Contacts of the strand formed by residues 34 - 39 (chain N) 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 N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80M  PHE*     5.4     9.5    -      -       -      -
     30N  ASN*     4.1     0.2    -      -       -      -
     31N  VAL      2.8    37.7    +      -       -      +
     32N  GLY      3.4     0.8    +      -       -      -
     33N  GLY*     1.3    83.9    -      -       -      +
     35N  VAL*     1.3    65.8    +      -       -      +
     36N  TYR*     3.5    18.8    -      -       +      +
     79N  GLY*     3.6    26.2    -      -       -      +
     80N  PHE*     3.8    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 35 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32M  GLY      4.6     4.0    -      -       -      +
     33M  GLY*     5.4     3.1    -      -       -      +
     28N  GLU*     4.6     5.6    -      -       +      +
     29N  LEU      3.3    12.8    -      -       -      +
     30N  ASN*     4.4     6.3    -      -       -      +
     33N  GLY      4.8     6.1    -      -       -      +
     34N  GLN*     1.3    76.2    -      -       -      +
     36N  TYR*     1.3    72.2    +      -       -      +
     37N  PHE*     3.6    29.3    -      -       +      -
     72N  ARG*     3.5    35.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32M  GLY      4.2     9.2    -      -       -      -
     80M  PHE*     5.9     6.9    -      +       -      -
     28N  GLU      3.6     0.2    -      -       -      -
     29N  LEU*     2.6    55.1    +      -       +      +
     31N  VAL*     4.1     6.1    -      -       +      -
     34N  GLN*     3.5    32.6    -      -       +      +
     35N  VAL*     1.3    74.3    -      -       -      +
     37N  PHE*     1.3    63.0    +      -       -      +
     38N  THR*     6.1     0.7    -      -       +      -
     79N  GLY      2.5    30.0    +      -       -      -
     80N  PHE*     3.9     2.4    +      -       -      -
     82N  PHE*     3.7    25.6    -      +       +      -
     83N  ARG*     3.2    42.8    +      -       +      +
     86N  LEU*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 37 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30M  ASN*     3.5    22.9    -      -       -      -
     32M  GLY*     3.6     9.6    +      -       -      -
     33M  GLY*     3.2    31.0    -      -       -      +
     68M  ASP*     4.6    10.8    -      -       +      -
     69M  SER*     5.3     4.5    -      -       -      -
     72M  ARG*     5.2     6.5    -      -       -      -
     74M  PHE*     3.3    28.6    -      +       +      -
     26N  VAL*     4.7     8.5    -      -       +      -
     27N  VAL      3.4     6.7    -      -       -      -
     28N  GLU*     3.3    39.5    -      -       +      -
     35N  VAL*     3.6    24.2    -      -       +      -
     36N  TYR*     1.3    79.9    -      -       -      +
     38N  THR*     1.3    63.5    +      -       -      +
     86N  LEU*     4.2     2.1    -      -       -      +
     90N  ARG*     3.6    14.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 38 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74M  PHE*     3.5    14.1    -      -       -      -
     76M  ASP*     2.9    19.5    +      -       -      -
     26N  VAL*     3.5     0.6    -      -       -      +
     27N  VAL*     2.6    42.4    +      -       +      +
     29N  LEU*     5.6     8.7    -      -       +      -
     36N  TYR*     5.7     0.7    -      -       +      -
     37N  PHE*     1.3    78.6    -      -       -      +
     39N  ARG*     1.3    65.7    +      -       -      +
     42N  THR*     3.3    16.5    -      -       -      +
     43N  LEU*     3.8    33.9    -      -       +      -
     86N  LEU*     3.8    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 39 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54M  MET*     6.1     2.6    -      -       -      +
     66M  ALA*     3.2    31.1    -      -       -      +
     74M  PHE*     3.9    21.5    +      -       +      -
     76M  ASP*     3.2    25.0    +      -       -      +
     25N  GLU*     3.1    44.8    +      -       +      +
     26N  VAL*     4.2     1.8    -      -       +      +
     38N  THR*     1.3    84.8    +      -       -      +
     40N  HIS*     1.3    66.7    +      -       -      +
     41N  SER*     3.5    22.0    +      -       -      +
     42N  THR*     3.1    18.6    +      -       -      +
     43N  LEU*     3.7     3.5    +      -       -      +
----------------------------------------------------------
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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