Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 1S9V


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 GLU 88 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  VAL      3.9     1.3    +      -       -      +
     87A  PRO*     1.3    73.4    -      -       -      +
     89A  VAL*     1.3    65.8    +      -       -      +
     90A  THR*     5.1     5.7    +      -       -      +
    108A  LEU*     3.3     2.4    -      -       -      +
    109A  VAL*     3.5     0.5    -      -       -      -
    110A  ASP*     2.7    55.5    +      -       +      +
    111A  ASN*     5.0     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  PRO*     4.1     3.3    +      -       +      +
     88A  GLU*     1.3    80.4    -      -       -      +
     90A  THR*     1.3    71.4    +      -       -      +
    107A  CYS*     3.7    28.0    -      -       -      -
    108A  LEU      3.3     2.7    -      -       -      +
    109A  VAL*     4.3     9.9    -      -       +      -
    163A  CYS*     4.5     1.1    -      -       -      +
    165A  VAL*     3.7    28.0    -      -       +      -
    174A  LEU*     3.7    30.0    -      -       +      +
    176A  LYS*     3.5    47.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  GLU*     5.1     7.1    +      -       -      +
     89A  VAL*     1.3    79.9    +      -       -      +
     91A  VAL*     1.3    69.7    +      -       -      +
     92A  PHE*     4.1    17.9    -      -       +      -
    106A  ILE      3.6     1.2    -      -       -      +
    107A  CYS*     3.4     2.1    -      -       -      -
    108A  LEU*     2.7    56.3    +      -       +      +
    176A  LYS*     4.6     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  THR*     1.3    83.9    -      -       -      +
     92A  PHE*     1.3    70.2    +      -       -      +
    105A  LEU*     4.6     3.1    -      -       +      -
    106A  ILE      3.1     9.0    -      -       -      +
    107A  CYS*     4.1     5.6    -      -       +      -
    121A  TRP*     4.2    16.2    -      -       +      -
    163A  CYS*     3.5    31.0    -      -       +      +
    176A  LYS*     3.7    26.6    -      -       +      +
    177A  HIS      4.8     3.5    -      -       -      +
    178A  TRP*     3.6    39.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  THR*     4.1    25.8    -      -       +      -
     91A  VAL*     1.3    82.1    -      -       -      +
     93A  SER*     1.3    66.4    +      -       -      +
    105A  LEU*     4.5     2.5    -      -       -      -
    106A  ILE*     2.6    84.8    +      -       +      +
    108A  LEU*     4.3    17.3    -      -       +      -
    148A  ILE*     6.5     0.2    -      -       +      -
    178A  TRP*     4.0    11.0    -      -       -      +
    148B  ILE*     3.5    36.1    -      -       +      -
    149B  ARG      4.2     8.7    -      -       -      -
    150B  ASN*     3.7     1.6    -      -       -      -
    156B  GLN*     3.7    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  PHE*     1.3    80.0    -      -       -      +
     94A  LYS*     1.3    61.9    +      -       -      +
     95A  SER      2.8    23.7    +      -       -      -
     96A  PRO*     4.7     1.0    -      -       -      +
     97A  VAL*     4.0     9.3    -      -       -      +
    103A  ASN*     4.0     9.2    -      -       -      -
    104A  ILE      3.4     9.6    -      -       -      -
    105A  LEU*     4.0     6.3    -      -       -      -
    106A  ILE*     4.4     0.4    -      -       -      -
    178A  TRP*     4.0    23.4    +      -       -      +
    156B  GLN*     3.1    21.9    +      -       -      +
----------------------------------------------------------
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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