Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 6IAP


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 33 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  MET*     3.6    29.6    -      -       +      -
     23D  CYS*     4.0     9.6    -      -       -      -
     29D  ILE*     3.7    16.6    -      -       +      -
     31D  SER      2.8    11.9    +      -       -      +
     32D  ASN*     1.3    73.7    -      -       -      +
     34D  ALA*     1.3    63.8    +      -       -      +
     35D  TRP*     3.3    38.5    -      -       +      +
     48D  VAL      4.2     0.5    -      -       -      +
     49D  TYR      3.6     0.5    -      -       -      -
     50D  ALA      3.1     8.3    +      -       -      -
     51D  ALA*     2.8    30.8    +      -       -      -
     71D  TYR*     3.5    38.6    -      -       +      -
     88D  CYS*     4.1     3.4    -      -       +      -
     89D  GLN      3.2    12.8    -      -       -      +
     91D  PHE*     3.5     4.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  LEU*     1.3    74.3    -      -       -      +
     35D  TRP*     1.3    64.4    +      -       -      +
     36D  PHE*     3.9    25.6    -      -       +      -
     46D  LEU*     4.0     8.5    -      -       +      -
     48D  VAL      3.1    10.5    -      -       -      +
     49D  TYR*     4.5     2.9    -      -       +      -
     88D  CYS*     3.1     6.9    -      -       -      +
     89D  GLN*     2.7    37.2    +      -       -      +
     91D  PHE*     3.8    14.8    -      -       +      -
    102E  ARG      5.8     0.4    -      -       -      +
    103E  GLY*     5.8     0.7    -      -       -      -
    104E  PHE      5.8     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 35 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  GLN*     3.9     9.4    -      -       -      -
     21D  ILE*     3.7    33.9    -      -       +      -
     23D  CYS*     3.6    31.4    -      -       +      -
     33D  LEU*     3.3    23.7    -      -       +      +
     34D  ALA*     1.3    74.6    -      -       -      +
     36D  PHE*     1.3    59.6    +      -       -      +
     46D  LEU*     3.8     1.7    -      -       -      +
     47D  LEU*     2.8    35.9    +      -       +      -
     48D  VAL*     2.7    44.8    +      -       +      +
     51D  ALA      4.3     7.2    +      -       -      -
     64D  GLY*     5.0     1.1    -      -       -      -
     65D  SER      5.3     0.2    -      -       -      +
     71D  TYR*     4.3     1.7    -      -       -      +
     72D  THR*     3.9     9.4    +      -       -      -
     73D  LEU*     3.4    53.9    -      -       +      +
     86D  TYR*     4.9     1.3    -      -       +      -
     87D  TYR      3.2    22.9    -      -       -      -
     88D  CYS*     3.7    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 36 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  ALA*     3.9    19.7    -      -       +      -
     35D  TRP*     1.3    72.6    -      -       -      +
     37D  GLN*     1.3    59.7    +      -       -      +
     44D  PRO*     4.0    16.4    -      -       +      -
     45D  LYS      3.3     8.5    -      -       -      +
     46D  LEU*     3.7    32.5    -      -       +      -
     47D  LEU*     4.3     1.8    -      -       -      +
     85D  THR      3.8     0.7    -      -       -      +
     86D  TYR*     3.2    12.4    -      -       -      +
     87D  TYR*     2.7    51.9    +      -       +      +
     89D  GLN*     3.4    41.3    -      -       +      -
     98D  PHE*     4.2    13.2    -      +       -      -
     45E  LEU*     5.6     0.7    -      -       +      -
    104E  PHE*     3.8    17.3    -      +       +      -
    107E  TRP*     3.7    28.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 37 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  PHE*     1.3    72.3    -      -       -      +
     38D  GLN*     1.3    61.2    +      -       -      +
     39D  LYS*     3.8    26.0    +      -       +      +
     42D  LYS*     5.8     0.5    +      -       -      -
     43D  ALA      4.4     0.7    -      -       -      +
     44D  PRO*     3.6     0.6    -      -       -      +
     45D  LYS*     2.9    52.7    +      -       +      +
     47D  LEU*     3.7    18.5    -      -       +      +
     62D  PHE*     4.2    11.9    -      -       -      -
     81D  GLU      4.2     4.9    +      -       -      -
     82D  ASP*     4.0    15.4    +      -       -      +
     84D  ALA*     3.6    13.0    -      -       +      -
     85D  THR      3.8     2.7    -      -       -      -
     86D  TYR*     3.0    39.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  GLN*     1.3    74.3    -      -       -      +
     39D  LYS*     1.3    63.8    +      -       -      +
     40D  PRO*     4.6     0.2    -      -       -      +
     42D  LYS      3.2    27.7    +      -       -      +
     43D  ALA      4.7     0.4    -      -       -      -
     44D  PRO*     3.7    30.0    -      -       +      +
     84D  ALA*     3.8     3.0    -      -       -      -
     85D  THR*     2.8    47.9    +      -       -      +
     87D  TYR*     3.4    19.4    +      -       +      -
     39E  GLN*     3.0    41.3    +      -       -      +
     95E  TYR*     3.4     9.3    +      -       -      -
----------------------------------------------------------
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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