Contacts of the strand formed by residues 373 - 377 (chain A) in PDB entry 3ELP


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 LEU 373 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  PRO*     4.6    13.0    -      -       +      +
    163A  THR*     5.0     8.7    -      -       -      +
    290A  ILE*     5.6     0.2    -      -       +      -
    315A  THR*     3.7    21.5    -      -       +      -
    316A  PHE      3.7     3.8    -      -       -      +
    317A  TYR*     3.7    28.7    -      -       +      +
    350A  LEU*     3.1    21.0    -      -       -      +
    351A  PRO*     3.7    29.5    -      -       +      +
    352A  ALA      5.3     0.2    +      -       -      -
    369A  ILE*     3.7    22.4    -      -       +      -
    370A  SER*     3.0    20.9    +      -       -      +
    372A  THR*     1.3    76.7    -      -       -      +
    374A  ILE*     1.3    77.3    +      -       -      +
    375A  ARG*     4.0     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  VAL      3.8     0.9    -      -       -      +
    315A  THR*     3.2     3.6    -      -       -      +
    316A  PHE*     2.8    71.3    +      -       +      +
    318A  ILE*     4.1    18.2    -      -       +      -
    325A  ALA*     4.3     7.9    -      -       +      +
    328A  PHE*     3.3    35.4    -      -       +      -
    329A  LEU*     4.5     4.9    -      -       +      -
    349A  GLU      3.2    16.8    -      -       -      +
    350A  LEU*     4.0    13.2    -      -       +      -
    372A  THR      4.4     2.0    -      -       -      +
    373A  LEU*     1.3    85.8    -      -       -      +
    375A  ARG*     1.3    63.6    +      -       -      +
    376A  LEU*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  ASN*     3.4    29.9    +      -       -      +
    162A  PRO*     3.6    18.8    -      -       +      +
    313A  MET*     3.6    19.2    -      -       +      +
    314A  VAL      3.6     2.9    -      -       -      -
    315A  THR*     4.2    11.7    -      -       -      +
    339A  GLU      3.2    24.9    +      -       -      -
    340A  SER      3.8     6.7    +      -       -      -
    341A  LEU*     3.6    34.7    -      -       -      +
    347A  LEU      4.2     0.3    -      -       -      +
    348A  ALA*     3.8     1.9    -      -       -      -
    349A  GLU*     2.8    64.6    +      -       -      +
    351A  PRO*     4.4     4.4    -      -       +      +
    373A  LEU*     4.0     2.7    -      -       +      +
    374A  ILE*     1.3    74.4    -      -       -      +
    376A  LEU*     1.3    70.5    +      -       -      +
    377A  SER*     4.7     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  VAL*     3.7    29.6    -      -       +      -
    280A  LEU*     4.1    15.0    -      -       +      -
    313A  MET*     3.4     5.2    -      -       -      +
    314A  VAL*     2.6    42.1    +      -       +      +
    316A  PHE*     4.2    12.1    -      -       +      -
    328A  PHE*     5.0     3.1    -      -       +      -
    335A  PHE*     3.9    26.2    -      -       +      -
    347A  LEU      3.3     2.0    -      -       -      +
    348A  ALA*     3.9    26.9    -      -       +      -
    374A  ILE*     4.0    14.4    -      -       +      -
    375A  ARG*     1.3    82.8    +      -       -      +
    377A  SER*     1.3    60.7    +      -       -      +
    378A  VAL*     3.8     4.0    -      -       +      -
    390A  LEU*     4.1    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  HIS*     6.1     0.2    -      -       -      -
    312A  GLY      3.7     4.6    -      -       -      -
    313A  MET*     4.7     2.4    -      -       -      +
    340A  SER      4.6     1.6    -      -       -      -
    341A  LEU*     3.6    17.1    -      -       -      +
    342A  GLY*     3.3    24.9    +      -       -      -
    345A  GLU      3.8     2.6    +      -       -      +
    346A  SER*     3.1     3.5    -      -       -      -
    347A  LEU*     2.7    50.9    +      -       -      +
    375A  ARG*     4.7     3.6    -      -       -      -
    376A  LEU*     1.3    74.7    -      -       -      +
    378A  VAL*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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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