Contacts of the strand formed by residues 87 - 93 (chain K) in PDB entry 3STJ


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 87 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31K  VAL*     3.7    23.5    -      -       +      +
     32K  GLU      3.8     5.2    -      -       -      -
     61K  PHE*     4.4     1.0    -      -       -      -
     84K  ILE      3.0    17.1    +      -       -      +
     85K  ASN      3.5     0.4    +      -       -      -
     86K  GLN*     1.3    78.1    -      -       -      +
     88K  GLN*     1.3    60.7    +      -       -      +
     89K  LYS      4.2     1.1    -      -       -      +
     90K  ILE*     3.6    33.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 88 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32K  GLU      2.7     9.7    +      -       -      +
     33K  GLY*     3.7    22.8    -      -       -      +
     34K  THR*     3.4    30.6    -      -       -      +
     86K  GLN      3.6     4.0    +      -       -      +
     87K  ALA*     1.3    76.0    -      -       -      +
     89K  LYS*     1.3    68.1    +      -       +      +
     90K  ILE*     5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 89 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30K  ARG      4.0     0.4    -      -       -      +
     31K  VAL*     3.4     4.0    -      -       -      -
     32K  GLU*     2.9    58.8    +      -       +      +
     87K  ALA*     4.2     0.9    -      -       -      +
     88K  GLN*     1.3    83.9    -      -       +      +
     90K  ILE*     1.4    63.2    +      -       -      +
     91K  SER*     4.3     1.8    -      -       -      +
    101K  ASP*     5.4     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 90 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  VAL*     4.2    10.1    -      -       +      -
     30K  ARG      3.4     7.6    -      -       -      +
     31K  VAL*     3.9     4.0    -      -       +      -
     84K  ILE*     3.7    22.4    -      -       +      +
     87K  ALA*     3.6    23.1    -      -       +      +
     88K  GLN      6.1     0.4    -      -       -      -
     89K  LYS*     1.4    76.5    -      -       -      +
     91K  SER*     1.3    62.7    +      -       -      +
     92K  ILE*     4.0     6.1    -      -       +      -
    101K  ASP*     3.3    11.6    +      -       -      +
    102K  ALA*     2.9    54.8    +      -       +      +
    103K  LYS*     5.2     0.2    -      -       -      -
    104K  LEU*     4.5    15.7    -      -       +      +
    116K  LEU*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 91 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28K  SER      3.8     0.2    -      -       -      +
     30K  ARG*     2.8    58.9    +      -       -      +
     89K  LYS*     5.3     2.4    -      -       -      +
     90K  ILE*     1.3    74.2    -      -       -      +
     92K  ILE*     1.3    70.3    +      -       -      +
     99K  GLU*     5.8     5.4    -      -       -      -
    100K  PHE      3.3    12.1    -      -       -      -
    101K  ASP*     4.5     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 92 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27K  VAL*     3.9    32.8    -      -       +      -
     28K  SER      3.3     3.4    -      -       -      +
     29K  VAL*     4.0     7.6    -      -       +      -
     30K  ARG*     6.4     0.2    -      -       -      -
     77K  VAL*     4.6    10.1    -      -       +      -
     90K  ILE*     4.0     3.8    -      -       +      -
     91K  SER*     1.3    80.6    -      -       -      +
     93K  GLN*     1.3    60.5    +      -       -      +
     94K  LEU*     4.0    17.9    -      -       +      -
     98K  ARG      3.8     0.2    -      -       -      +
     99K  GLU*     3.3     7.0    -      -       -      +
    100K  PHE*     2.8    39.5    +      -       +      +
    102K  ALA*     3.6    24.9    -      -       +      -
    116K  LEU*     3.9    22.0    -      -       +      -
    118K  ILE*     4.0    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 93 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27K  VAL*     3.6     4.9    -      -       -      +
     28K  SER*     2.9    51.2    +      -       -      +
     30K  ARG*     6.5     0.9    -      -       +      -
     92K  ILE*     1.3    74.8    -      -       -      +
     94K  LEU*     1.3    77.2    +      -       -      +
     97K  GLY*     4.0    12.0    -      -       -      +
     98K  ARG      3.4     7.9    -      -       -      +
     99K  GLU*     3.3    28.6    -      -       +      +
----------------------------------------------------------
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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