Contacts of the strand formed by residues 93 - 98 (chain D) in PDB entry 3E5X


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 ASN 93 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  ARG*     5.2     1.6    -      -       -      +
     46D  PRO*     3.3    13.6    -      -       -      +
     47D  GLY*     2.8    35.8    +      -       -      +
     65D  ILE*     3.4     8.6    -      -       -      +
     66D  ILE*     2.9    63.2    +      -       -      +
     67D  PHE      5.2     1.6    +      -       -      -
     91D  GLY      4.0     1.2    +      -       -      -
     92D  ASN*     1.3    71.1    -      -       -      +
     94D  ILE*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  ILE*     3.5    24.6    -      -       +      +
     45D  MET      3.3    21.1    -      -       -      +
     48D  GLU      5.4     1.9    +      -       -      +
     63D  LEU*     3.7    30.1    -      -       +      -
     64D  ASP      3.4    12.6    -      -       -      +
     65D  ILE*     4.0     4.3    -      -       +      -
     75D  LEU*     3.9    23.8    -      -       +      -
     86D  LYS*     3.4    31.6    -      -       -      +
     92D  ASN*     3.6    20.7    +      -       +      +
     93D  ASN*     1.3    89.6    +      -       -      +
     95D  TYR*     1.3    66.2    +      -       -      +
    503D  3C4      3.5    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  GLY      4.8     3.6    +      -       -      -
     42D  ALA*     3.9    19.7    -      -       +      +
     44D  ILE      3.2    14.8    -      -       -      -
     46D  PRO*     3.5    21.3    -      -       +      -
     62D  LYS      3.8     1.4    -      -       -      +
     63D  LEU*     3.6     0.2    -      -       -      -
     64D  ASP*     2.7    38.6    +      -       -      +
     66D  ILE*     3.5    24.2    -      -       +      +
     72D  GLU*     3.5    29.2    -      -       -      +
     93D  ASN      4.3     0.2    -      -       -      -
     94D  ILE*     1.3    76.9    -      -       -      +
     96D  ALA*     1.3    59.4    +      -       -      +
     97D  THR*     3.0    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  ALA*     3.6     3.3    -      -       -      -
     43D  VAL*     2.8    28.3    +      -       +      -
     44D  ILE*     3.0    31.7    +      -       +      +
     61D  ILE*     3.9    15.9    -      -       +      -
     62D  LYS      3.1    10.1    -      -       -      +
     63D  LEU*     4.0    21.5    -      -       +      -
     84D  ILE*     5.0     1.3    -      -       +      -
     95D  TYR*     1.3    75.6    -      -       -      +
     97D  THR*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  GLY*     4.2    10.3    -      -       -      +
     41D  SER      3.4    12.1    -      -       -      +
     43D  VAL*     4.5     3.1    -      -       -      -
     61D  ILE*     3.3     4.6    -      -       -      -
     62D  LYS*     2.9    45.6    +      -       -      +
     95D  TYR*     3.0    46.3    -      -       +      +
     96D  ALA*     1.3    73.4    -      -       -      +
     98D  ALA*     1.3    68.8    +      -       -      +
     99D  MET*     3.4     3.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  PHE*     3.9    21.1    -      -       +      -
     38D  ALA      3.5    22.2    -      -       -      +
     40D  GLY*     2.8    27.7    +      -       -      -
     41D  SER      3.0     9.3    +      -       -      +
     43D  VAL*     4.1     4.0    -      -       +      +
     60D  LYS      3.5     5.8    -      -       -      -
     61D  ILE*     4.4     3.4    -      -       -      -
     97D  THR*     1.3    73.0    -      -       -      +
     99D  MET*     1.3    57.2    +      -       -      +
    100D  GLU      3.2    17.5    -      -       -      +
    102D  THR*     3.9     8.5    -      -       -      +
----------------------------------------------------------
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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