Contacts of the strand formed by residues 180 - 184 (chain I) in PDB entry 1SXG


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 ILE 180 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169I  VAL*     4.8     5.4    -      -       +      +
    172I  LEU*     3.4    29.4    -      -       +      -
    173I  ILE*     4.2    19.3    -      -       +      -
    177I  HIS*     3.4    47.8    -      -       +      +
    178I  LYS      3.4     9.7    +      -       -      +
    179I  ASN*     1.3    75.6    -      -       -      +
    181I  ALA*     1.3    62.8    +      -       -      +
    200I  TYR*     2.5    36.3    +      -       +      -
    204I  LEU*     4.1    16.6    -      -       +      +
    209I  LEU*     5.4     0.7    -      -       +      -
    215I  TYR*     3.3     8.1    -      -       -      -
    242I  ALA*     3.2    23.6    -      -       +      +
    244I  PHE*     4.6     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 181 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179I  ASN      4.0     1.0    +      -       -      -
    180I  ILE*     1.3    82.1    -      -       -      +
    182I  PHE*     1.3    64.1    +      -       -      +
    200I  TYR*     3.6     5.5    -      -       -      -
    215I  TYR*     3.3    19.9    -      -       +      +
    233I  LEU*     3.5    26.5    -      -       +      -
    240I  PRO*     3.8    12.3    -      -       +      -
    242I  ALA      2.8     7.7    +      -       -      -
    243I  ILE*     3.7    13.9    -      -       +      -
    244I  PHE*     3.1    21.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 182 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181I  ALA*     1.3    77.7    -      -       -      +
    183I  VAL*     1.3    73.9    +      -       -      +
    184I  SER*     3.2    33.0    +      -       -      -
    196I  LYS*     4.0    20.6    -      -       +      -
    197I  VAL*     3.9    31.6    -      -       +      -
    200I  TYR*     3.7    27.4    -      +       +      -
    215I  TYR      2.8    11.1    +      -       -      +
    216I  ILE*     3.5    15.3    -      -       +      +
    217I  VAL      3.1    24.4    +      -       -      +
    244I  PHE*     2.8    49.6    -      +       -      -
    246I  GLY*     3.6    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182I  PHE*     1.3    73.5    -      -       -      +
    184I  SER*     1.3    60.6    +      -       -      +
    217I  VAL*     3.3     9.4    -      -       +      +
    219I  GLY*     4.6     4.0    -      -       -      +
    225I  SER      4.9     1.1    -      -       -      +
    226I  GLY*     5.2     0.4    -      -       -      -
    229I  ALA*     3.4    36.1    -      -       +      -
    230I  VAL*     5.6     0.2    -      -       +      -
    233I  LEU*     4.4    11.2    -      -       +      -
    243I  ILE*     3.4    24.9    -      -       +      -
    244I  PHE      2.9     8.5    +      -       -      -
    245I  VAL*     3.4    18.5    -      -       +      +
    246I  GLY      2.8    27.2    +      -       -      -
    250I  MET*     4.3    17.1    -      -       +      +
    254I  VAL*     3.9    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 184 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182I  PHE*     3.2    35.1    +      -       -      -
    183I  VAL*     1.3    75.5    -      -       -      +
    185I  GLY*     1.3    80.0    +      -       -      +
    187I  LEU*     3.4    20.7    -      -       -      +
    192I  ASN*     3.4    15.8    -      -       -      +
    216I  ILE*     5.2     1.6    -      -       -      -
    217I  VAL      3.1     9.2    +      -       -      -
    218I  GLU*     3.8     0.3    -      -       -      -
    219I  GLY*     2.9    27.4    +      -       -      -
    246I  GLY*     4.7     1.1    -      -       -      +
    250I  MET*     3.7     6.1    -      -       -      +
----------------------------------------------------------
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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