Contacts of the strand formed by residues 34 - 38 (chain A) in PDB entry 1GO1


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 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LYS*     1.4    78.1    -      -       +      +
     35A  ILE*     1.4    60.0    +      -       -      +
     36A  ILE*     4.2    15.3    -      -       +      -
     58A  ILE*     4.4     0.2    -      -       -      -
     59A  PRO*     3.5    18.4    -      -       +      +
     61A  TYR*     4.7    10.1    -      -       +      -
     85A  VAL*     2.7    47.5    +      -       +      +
     93A  ILE*     3.2    49.8    -      -       +      +
     94A  LEU*     4.1    11.2    -      -       +      +
     96A  LEU*     5.3     1.1    -      -       +      -
     97A  GLY*     3.3    34.1    -      -       -      +
     98A  GLY*     3.7    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  SER*     4.3    15.0    -      -       -      +
     27A  ALA*     4.0    28.5    -      -       +      +
     32A  ALA*     4.1    13.7    -      -       +      -
     34A  LEU*     1.4    75.5    -      -       -      +
     36A  ILE*     1.4    60.3    +      -       -      +
     37A  VAL*     4.5     7.4    -      -       +      -
     49A  ILE*     3.5    24.9    -      -       +      -
     53A  ALA*     4.0    10.1    -      -       +      -
     58A  ILE*     3.7    28.5    -      -       +      -
     59A  PRO      3.1    10.6    +      -       -      +
     60A  VAL*     3.2    14.3    -      -       +      +
     61A  TYR      3.0    22.1    +      -       -      -
     83A  LEU      3.6    16.4    -      -       -      +
     84A  ALA*     4.1     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.7    30.7    -      -       +      -
      7A  LEU*     4.2     2.0    -      -       +      -
     34A  LEU*     4.1     9.8    +      -       +      -
     35A  ILE*     1.4    72.7    -      -       -      +
     37A  VAL*     1.4    61.6    +      -       -      +
     38A  ALA      4.5     0.2    +      -       -      -
     61A  TYR*     3.4    35.7    -      -       +      +
     63A  PHE*     3.9    22.2    -      -       +      -
     70A  LEU*     5.1     2.7    -      -       +      +
     82A  ALA*     3.5     1.7    -      -       -      -
     83A  LEU*     2.9    64.4    +      -       +      +
     85A  VAL*     4.2     3.8    -      -       +      -
     93A  ILE*     3.7    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     4.0     1.8    +      -       +      -
     36A  ILE*     1.4    78.3    -      -       -      +
     38A  ALA*     1.4    59.7    +      -       -      +
     46A  LYS*     4.5    26.0    -      -       +      +
     49A  ILE*     4.1    24.0    -      -       +      -
     50A  GLU*     4.8     8.1    -      -       +      -
     60A  VAL*     3.7    28.5    -      -       +      -
     61A  TYR      3.0    11.6    +      -       -      +
     62A  GLU*     3.5    16.5    -      -       +      -
     63A  PHE*     2.8    33.0    +      -       -      -
     81A  SER      3.9     4.0    -      -       -      +
     82A  ALA*     3.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ILE      4.5     0.2    +      -       -      -
     37A  VAL*     1.4    70.1    -      -       -      +
     39A  ARG*     1.4    64.7    +      -       -      +
     40A  ASN      3.3     0.4    -      -       -      +
     41A  ALA*     3.2    23.2    +      -       +      +
     46A  LYS*     3.5    11.1    -      -       -      +
     63A  PHE*     4.1    11.4    -      -       +      -
     66A  THR      4.4     4.3    -      -       -      -
     67A  SER*     4.2    18.2    -      -       -      +
     70A  LEU*     4.0    18.2    -      -       +      +
     80A  VAL      4.0     7.9    -      -       -      +
     81A  SER      2.9    20.4    +      -       -      +
----------------------------------------------------------
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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