Contacts of the strand formed by residues 265 - 271 (chain E) in PDB entry 4GDK


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 265 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185E  ILE*     4.5     7.9    -      -       +      -
    186E  PRO      2.9    18.7    +      -       -      +
    187E  PHE*     3.4     5.7    -      -       +      +
    188E  ARG      3.1    21.0    +      -       -      +
    240E  ILE*     4.2    16.2    -      -       +      -
    251E  LEU*     4.1    26.0    -      -       +      -
    254E  LEU*     4.0    27.4    -      -       +      +
    255E  SER*     4.4     9.4    -      -       -      +
    258E  LEU*     3.5    32.3    -      -       +      +
    259E  SER*     4.2     5.6    -      -       -      +
    264E  PHE*     1.3    70.1    -      -       -      +
    266E  HIS*     1.3    63.0    +      -       -      +
    267E  ILE*     3.5    23.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 266 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  TYR*     6.2     0.4    -      +       -      -
     82E  PRO*     4.1    15.5    -      -       +      +
     85E  LEU*     3.7    18.1    -      -       +      +
    128E  CYS*     6.2     0.2    -      -       -      -
    188E  ARG*     3.5    24.0    -      -       -      +
    190E  TYR*     2.7    36.7    +      -       +      -
    240E  ILE*     3.7    21.8    -      -       -      +
    260E  TYR*     3.4    43.4    +      +       +      -
    262E  ASP*     2.9    25.7    +      -       -      -
    264E  PHE*     3.5    21.6    +      -       +      +
    265E  LEU*     1.3    70.7    -      -       -      +
    267E  ILE*     1.3    59.7    +      -       -      +
    268E  SER*     4.3     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 267 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  PHE*     4.6     2.7    -      -       +      -
    188E  ARG      2.9    10.3    +      -       -      +
    189E  ILE*     3.5    18.1    -      -       +      +
    190E  TYR*     2.8    35.0    +      -       -      -
    215E  LEU*     4.2    21.1    -      -       +      -
    218E  LEU*     4.2    18.4    -      -       +      -
    219E  LEU*     5.0     2.9    -      -       +      -
    238E  VAL*     3.8    28.0    -      -       +      -
    239E  MET      3.9     5.4    -      -       -      +
    240E  ILE*     4.2    11.0    -      -       +      -
    265E  LEU*     3.6    28.3    -      -       +      +
    266E  HIS*     1.3    78.3    -      -       -      +
    268E  SER*     1.3    60.9    +      -       -      +
    269E  ILE*     3.9    12.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 268 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85E  LEU*     3.6    24.3    +      -       -      +
     88E  ASP*     3.8    19.3    -      -       -      +
     89E  LEU*     4.1    16.3    +      -       -      +
    190E  TYR*     3.8     3.6    -      -       -      -
    237E  GLN      3.4     1.9    -      -       -      +
    239E  MET*     2.8    55.1    +      -       -      +
    266E  HIS      4.3     0.4    +      -       -      -
    267E  ILE*     1.3    71.6    -      -       -      +
    269E  ILE*     1.3    66.2    +      -       -      +
    270E  ILE*     3.8     8.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 269 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89E  LEU*     4.7     0.5    -      -       -      +
    189E  ILE*     3.7    26.0    -      -       +      -
    190E  TYR      2.9    13.4    +      -       -      +
    191E  GLN*     3.6    41.9    +      -       +      +
    192E  THR*     4.4     3.3    +      -       -      -
    219E  LEU*     4.6     8.1    -      -       +      -
    223E  CYS*     5.0     3.1    -      -       -      -
    226E  ALA*     3.8    28.7    -      -       +      -
    236E  ASN*     4.2    13.9    -      -       +      -
    237E  GLN      3.4     5.8    -      -       -      +
    238E  VAL*     3.7    31.0    -      -       +      -
    267E  ILE*     4.2     7.6    -      -       +      -
    268E  SER*     1.3    79.2    -      -       -      +
    270E  ILE*     1.3    62.8    +      -       -      +
    271E  PRO*     4.5     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 270 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  ASP      3.6    16.4    -      -       -      +
     89E  LEU*     4.0    26.9    -      -       +      +
     92E  SER*     3.5    24.5    -      -       -      +
     93E  SER*     5.8     2.2    -      -       -      +
    192E  THR*     5.4     2.2    -      -       -      +
    236E  ASN*     3.5     4.5    -      -       -      -
    237E  GLN*     2.5    60.8    +      -       +      +
    239E  MET*     3.6    28.5    -      -       +      -
    268E  SER*     4.3     5.8    -      -       -      -
    269E  ILE*     1.3    79.7    -      -       -      +
    271E  PRO*     1.3    69.9    -      -       +      +
    273E  PRO*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 271 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192E  THR*     4.6    12.3    -      -       -      +
    193E  THR*     5.8     6.7    -      -       +      -
    235E  LYS      4.0     1.3    -      -       -      +
    236E  ASN*     3.8    17.9    -      -       -      +
    237E  GLN*     4.6     0.2    -      -       -      -
    269E  ILE      4.5     1.6    -      -       -      +
    270E  ILE*     1.3    98.0    -      -       +      +
    272E  GLN*     1.3    67.4    +      -       -      +
    273E  PRO*     3.4     8.0    -      -       -      +
----------------------------------------------------------
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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