Contacts of the strand formed by residues 34 - 39 (chain K) in PDB entry 5A15


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 GLN 34 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30K  ASN*     3.6     0.6    -      -       -      -
     31K  VAL      2.7    39.9    +      -       -      +
     32K  GLY      3.4     0.4    -      -       -      -
     33K  GLY*     1.3    83.0    -      -       -      +
     35K  VAL*     1.3    65.7    +      -       -      +
     36K  TYR*     3.5    36.9    +      -       +      +
     79K  GLY*     3.7    11.7    -      -       -      +
     80K  PHE*     3.9    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 35 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28K  GLU*     4.1    13.7    -      -       +      +
     29K  LEU      3.2    12.6    -      -       -      +
     30K  ASN*     5.0     6.7    -      -       -      +
     33K  GLY      3.9     6.0    +      -       -      +
     34K  GLN*     1.3    78.2    -      -       -      +
     36K  TYR*     1.3    71.9    +      -       -      +
     37K  PHE*     3.6    29.7    -      -       +      -
     72K  ARG*     3.9    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27K  VAL      3.8     0.2    -      -       -      +
     28K  GLU*     3.6     1.4    -      -       -      -
     29K  LEU*     2.6    50.1    +      -       +      +
     31K  VAL*     4.0     5.8    -      -       +      -
     34K  GLN*     3.5    33.8    -      -       +      +
     35K  VAL*     1.3    75.8    -      -       -      +
     37K  PHE*     1.3    63.0    +      -       -      +
     79K  GLY      2.5    31.3    +      -       -      -
     80K  PHE*     3.7     4.2    +      -       -      -
     82K  PHE*     3.7    22.4    -      +       +      -
     83K  ARG*     3.5    40.6    +      -       +      +
     86K  LEU*     4.3    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 37 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26K  VAL*     4.7    17.7    -      -       +      -
     27K  VAL      3.4     5.4    -      -       -      +
     28K  GLU*     3.2    44.4    -      -       +      -
     35K  VAL*     3.6    23.3    -      -       +      -
     36K  TYR*     1.3    80.9    -      -       -      +
     38K  THR*     1.3    63.7    +      -       -      +
     86K  LEU*     4.2     7.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 38 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26K  VAL*     4.4     6.4    -      -       -      +
     27K  VAL*     2.6    43.3    +      -       -      +
     29K  LEU*     3.9    16.2    -      -       +      -
     37K  PHE*     1.3    76.7    -      -       -      +
     39K  ARG*     1.3    68.1    +      -       -      +
     42K  THR*     3.6    15.8    +      -       -      +
     43K  LEU*     3.8    31.4    -      -       +      -
     86K  LEU*     3.5    29.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 39 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25K  GLU*     3.2    18.6    +      -       -      +
     26K  VAL*     4.4     8.6    -      -       +      +
     27K  VAL*     4.6     0.7    -      -       -      -
     38K  THR*     1.3    82.5    +      -       -      +
     40K  HIS*     1.3    65.5    +      -       -      +
     41K  SER*     3.7    18.6    -      -       -      +
     42K  THR*     3.1    27.5    +      -       -      +
     43K  LEU*     3.5     8.3    +      -       -      +
----------------------------------------------------------
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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