Contacts of the strand formed by residues 352 - 357 (chain E) in PDB entry 6GL7


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 HIS 352 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324E  TRP*     3.1    51.1    +      +       +      +
    329E  PHE*     5.4     2.7    -      +       -      +
    350E  THR*     3.5     3.9    +      -       +      -
    351E  VAL*     1.3    75.3    -      -       -      +
    353E  ASP*     1.3    59.2    +      -       -      +
    354E  TYR*     3.4    52.7    -      +       +      +
    372E  LEU      4.9     1.8    -      -       -      -
    373E  ALA*     2.9     6.2    -      -       -      +
    374E  VAL*     2.8    65.3    +      -       +      +
    375E  LEU*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 353 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278E  THR*     3.5    18.4    +      -       -      +
    320E  PRO*     5.6     0.7    -      -       -      +
    352E  HIS*     1.3    76.9    -      -       -      +
    354E  TYR*     1.3    64.5    +      -       -      +
    355E  ARG      4.1     0.5    +      -       -      -
    371E  GLN*     3.4    21.0    -      -       -      +
    372E  LEU      3.1    18.4    -      -       -      +
    373E  ALA*     3.8    14.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 354 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317E  THR*     4.5    14.8    -      -       +      +
    320E  PRO*     3.5    59.4    +      -       +      +
    323E  THR*     4.2     7.1    +      -       -      -
    324E  TRP*     3.7    34.4    +      -       +      +
    325E  ALA*     4.1    13.5    -      -       +      -
    352E  HIS*     3.4    39.5    -      +       +      +
    353E  ASP*     1.3    81.7    -      -       -      +
    355E  ARG*     1.3    60.0    +      -       -      +
    356E  LEU*     3.3    14.4    -      -       +      +
    371E  GLN*     3.3     2.6    -      -       -      -
    372E  LEU      3.0    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 355 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317E  THR*     3.2    20.4    +      -       -      -
    318E  LEU      5.1     0.2    +      -       -      -
    319E  LEU      5.0     6.8    +      -       -      +
    320E  PRO*     5.6     0.6    -      -       -      +
    353E  ASP      4.1     1.4    +      -       -      -
    354E  TYR*     1.3    70.7    -      -       -      +
    356E  LEU*     1.3    63.3    +      -       -      +
    357E  VAL*     3.8     5.2    +      -       +      +
    367E  ASN*     5.6     4.0    -      -       -      +
    369E  THR*     2.9    41.3    +      -       +      +
    370E  MET      3.3     9.4    -      -       -      +
    371E  GLN*     4.1    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 356 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317E  THR*     4.2     5.8    -      -       -      -
    331E  VAL*     3.6    35.2    -      -       +      -
    338E  THR*     3.4    32.5    -      -       +      -
    340E  VAL*     3.9     8.1    -      -       +      -
    354E  TYR*     3.3    26.9    -      -       +      +
    355E  ARG*     1.3    73.9    -      -       -      +
    357E  VAL*     1.3    61.8    +      -       -      +
    358E  LEU*     4.6     2.8    -      -       +      +
    369E  THR*     3.0     9.9    -      -       -      -
    370E  MET*     2.5    41.0    +      -       +      +
    372E  LEU*     3.8    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 357 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315E  THR*     2.9    50.8    -      -       -      +
    316E  SER*     3.3    27.4    -      -       -      +
    317E  THR*     3.8    10.7    -      -       -      +
    318E  LEU*     5.0     2.5    -      -       +      +
    331E  VAL*     5.6     1.2    -      -       -      +
    333E  HIS*     4.2     2.8    -      -       -      +
    355E  ARG*     4.5     5.8    -      -       +      +
    356E  LEU*     1.3    76.4    -      -       -      +
    358E  LEU*     1.3    66.0    +      -       -      +
    359E  ASN*     3.7     7.4    -      -       +      +
    362E  LEU*     3.8    30.7    -      -       +      -
    367E  ASN*     5.5     0.2    -      -       -      -
    368E  ARG      4.0     3.4    -      -       -      +
    369E  THR*     4.1    12.1    -      -       +      -
----------------------------------------------------------
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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