Contacts of the strand formed by residues 645 - 652 (chain A) in PDB entry 5L6P


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 GLY 645 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641A  ALA*     3.8     5.2    -      -       -      +
    642A  GLY*     2.8    35.5    +      -       -      +
    643A  GLU      3.7     0.4    -      -       -      -
    644A  PHE*     1.3    79.6    -      -       -      +
    646A  GLU*     1.3    61.2    +      -       -      -
    666A  THR      3.3     8.7    +      -       -      -
    668A  LYS*     4.1    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 646 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    638A  VAL*     4.7    22.3    -      -       +      +
    640A  GLY      4.0     9.6    -      -       -      +
    641A  ALA*     4.4     2.9    -      -       +      +
    642A  GLY      4.3     0.2    -      -       -      +
    645A  GLY*     1.3    75.8    -      -       -      +
    647A  VAL*     1.3    65.1    +      -       -      +
    648A  CYS*     5.0     4.9    -      -       -      -
    664A  ILE      4.5     0.2    -      -       -      -
    665A  LYS*     3.5     4.5    -      -       -      +
    666A  THR*     2.9    46.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 647 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    638A  VAL*     3.9     1.6    -      -       -      +
    639A  ILE*     3.2    16.1    +      -       +      -
    640A  GLY      3.0    30.5    +      -       -      +
    642A  GLY*     3.7    22.4    -      -       -      +
    646A  GLU*     1.3    77.9    -      -       -      +
    648A  CYS*     1.3    64.1    +      -       -      +
    663A  ALA*     5.3     2.2    -      -       +      -
    664A  ILE      3.5     8.3    -      -       -      +
    665A  LYS*     4.0    14.4    -      -       +      -
    778A  GLY      4.6     7.2    -      -       -      +
    779A  LEU*     3.4    34.3    -      -       +      +
   1001A  6P8      4.3    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 648 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635A  ILE*     3.8    37.7    -      -       +      -
    637A  GLU      3.4    13.2    -      -       -      +
    638A  VAL*     3.7    16.4    -      -       +      -
    639A  ILE*     3.8     7.9    -      -       -      -
    646A  GLU*     5.0     2.7    -      -       -      -
    647A  VAL*     1.3    79.1    -      -       -      +
    649A  ARG*     1.3    62.8    +      -       -      +
    663A  ALA*     3.5     3.1    -      -       -      +
    664A  ILE*     2.8    58.7    +      -       -      +
    666A  THR*     4.6    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 649 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635A  ILE*     3.9     3.1    -      -       -      +
    636A  GLU*     2.8    50.3    +      -       -      +
    637A  GLU*     2.8    27.4    +      -       -      +
    639A  ILE*     4.0    13.7    -      -       +      +
    648A  CYS*     1.3    73.2    -      -       -      +
    650A  GLY*     1.3    58.1    +      -       -      +
    661A  PHE*     3.6    33.7    -      -       +      -
    662A  VAL      3.6     4.9    -      -       -      +
    664A  ILE*     4.7     1.1    -      -       -      -
    713A  PHE*     3.6    49.8    -      -       +      -
    715A  GLU*     6.0     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 650 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634A  LYS      3.3    13.2    -      -       -      -
    636A  GLU*     3.8     9.6    -      -       -      -
    648A  CYS      4.0     0.4    +      -       -      -
    649A  ARG*     1.3    75.7    -      -       -      +
    651A  ARG*     1.3    59.7    +      -       -      -
    661A  PHE*     3.5    16.7    -      -       -      -
    662A  VAL*     2.8    33.2    +      -       -      -
    664A  ILE*     3.8    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 651 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  CYS      3.7     0.9    -      -       -      +
    633A  VAL*     3.5     7.3    -      -       -      +
    634A  LYS*     2.9    36.9    +      -       +      +
    636A  GLU*     5.4     2.0    -      -       +      +
    650A  GLY*     1.3    73.7    -      -       -      +
    652A  LEU*     1.3    60.4    +      -       -      +
    659A  GLU*     3.5    30.3    -      -       -      +
    660A  VAL      3.5     9.0    -      -       -      +
    661A  PHE*     5.3     7.2    -      -       +      -
    662A  VAL*     3.9     3.5    -      -       -      +
    664A  ILE*     4.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 652 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  CYS*     3.5    13.7    -      -       +      +
    633A  VAL*     3.7    19.5    -      -       +      -
    651A  ARG*     1.3    73.8    -      -       -      +
    653A  LYS*     1.3    65.4    +      -       -      +
    654A  GLN*     3.8    16.9    +      -       +      +
    658A  ARG      4.3     0.5    -      -       -      +
    659A  GLU*     3.4     8.6    -      -       -      +
    660A  VAL*     3.1    37.1    +      -       +      +
    662A  VAL*     3.8    26.0    -      -       +      +
    698A  GLU*     4.1    34.5    -      -       +      +
    710A  LEU*     4.6    11.0    -      -       +      -
----------------------------------------------------------
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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