Contacts of the strand formed by residues 244 - 250 (chain A) in PDB entry 3SRG


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 LYS 244 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  GLU*     2.8    50.4    +      -       +      +
    242A  ALA*     3.6    17.2    -      -       +      +
    243A  HIS*     1.4    83.1    -      -       -      +
    245A  ILE*     1.3    62.0    +      -       -      +
    246A  HIS*     3.7    17.8    -      -       +      +
    261A  VAL*     3.7    19.3    -      -       +      -
    262A  LEU      3.1    11.7    -      -       -      +
    263A  SER*     3.9    17.7    -      -       -      +
    264A  PHE*     4.3     0.4    -      -       -      -
    268A  VAL*     3.3     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  TYR*     4.4     2.2    -      -       +      -
    237A  ILE      3.3     8.3    -      -       -      +
    238A  ALA*     4.3     6.1    -      -       -      -
    244A  LYS*     1.3    78.9    -      -       -      +
    246A  HIS*     1.3    69.8    +      -       -      +
    247A  VAL*     4.1     1.0    +      -       +      +
    261A  VAL*     3.6     1.8    -      -       -      -
    262A  LEU*     2.9    36.5    +      -       +      +
    264A  PHE*     3.8    16.8    -      -       +      -
    268A  VAL*     4.1    11.9    -      -       +      -
    271A  ILE*     4.1    20.0    -      -       +      -
    280A  LEU*     4.2    14.4    -      -       +      -
    282A  VAL*     3.8    28.7    -      -       +      -
    305A  LEU*     5.9     0.2    -      -       +      -
    307A  ILE*     3.7    27.1    -      -       +      -
    310A  ILE*     4.7     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  PHE*     3.8    22.1    -      +       -      -
    235A  VAL      3.7     0.5    -      -       -      +
    236A  TYR*     3.2     5.4    -      -       -      -
    237A  ILE*     2.8    43.3    +      -       +      +
    239A  GLU*     2.6    38.5    +      -       +      -
    244A  LYS*     3.7    12.9    -      -       +      +
    245A  ILE*     1.3    77.3    -      -       -      +
    247A  VAL*     1.3    62.0    +      -       -      +
    248A  TYR*     3.5    27.4    +      -       +      -
    260A  ARG      3.6     6.3    -      -       -      +
    261A  VAL*     3.8    26.8    -      -       +      +
   1363A   CA      4.2    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  TYR*     4.3     7.2    -      -       +      -
    235A  VAL      3.5     3.8    -      -       -      +
    236A  TYR*     3.9    21.3    -      -       +      -
    245A  ILE*     4.7     2.9    -      -       +      +
    246A  HIS*     1.3    77.6    -      -       -      +
    248A  TYR*     1.3    64.8    +      -       -      +
    258A  PRO*     4.2     0.5    -      -       -      +
    259A  LEU*     3.0    31.3    +      -       +      +
    260A  ARG*     2.8    36.8    +      -       +      +
    262A  LEU*     4.2     6.1    -      -       +      -
    310A  ILE*     3.7    33.2    -      -       +      -
    311A  LEU*     4.1    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  VAL      5.0     1.3    -      -       -      -
    217A  ALA*     3.7    21.2    -      -       +      +
    218A  GLU      5.4     0.5    +      -       -      -
    220A  PHE*     3.7    16.8    -      +       -      -
    234A  TYR*     3.1    10.7    -      -       -      +
    235A  VAL*     2.8    37.0    +      -       +      +
    237A  ILE*     3.8    23.3    -      -       +      -
    246A  HIS*     3.5    33.8    +      +       +      -
    247A  VAL*     1.3    79.0    -      -       -      +
    249A  GLU*     1.3    66.3    +      -       -      +
    256A  LEU*     3.6    27.8    -      -       +      -
    257A  THR      3.3    24.2    -      -       -      +
    258A  PRO*     3.5    26.5    -      -       +      +
    259A  LEU*     4.2     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LYS      3.5     5.6    -      -       -      +
    234A  TYR*     3.9    24.5    +      -       +      -
    248A  TYR*     1.3    72.7    -      -       -      +
    250A  LYS*     1.3    61.1    -      -       -      +
    251A  HIS*     3.7    23.8    -      -       +      +
    255A  THR      3.8     0.3    -      -       -      +
    256A  LEU*     3.2     6.9    -      -       -      -
    257A  THR*     2.9    43.8    +      -       -      +
    258A  PRO      5.9     0.7    -      -       -      +
    259A  LEU*     4.0    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  VAL*     4.5     0.6    -      -       -      +
    179A  TYR*     3.5    22.9    -      -       +      +
    228A  ILE*     3.6    19.5    -      -       +      +
    232A  GLY*     2.8    30.4    +      -       -      +
    233A  LYS*     2.7    31.7    +      -       -      +
    235A  VAL*     3.7    23.8    -      -       +      -
    248A  TYR      3.6     0.6    +      -       -      -
    249A  GLU*     1.3    74.2    -      -       -      +
    251A  HIS*     1.3    71.9    +      -       -      +
    254A  TRP*     3.6    36.6    -      -       -      -
    255A  THR      3.6     3.8    -      -       -      -
    256A  LEU*     3.8     8.5    -      -       +      -
----------------------------------------------------------
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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