Contacts of the strand formed by residues 148 - 155 (chain A) 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 GLN 148 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  SER*     5.6     1.9    +      -       -      -
    119A  TYR*     3.6    29.6    -      -       +      +
    120A  CYS      3.4    16.8    -      -       -      +
    121A  ARG*     3.1    40.4    +      -       +      +
    129A  PHE*     5.0     0.2    -      -       -      -
    145A  GLY*     3.6    16.6    -      -       -      -
    146A  LYS      2.8    13.0    +      -       -      +
    147A  VAL*     1.3    75.7    -      -       +      +
    149A  ALA*     1.3    64.6    +      -       -      +
    150A  GLU      4.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  PHE      3.9     0.3    -      -       -      +
    119A  TYR*     3.5     8.8    -      -       -      +
    120A  CYS      2.7    35.2    +      -       -      +
    129A  PHE*     3.6    40.4    -      -       +      -
    143A  GLY*     4.4     2.9    -      -       -      -
    144A  TYR      4.0    19.3    -      -       -      +
    145A  GLY*     4.3     0.4    -      -       -      +
    148A  GLN*     1.3    75.3    -      -       -      +
    150A  GLU*     1.3    61.4    +      -       -      +
    151A  PHE*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  THR*     4.6    10.7    -      -       -      +
    118A  PHE      3.8     2.7    -      -       -      -
    119A  TYR*     3.2    40.6    +      -       +      -
    143A  GLY*     4.9     7.8    -      -       -      -
    144A  TYR      4.3     8.8    +      -       -      +
    148A  GLN      4.3     1.0    +      -       -      -
    149A  ALA*     1.3    71.2    -      -       -      +
    151A  PHE*     1.3    64.5    +      -       -      +
    152A  PRO*     3.3    29.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  THR*     4.2     0.4    -      -       -      -
    118A  PHE*     2.7    45.7    +      -       +      +
    120A  CYS*     4.1    14.8    -      -       +      -
    129A  PHE*     3.5    40.6    -      -       +      -
    130A  LEU      3.8     2.5    -      -       -      -
    131A  LEU*     3.5    33.9    -      -       +      -
    141A  GLN*     3.3    23.1    -      -       +      -
    142A  ARG      3.7     3.4    -      -       -      -
    143A  GLY*     3.3    30.5    -      -       -      -
    149A  ALA*     3.9    17.0    -      -       +      -
    150A  GLU*     1.3    72.2    -      -       -      +
    152A  PRO*     1.4    65.4    -      -       -      +
    153A  LEU*     3.3     9.2    -      -       +      +
    166A  CYS*     4.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  THR*     3.7    22.0    -      -       +      -
    150A  GLU*     3.3    33.0    -      -       +      +
    151A  PHE*     1.4    84.2    -      -       -      +
    153A  LEU*     1.3    63.3    +      -       -      +
    154A  GLY*     4.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  VAL*     2.8    25.9    +      -       +      +
    118A  PHE*     3.6    35.7    -      -       +      -
    131A  LEU*     4.4    11.4    -      -       +      -
    141A  GLN*     5.1     7.9    -      -       -      +
    151A  PHE*     3.3    19.7    -      -       +      +
    152A  PRO*     1.3    76.7    -      -       -      +
    154A  GLY*     1.3    64.5    -      -       -      +
    155A  PRO*     4.1     2.8    -      -       -      +
    156A  VAL*     5.2     1.6    -      -       +      -
    160A  HIS*     3.7    42.3    +      -       +      +
    164A  TYR*     4.4    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU      3.0     7.8    -      -       -      +
    115A  LYS*     3.6    13.2    -      -       -      -
    116A  VAL*     3.1    16.3    +      -       -      -
    117A  THR*     5.7     1.3    -      -       -      -
    152A  PRO*     3.7     3.9    -      -       -      +
    153A  LEU*     1.3    79.7    -      -       -      +
    155A  PRO*     1.4    70.5    -      -       -      +
    156A  VAL*     2.9    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  GLY*     3.5    23.8    -      -       -      +
    114A  GLU      3.3     7.9    -      -       -      +
    115A  LYS*     4.1     9.8    -      -       +      -
    153A  LEU      4.5     2.8    -      -       -      +
    154A  GLY*     1.4    76.7    -      -       -      +
    156A  VAL*     1.3    66.1    +      -       -      +
    157A  THR*     4.4     6.4    +      -       -      +
    160A  HIS*     4.4     8.1    +      -       -      -
----------------------------------------------------------
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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