Contacts of the strand formed by residues 513 - 519 (chain D) in PDB entry 4G7Z


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 ILE 513 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  PRO*     4.5     6.8    -      -       -      +
     98D  PRO*     3.5    32.3    -      -       +      -
     99D  ALA      3.6     8.7    -      -       -      +
    100D  ALA*     4.2     6.5    -      -       +      +
    112D  ILE*     4.0     9.2    -      -       +      -
    458D  ALA*     3.8    22.9    -      -       +      +
    461D  ILE*     3.8    16.2    -      -       +      -
    462D  GLN*     3.6    25.2    +      -       +      +
    465D  LEU*     3.5    32.1    -      -       +      -
    510D  GLU      3.1    15.9    +      -       -      +
    511D  TRP*     3.0    12.1    -      -       -      +
    512D  MET*     1.3    81.8    -      -       -      +
    514D  LEU*     1.3    62.7    +      -       -      +
    515D  GLU      4.1     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 514 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1096C  ALA*     3.9    24.5    -      -       +      -
     15D  PRO*     4.9     2.7    -      -       +      -
     18D  ILE*     4.5     8.1    -      -       +      -
     95D  LEU*     4.1     5.0    -      -       +      +
     98D  PRO*     3.4     4.9    -      -       -      +
     99D  ALA      2.6    42.1    +      -       -      +
    100D  ALA      4.5     1.6    -      -       -      +
    101D  HIS*     3.8    33.9    -      -       +      -
    511D  TRP      4.8     7.6    -      -       -      +
    513D  ILE*     1.3    76.1    -      -       -      +
    515D  GLU*     1.3    61.4    +      -       -      +
    516D  ALA      3.5    21.1    -      -       -      +
    517D  VAL*     4.5    17.7    -      -       +      -
    518D  PRO*     4.6     5.2    -      -       +      -
    578D  VAL*     4.7     4.5    -      -       +      -
    582D  LEU*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 515 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  PRO*     4.0    16.8    -      -       +      +
     16D  GLU*     5.4     1.4    -      -       -      +
     19D  ARG*     3.7    15.5    +      -       -      +
     93D  ILE      3.4     2.3    -      -       -      +
     94D  GLU*     3.6    13.7    -      -       -      +
     95D  LEU*     2.9    46.0    +      -       -      +
     98D  PRO*     3.9    17.1    -      -       +      +
    462D  GLN*     2.6    38.4    +      -       -      +
    466D  LYS*     4.5     4.5    +      -       -      -
    514D  LEU*     1.3    75.5    -      -       -      +
    516D  ALA*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 516 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  PRO*     3.8    28.2    -      -       +      +
     18D  ILE*     3.3    28.1    -      -       +      +
     19D  ARG*     4.0    15.0    -      -       +      +
     92D  HIS*     4.4     5.8    -      -       +      -
     93D  ILE      3.8     4.7    -      -       -      -
     94D  GLU*     3.5    16.3    +      -       -      +
    514D  LEU*     3.5    13.3    -      -       -      +
    515D  GLU*     1.3    79.6    +      -       -      +
    517D  VAL*     1.3    60.4    +      -       -      +
    518D  PRO*     3.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 517 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1094C  ALA      5.7     0.9    -      -       -      +
     92D  HIS*     3.2     5.6    -      -       -      -
     93D  ILE*     2.9    53.2    +      -       +      +
     95D  LEU*     4.1    27.8    -      -       +      -
    514D  LEU*     4.5    15.7    -      -       +      -
    516D  ALA*     1.3    72.6    -      -       -      +
    518D  PRO*     1.3    78.6    -      -       +      +
    519D  VAL*     4.0     0.7    -      -       -      +
    544D  TYR*     4.6     0.9    -      -       +      -
    547D  LEU*     4.5     5.4    -      -       +      -
    578D  VAL*     4.3    14.8    -      -       +      -
    581D  LEU*     4.4    20.0    -      -       +      -
    582D  LEU*     5.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 518 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1093C  GLN      3.2    28.0    -      -       -      +
   1094C  ALA*     3.7    15.9    -      -       -      +
   1096C  ALA*     4.4     9.2    -      -       +      +
     18D  ILE*     3.4    34.8    -      -       +      -
     21D  TRP*     4.5     3.6    -      -       +      -
     90D  MET*     4.2     7.9    -      -       +      -
     91D  GLY      3.4     6.5    -      -       -      +
    514D  LEU*     4.6     7.4    -      -       +      -
    516D  ALA      3.5     9.9    -      -       -      +
    517D  VAL*     1.3    93.8    -      -       +      +
    519D  VAL*     1.3    59.7    +      -       -      +
    520D  LEU      3.9     0.2    +      -       -      -
    544D  TYR*     2.9    15.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 519 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  VAL*     4.0    14.8    -      -       +      -
     44D  LEU*     4.7     5.6    -      -       +      -
     50D  PHE*     4.3    12.7    -      -       +      -
     90D  MET*     3.0    16.9    -      -       -      +
     91D  GLY*     2.6    39.3    +      -       -      +
     93D  ILE*     3.6    36.1    -      -       +      -
    517D  VAL      4.0     0.4    -      -       -      +
    518D  PRO*     1.3    74.5    -      -       -      +
    520D  LEU*     1.3    65.3    +      -       -      +
    525D  ARG*     3.6    23.8    -      -       -      +
    544D  TYR*     3.6    17.3    -      -       +      -
----------------------------------------------------------
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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