Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 3T2D


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 ARG 2 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     1.3    78.4    -      -       -      +
      3A  VAL*     1.3    60.2    +      -       -      +
     61A  THR*     3.6    21.5    -      -       -      +
    117A  GLU*     3.9    35.5    +      -       +      +
    118A  PHE*     3.3    24.3    -      -       -      +
    119A  GLU*     3.3    38.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 3 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     4.5    10.1    -      -       +      -
      2A  ARG*     1.3    75.5    -      -       -      +
      4A  THR*     1.3    73.6    +      -       -      +
      5A  VAL*     4.7     0.9    -      -       +      -
     43A  ILE*     4.9     0.7    -      -       +      -
     59A  THR*     4.4     6.3    -      -       +      -
     60A  HIS      3.6    17.3    -      -       -      +
     61A  THR*     5.2     0.4    -      -       -      +
    116A  MET      3.9     0.9    -      -       -      +
    117A  GLU*     3.2     3.7    -      -       -      -
    118A  PHE*     2.9    64.4    +      -       +      +
    120A  GLU*     4.2    17.5    -      -       +      +
    309A  LEU*     4.3     8.5    -      -       +      -
    312A  GLY*     3.9    23.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 4 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL*     1.3    76.6    -      -       -      +
      5A  VAL*     1.4    68.3    +      -       -      +
      6A  SER*     3.7     9.2    -      -       -      +
     59A  THR*     3.3     5.5    -      -       -      -
     60A  HIS*     2.8    66.4    +      -       +      +
     61A  THR*     4.7     1.2    -      -       -      +
     62A  LYS      4.4     0.2    +      -       -      -
     63A  GLY*     3.2    35.7    +      -       -      +
     64A  GLU*     4.1     8.1    -      -       +      +
    115A  GLU*     4.5     0.9    -      -       +      +
    116A  MET      3.3    15.0    -      -       -      +
    117A  GLU*     3.6    10.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL*     4.7     1.8    -      -       +      -
      4A  THR*     1.4    78.1    -      -       -      +
      6A  SER*     1.3    63.1    -      -       -      +
     57A  LEU*     3.5    26.7    -      -       +      -
     58A  MET      3.7     2.0    -      -       -      -
     59A  THR*     4.1    13.0    -      -       +      -
    115A  GLU*     3.1     4.2    -      -       -      +
    116A  MET*     2.9    33.9    +      -       +      +
    118A  PHE*     3.7    18.6    -      -       +      -
    126A  ILE*     4.0    12.1    -      -       +      -
    238A  LEU*     3.4    23.1    -      -       +      +
    309A  LEU*     3.6    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  THR*     3.7     1.4    -      -       -      +
      5A  VAL*     1.3    74.2    -      -       -      +
      7A  ILE*     1.3    62.5    +      -       -      +
      8A  ILE*     4.6     8.7    -      -       -      -
     56A  LEU      3.4     3.1    -      -       -      +
     57A  LEU*     3.5     2.1    -      -       -      -
     58A  MET*     2.8    41.2    +      -       -      +
     60A  HIS*     2.9    28.0    +      -       -      -
     69A  ILE*     4.3    11.1    -      -       -      +
    114A  ALA      3.6     4.7    -      -       -      -
    115A  GLU*     2.7    29.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  SER*     1.3    70.8    -      -       -      +
      8A  ILE*     1.3    66.0    +      -       -      +
      9A  LYS      4.1     0.2    -      -       -      -
     48A  TYR*     4.1     5.2    -      -       -      +
     55A  SER*     3.8    31.6    -      -       -      +
     56A  LEU      3.4     6.3    -      -       -      +
     57A  LEU*     3.7    20.6    -      -       +      -
    112A  GLN      3.7     0.7    -      -       -      +
    113A  VAL*     3.3     5.5    -      -       -      +
    114A  ALA*     2.8    38.7    +      -       +      +
    128A  ALA*     3.9    12.8    -      -       +      -
    129A  PHE      4.5     1.6    -      -       -      +
    236A  VAL*     3.8    19.2    -      -       +      +
    237A  LEU      3.7    25.1    -      -       -      +
    238A  LEU*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  SER*     4.6     5.2    -      -       -      -
      7A  ILE*     1.3    79.4    -      -       -      +
      9A  LYS*     1.3    62.6    +      -       -      +
     56A  LEU*     2.8    34.6    +      -       -      +
     58A  MET*     3.9    17.9    -      -       +      -
     69A  ILE*     4.0     5.4    -      -       +      +
     70A  HIS*     3.8    47.6    -      -       +      +
     73A  ALA*     3.5    27.8    -      -       +      -
     77A  PHE*     3.5     6.4    -      -       +      -
    111A  PRO*     3.9    20.2    -      -       +      -
    112A  GLN      3.3     9.4    -      -       -      +
    113A  VAL*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     4.7     0.2    -      -       +      -
      8A  ILE*     1.3    75.2    -      -       -      +
     10A  ALA*     1.3    77.3    +      -       -      +
     53A  ASP*     3.1    36.0    +      -       +      -
     54A  ILE      3.1    16.2    -      -       -      +
     55A  SER*     3.8     9.4    -      -       -      +
     77A  PHE*     3.7     2.2    -      -       -      -
     96A  ASP*     4.1     9.5    +      -       -      +
    111A  PRO*     3.1     5.7    -      -       -      +
    112A  GLN*     2.9    47.3    +      -       +      +
    130A  ALA*     6.0     0.4    -      -       +      -
    131A  ALA      5.8     0.2    -      -       -      +
    233A  ASP      3.1    17.4    +      -       -      -
    234A  ASP*     3.1    30.1    +      -       -      +
    236A  VAL*     3.7    29.4    -      -       +      -
    410A   MG      4.2     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  LYS*     1.3    83.3    -      -       -      +
     11A  ASP*     1.3    61.1    +      -       -      +
     12A  VAL*     4.0     3.9    +      -       +      -
     54A  ILE*     2.9    36.1    +      -       -      +
     77A  PHE*     3.4    33.8    -      -       +      -
     96A  ASP*     3.6    17.7    -      -       +      +
     97A  LEU*     4.4     7.9    -      -       +      -
    111A  PRO*     4.2     9.9    -      -       +      -
----------------------------------------------------------
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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