Contacts of the strand formed by residues 480 - 485 (chain A) in PDB entry 1IEQ


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 ALA 480 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406A  LEU*     5.8     0.2    -      -       -      +
    414A  LEU*     3.1    23.1    -      -       +      +
    479A  TYR*     1.3    81.7    -      -       -      +
    481A  ILE*     1.3    61.7    +      -       -      +
    482A  VAL*     4.0     1.1    -      -       +      -
    512A  VAL*     3.5    31.4    -      -       +      -
    516A  VAL*     3.8     9.6    -      -       +      -
    517A  ARG      2.9     8.1    +      -       -      +
    518A  CYS*     3.3     2.0    -      -       +      -
    519A  ALA*     2.8    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 481 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406A  LEU*     3.8    28.9    -      -       +      -
    413A  ILE*     5.4     0.4    -      -       +      -
    414A  LEU      2.8     9.6    +      -       -      +
    415A  VAL*     3.2    11.0    -      -       +      +
    416A  ALA      2.8    24.9    +      -       -      +
    420A  ALA*     5.3     0.2    -      -       -      +
    447A  ILE*     4.5    15.9    -      -       +      -
    451A  VAL*     4.1    24.7    -      -       +      -
    479A  TYR*     4.5     9.0    -      -       +      -
    480A  ALA*     1.3    76.3    -      -       -      +
    482A  VAL*     1.3    62.9    +      -       -      +
    483A  ALA*     5.8     0.4    -      -       +      -
    519A  ALA*     3.4    11.9    -      -       +      +
    521A  VAL*     4.1    10.8    -      -       +      -
    557A  LEU*     3.9    29.4    -      -       +      -
    558A  PHE*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 482 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  ALA*     3.0    17.9    -      -       +      +
    417A  GLY*     4.1     3.4    -      -       -      -
    480A  ALA*     4.7     0.2    -      -       +      -
    481A  ILE*     1.3    78.4    -      -       -      +
    483A  ALA*     1.3    62.5    +      -       -      +
    484A  VAL*     4.2     4.0    -      -       +      -
    508A  THR*     4.1    18.8    -      -       +      -
    509A  VAL*     3.9    28.0    -      -       +      -
    512A  VAL*     3.4    37.9    -      -       +      -
    518A  CYS*     4.6    11.4    -      -       +      -
    519A  ALA      3.1     6.4    +      -       -      +
    520A  THR*     3.4     8.9    -      -       -      +
    521A  VAL*     2.8    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 483 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  ALA      2.8     9.3    +      -       -      -
    417A  GLY*     3.1    13.5    -      -       -      -
    419A  HIS*     3.0    33.7    +      -       +      +
    420A  ALA*     3.5    26.9    -      -       +      +
    447A  ILE*     3.8    21.5    -      -       +      -
    481A  ILE*     4.2     0.9    -      -       +      -
    482A  VAL*     1.3    73.0    -      -       -      +
    484A  VAL*     1.3    61.4    +      -       -      +
    521A  VAL*     3.3    11.4    -      -       +      +
    523A  ILE*     5.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 484 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  GLY*     4.3     6.7    -      -       -      -
    418A  SER*     4.2     6.7    -      -       -      +
    419A  HIS*     3.6    13.2    -      -       -      +
    482A  VAL*     4.2    14.4    -      -       +      -
    483A  ALA*     1.3    80.6    -      -       -      +
    485A  GLY*     1.3    60.5    +      -       -      +
    501A  ILE*     4.2    15.9    -      -       +      -
    504A  PRO      4.6     1.1    -      -       -      +
    505A  GLY*     3.7    33.2    -      -       -      +
    508A  THR*     4.7     3.6    -      -       -      -
    509A  VAL*     4.0    16.8    -      -       +      -
    520A  THR*     4.5     5.8    -      -       +      -
    521A  VAL      3.2     9.4    +      -       -      +
    522A  LEU*     3.5     6.4    -      -       +      +
    523A  ILE*     2.9    23.2    +      -       -      +
    533A  LEU*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 485 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  SER*     4.6     0.6    +      -       -      -
    419A  HIS*     3.1    19.1    -      -       -      -
    484A  VAL*     1.3    79.6    -      -       -      +
    486A  GLU*     1.3    64.9    +      -       -      -
    487A  HIS*     4.1     2.6    +      -       -      -
    501A  ILE*     4.0    22.8    -      -       -      +
    502A  PRO*     3.4    16.9    +      -       -      +
    522A  LEU*     4.2     2.9    -      -       -      -
    523A  ILE      3.0    11.2    -      -       -      -
----------------------------------------------------------
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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