Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 1EKV


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 HIS 37 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLU      3.5    19.3    -      -       -      -
     14A  MET*     3.4    10.5    -      -       +      -
     15A  THR*     2.9    32.7    +      -       +      -
     35A  THR*     3.4    14.4    +      -       -      -
     36A  ASP*     1.3    93.8    -      -       +      +
     38A  MET*     1.3    64.5    +      -       -      +
     53A  ILE*     3.8     8.5    -      -       +      -
     54A  GLN      3.4    14.4    -      -       -      +
     55A  PRO*     4.0     3.1    -      -       +      -
     56A  PHE*     3.8     9.9    -      -       -      +
    124A  LEU*     3.8    19.8    -      -       +      +
    127A  VAL*     3.5    20.3    -      -       +      +
    128A  ASP*     3.0    28.0    +      -       -      +
    165A  VAL      4.8     0.5    -      -       -      +
    167A  LEU*     4.8     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  HIS*     1.3    75.9    -      -       -      +
     39A  LEU*     1.3    63.5    +      -       -      +
     40A  MET*     3.7    20.0    -      -       +      -
     53A  ILE*     3.4     4.5    -      -       -      +
     54A  GLN*     2.8    59.0    +      -       +      +
     55A  PRO      3.7     2.5    -      -       -      +
     56A  PHE*     3.8     3.8    -      -       +      -
     57A  GLN*     3.4    40.2    -      -       -      +
     59A  LEU*     4.3     7.0    -      -       +      -
    124A  LEU*     3.6     8.1    -      -       -      -
    164A  PHE*     4.4     9.6    -      -       +      -
    165A  VAL      3.2    17.0    -      -       -      +
    166A  ILE*     4.1    15.3    -      -       +      -
     63B  PRO*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     3.5    31.2    -      -       +      -
     38A  MET*     1.3    76.3    -      -       -      +
     40A  MET*     1.3    70.3    +      -       -      +
     41A  VAL*     4.4    11.0    -      -       +      -
     51A  PRO*     4.5     3.8    -      -       +      -
     52A  ARG      3.7    13.9    -      -       -      +
     53A  ILE*     4.3     6.3    -      -       +      +
    117A  LEU*     3.9    21.5    -      -       +      -
    120A  CYS*     3.9    25.8    -      -       +      +
    121A  ILE*     4.8     1.6    -      -       +      -
    124A  LEU*     3.8    12.8    -      -       +      +
    163A  LEU*     4.5     2.9    -      -       +      -
    164A  PHE*     3.2     8.4    -      -       -      +
    165A  VAL*     3.1    49.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  MET*     3.7    23.8    -      -       +      -
     39A  LEU*     1.3    80.9    -      -       -      +
     41A  VAL*     1.3    63.9    +      -       -      +
     42A  GLU*     5.1     0.4    -      -       +      -
     51A  PRO*     3.6     0.5    -      -       -      +
     52A  ARG*     2.8    66.4    +      -       -      +
     54A  GLN*     2.8    43.7    -      -       -      +
     57A  GLN*     5.1     2.5    -      -       +      -
     58A  ASN      5.4     1.8    -      -       -      +
     59A  LEU*     4.1    11.7    -      -       +      -
    162A  LEU*     3.7    36.8    -      -       +      -
    163A  LEU      3.5     5.4    -      -       -      -
    164A  PHE*     4.4     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     3.4    51.8    -      -       +      -
     39A  LEU*     4.4    13.2    -      -       +      -
     40A  MET*     1.3    80.5    -      -       -      +
     42A  GLU*     1.3    66.0    +      -       -      +
     48A  TRP*     3.4    16.6    -      -       +      -
     49A  GLY      3.9    11.4    -      -       -      +
     50A  GLN      4.4     3.4    -      -       -      +
     51A  PRO*     3.6    23.1    -      -       +      -
     52A  ARG*     4.8     0.4    -      -       -      +
    162A  LEU*     3.5     3.6    -      -       -      +
    163A  LEU*     2.9    40.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  VAL*     1.3    76.0    -      -       -      +
     43A  TRP*     1.3    63.0    +      -       -      +
     44A  ASN*     6.0     3.6    -      -       -      +
     48A  TRP*     3.3     7.7    -      -       -      -
     49A  GLY*     2.8    31.5    +      -       -      +
     50A  GLN      4.9     1.8    +      -       -      -
     52A  ARG*     3.8    30.4    +      -       -      +
    161A  ALA      4.0     5.4    -      -       -      +
    162A  LEU*     3.5    21.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  SER      5.4     1.0    +      -       -      -
     42A  GLU*     1.3    78.3    -      -       -      +
     44A  ASN*     1.3    71.5    +      -       -      +
     45A  ASP*     5.3     2.9    -      -       -      -
     47A  GLY*     3.5    31.4    -      -       -      -
     48A  TRP*     3.6    39.0    -      +       +      +
    110A  PRO*     3.4    31.6    -      -       +      +
    157A  GLN*     5.4     7.6    -      -       -      -
    158A  PRO*     3.6    17.9    -      -       +      -
    159A  ARG*     3.2    30.1    -      -       -      -
    160A  ARG*     3.2     7.9    -      -       -      +
    161A  ALA*     2.8    55.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     6.0     3.2    -      -       -      +
     43A  TRP*     1.3    87.1    -      -       -      +
     45A  ASP*     1.3    60.7    +      -       -      +
     46A  LYS*     2.5    59.0    +      -       -      +
     47A  GLY*     2.9    17.4    +      -       -      +
    159A  ARG      3.0    16.2    -      -       -      +
    160A  ARG*     4.5    14.1    -      -       +      +
----------------------------------------------------------
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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