Contacts of the strand formed by residues 539 - 544 (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 539 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  LYS*     3.0    14.8    -      -       -      +
    394A  ASN*     3.6    20.6    -      -       -      +
    403A  LEU*     3.8    19.7    -      -       +      -
    404A  LEU*     3.8    16.2    -      -       +      -
    518A  CYS      3.3     2.4    +      -       -      -
    519A  ALA*     3.4     3.7    -      -       -      -
    520A  THR      2.8    23.8    +      -       -      -
    537A  SER*     3.6     6.7    -      -       -      -
    538A  ASP*     1.3    79.4    -      -       -      +
    540A  LEU*     1.3    61.8    +      -       -      +
    541A  VAL*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  LEU*     3.9     0.2    -      -       -      +
    392A  LEU*     3.0    53.7    +      -       +      -
    393A  LYS*     2.9    14.2    +      -       +      +
    520A  THR*     3.3    24.7    -      -       +      +
    522A  LEU*     4.7     8.5    -      -       +      -
    530A  VAL*     3.9     9.2    -      -       +      -
    533A  LEU*     3.8    32.3    -      -       +      +
    534A  LEU*     3.5    33.2    -      -       +      +
    537A  SER*     4.5     3.6    -      -       -      -
    539A  ALA*     1.3    74.8    -      -       -      +
    541A  VAL*     1.3    76.2    +      -       -      +
    542A  ALA      4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  LEU*     3.8    23.6    -      -       +      -
    390A  VAL      3.5     9.9    -      -       -      +
    391A  LEU*     3.8    13.9    -      -       +      -
    404A  LEU*     4.0     8.3    -      -       +      -
    519A  ALA*     6.2     1.1    -      -       +      -
    520A  THR      2.7    15.4    +      -       -      +
    521A  VAL*     3.7     8.5    -      -       +      -
    522A  LEU*     2.7    35.2    +      -       -      +
    540A  LEU*     1.3    81.5    -      -       -      +
    542A  ALA*     1.3    64.0    +      -       -      +
    543A  ALA*     3.5     2.4    +      -       +      +
    553A  VAL*     6.3     1.1    -      -       +      -
    557A  LEU*     4.4    10.8    -      -       +      -
    563A  PHE*     3.8    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 542 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  LEU*     3.5     3.1    -      -       -      -
    390A  VAL*     2.8    46.1    +      -       +      +
    392A  LEU*     4.3     7.0    -      -       +      -
    522A  LEU*     3.9     8.5    -      -       +      -
    524A  SER*     6.0     1.1    -      -       -      +
    540A  LEU*     4.4     1.0    +      -       -      +
    541A  VAL*     1.3    70.0    -      -       -      +
    543A  ALA*     1.3    62.1    +      -       -      +
    544A  TRP*     3.4    18.5    +      -       +      +
    571A  TRP*     4.0    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 543 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388A  SER*     4.5     3.5    +      -       -      -
    389A  LEU*     3.6    26.3    -      -       +      +
    521A  VAL*     3.8    15.7    -      -       +      -
    522A  LEU      2.9     7.9    +      -       -      +
    523A  ILE*     3.6    26.5    -      -       +      -
    541A  VAL*     3.5     1.9    +      -       +      -
    542A  ALA*     1.3    72.7    -      -       -      +
    544A  TRP*     1.3    76.7    +      -       -      +
    545A  LEU      3.2     0.7    +      -       -      -
    546A  PRO*     3.2    19.3    -      -       +      +
    553A  VAL*     4.7     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 544 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  PRO*     6.5     0.2    -      -       +      -
    113A  VAL*     3.9    34.3    -      -       +      -
    114A  GLY*     3.5    21.5    -      -       -      +
    117A  ALA*     3.8     6.7    -      -       +      +
    388A  SER*     3.0    31.4    +      -       -      -
    390A  VAL*     3.9     6.2    -      -       +      +
    522A  LEU      3.6     4.2    +      -       -      -
    523A  ILE*     3.3     8.0    -      -       -      +
    524A  SER*     2.7    49.3    +      -       -      +
    526A  ARG      4.3    19.5    -      -       -      -
    527A  PRO*     4.4     7.6    -      -       +      -
    542A  ALA*     3.4    15.3    +      -       +      +
    543A  ALA*     1.3    84.1    -      -       -      +
    545A  LEU*     1.3    61.6    +      -       -      +
    546A  PRO*     3.3     5.0    -      -       -      +
    567A  LEU*     3.8    26.2    -      -       +      -
    568A  PRO*     3.7    26.5    -      -       +      -
    569A  ARG*     5.5     2.5    -      -       +      -
    571A  TRP*     4.0    20.0    -      +       -      -
----------------------------------------------------------
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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