.0     8.5    -      -       -      +
    337D  LEU*     3.3     9.7    -      -       -      +
    338D  GLU*     2.8    52.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235D  ALA*     3.1    19.3    -      -       -      +
    236D  TYR*     2.6    43.3    +      -       +      +
    313D  MET*     3.8     6.7    -      -       +      -
    318D  ARG*     1.3    82.5    +      -       -      +
    320D  ALA*     1.3    65.6    +      -       -      +
    321D  GLN      3.5     0.9    -      -       -      +
    322D  VAL*     4.6     9.4    -      -       +      -
    335D  LEU*     4.6     9.6    -      -       +      -
    336D  PHE      3.9     3.6    -      -       -      +
    337D  LEU*     4.4     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 320 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234D  GLU      3.6     1.4    -      -       -      +
    235D  ALA*     3.3    17.5    -      -       -      +
    318D  ARG*     4.0    12.0    +      -       -      +
    319D  ALA*     1.3    71.0    -      -       -      +
    321D  GLN*     1.3    71.6    +      -       +      +
    336D  PHE*     3.1    18.2    +      -       +      +
    338D  GLU*     3.9    25.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 321 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234D  GLU      3.5     3.8    -      -       -      -
    319D  ALA*     4.9     0.3    -      -       -      +
    320D  ALA*     1.3    91.4    +      -       +      +
    322D  VAL*     1.3    67.0    +      -       -      +
    323D  GLU*     4.1     8.6    -      -       +      +
    334D  THR      4.2     0.3    -      -       -      +
    335D  LEU*     3.8     4.7    -      -       -      +
    336D  PHE*     3.2    60.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 322 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  TRP*     3.9    25.8    -      -       +      -
    233D  LYS      3.5    21.0    -      -       -      +
    234D  GLU*     2.9    25.3    +      -       -      +
    235D  ALA*     4.0     3.6    -      -       -      -
    236D  TYR*     3.5    30.5    -      -       +      -
    319D  ALA*     4.6     3.4    -      -       +      -
    321D  GLN*     1.3    74.3    -      -       -      +
    323D  GLU*     1.3    61.5    +      -       -      +
    324D  ALA*     3.5     3.5    +      -       -      +
    333D  LEU*     4.1    11.4    -      -       +      -
    335D  LEU*     3.5    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 323 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321D  GLN*     4.1     7.1    -      -       +      +
    322D  VAL*     1.3    71.2    -      -       -      +
    324D  ALA*     1.3    61.8    +      -       -      +
    325D  GLU*     3.7     1.7    +      -       -      +
    333D  LEU*     3.8     0.7    -      -       -      -
    334D  THR*     3.0    52.9    +      -       -      +
    336D  PHE*     3.3    35.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 324 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  TRP*     3.7    32.8    -      -       +      -
    322D  VAL*     3.5     5.2    +      -       +      +
    323D  GLU*     1.3    70.6    -      -       -      +
    325D  GLU*     1.3    60.1    +      -       -      +
    326D  GLU*     4.1     5.1    +      -       +      +
    331D  VAL*     3.9     6.3    -      -       +      -
    332D  TYR      3.7     4.5    -      -       -      -
    333D  LEU*     3.7    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 325 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224D  ARG*     4.8     0.7    +      -       -      -
    323D  GLU      3.7     2.6    +      -       -      +
    324D  ALA*     1.3    73.5    -      -       -      +
    326D  GLU*     1.3    66.4    +      -       -      +
    327D  GLU*     3.2    28.2    -      -       +      +
    331D  VAL*     3.2     3.3    -      -       -      +
    332D  TYR*     2.7    59.4    +      -       +      +
    334D  THR*     5.6     2.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 326 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227D  LEU*     3.3    33.5    -      -       +      +
    230D  TRP*     4.4     0.9    +      -       -      -
    232D  GLU*     3.4    22.2    -      -       -      +
    324D  ALA*     4.1     5.9    +      -       +      +
    325D  GLU*     1.3    78.7    -      -       -      +
    327D  GLU*     1.3    61.8    +      -       -      +
    328D  GLY      4.3     3.4    -      -       -      +
    330D  THR      3.6     6.1    -      -       -      +
    331D  VAL*     3.6    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 327 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224D  ARG*     3.2    33.9    +      -       -      +
    325D  GLU*     3.2    23.2    +      -       -      +
    326D  GLU*     1.3    74.6    -      -       -      +
    328D  GLY*     1.3    62.8    +      -       -      +
    330D  THR*     2.9    34.5    +      -       -      +
    332D  TYR*     5.5     0.2    -      -       +      -
----------------------------------------------------------
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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