Contacts of the strand formed by residues 713 - 721 (chain N) 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 713 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032M  PHE*     4.2    19.7    -      -       +      -
   1036M  GLU*     3.7    17.7    -      -       -      +
   1039M  ALA*     3.5    26.9    -      -       +      -
   1040M  LEU*     4.5     5.2    -      -       +      -
   1043M  TYR*     2.7    36.4    +      -       +      -
    701N  LEU*     4.2    17.0    -      -       +      -
    702N  LEU      3.2    11.9    -      -       -      +
    703N  ASN*     3.2    27.6    -      -       +      +
    707N  THR*     4.2     1.1    -      -       +      -
    710N  ARG      3.1     6.3    +      -       -      +
    712N  GLY*     1.3    77.5    -      -       -      +
    714N  GLN*     1.3    58.3    +      -       -      +
    763N  MET*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 714 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1043M  TYR*     3.5    11.4    -      -       -      +
    701N  LEU*     3.5     3.2    -      -       -      -
    702N  LEU      2.9    31.7    +      -       -      -
    711N  LEU*     3.0    32.8    +      -       +      +
    713N  ILE*     1.3    82.7    -      -       -      +
    715N  ALA*     1.3    61.2    +      -       -      +
    716N  PHE*     3.4    21.4    -      -       +      -
    732N  VAL*     3.4    14.1    -      -       -      +
    735N  ALA*     3.7    19.6    -      -       -      +
    736N  PHE*     3.5    18.2    -      -       +      -
    763N  MET*     3.8     5.8    -      -       -      +
    765N  SER*     3.1    32.4    -      -       -      +
    768N  ASN*     5.3     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 715 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    699N  VAL*     4.0    10.8    -      -       +      -
    700N  VAL      3.3     8.3    -      -       -      +
    701N  LEU*     4.2     7.2    -      -       +      -
    714N  GLN*     1.3    69.4    -      -       -      +
    716N  PHE*     1.3    62.8    +      -       -      +
    759N  ALA      3.2    31.4    -      -       -      +
    763N  MET*     2.8    24.5    +      -       +      +
    764N  LEU*     3.5     9.7    -      -       +      +
    765N  SER*     3.0    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 716 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    639N  LEU      3.6    20.6    -      -       -      -
    640N  HIS      3.3     6.1    -      -       -      +
    641N  GLN      3.2    24.7    -      -       -      -
    642N  CYS*     3.4    27.6    -      -       +      +
    699N  VAL*     3.7     4.7    -      -       -      -
    700N  VAL*     2.7    40.4    +      -       +      +
    702N  LEU*     4.2    14.4    -      -       +      -
    714N  GLN*     3.4    32.8    -      -       +      -
    715N  ALA*     1.3    77.4    -      -       -      +
    717N  GLN*     1.3    59.2    +      -       -      +
    718N  PRO*     3.4     1.4    -      -       -      +
    728N  LEU*     4.2     8.3    -      -       +      -
    729N  HIS*     4.3     4.5    -      -       +      -
    732N  VAL*     3.6    33.7    -      -       +      -
    736N  PHE*     4.2     8.7    -      +       -      -
    764N  LEU*     4.7     0.7    -      -       -      -
    765N  SER*     3.7    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 717 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    640N  HIS*     2.7    29.9    +      -       +      +
    641N  GLN*     3.3    45.2    +      -       +      +
    642N  CYS      3.4     3.6    +      -       -      -
    695N  ILE      5.6     0.9    -      -       -      +
    697N  GLY*     4.6    21.2    +      -       -      +
    698N  LYS      3.6    16.2    -      -       -      +
    699N  VAL*     3.7    12.4    -      -       +      +
    716N  PHE*     1.3    70.8    -      -       -      +
    718N  PRO*     1.3    75.2    -      -       +      +
    719N  VAL*     3.7     1.9    +      -       -      +
    760N  ARG*     5.8     1.2    -      -       -      +
    764N  LEU*     4.9     1.0    -      -       +      +
      3O  GLU*     5.6     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 718 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642N  CYS*     3.6     9.6    -      -       -      +
    644N  LEU*     3.7    31.0    -      -       +      -
    653N  PHE*     5.0     3.6    -      -       +      -
    695N  ILE*     3.7    34.5    -      -       +      +
    698N  LYS      3.2    18.6    -      -       -      +
    699N  VAL*     3.7     5.6    -      -       -      -
    700N  VAL*     4.0    18.4    -      -       +      +
    716N  PHE      3.4     9.2    -      -       -      +
    717N  GLN*     1.3    92.5    -      -       +      +
    719N  VAL*     1.3    62.0    +      -       -      +
    720N  LEU*     4.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 719 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185L  ARG*     4.2    16.4    -      -       -      +
    637N  LEU*     5.5     5.8    -      -       +      -
    641N  GLN*     3.9    41.7    -      -       +      +
    642N  CYS      3.1    11.7    +      -       -      +
    643N  GLY*     3.6     1.6    -      -       -      -
    644N  LEU      3.0    20.6    +      -       -      +
    695N  ILE*     5.3     0.2    -      -       -      -
    717N  GLN*     4.3     2.7    -      -       -      +
    718N  PRO*     1.3    77.2    -      -       -      +
    720N  LEU*     1.3    73.4    +      -       -      +
    721N  VAL*     3.3    11.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 720 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185L  ARG*     3.4    28.7    +      -       -      -
    644N  LEU*     3.2    17.3    -      -       +      +
    645N  PRO      4.9     0.7    -      -       -      +
    646N  LYS*     4.8    14.8    -      -       +      -
    649N  ALA*     3.7    25.6    -      -       +      -
    688N  TRP*     5.2     3.1    -      -       +      +
    691N  LEU*     3.7    35.7    -      -       +      -
    692N  GLU*     4.3    31.6    +      -       +      +
    695N  ILE*     3.7    27.3    -      -       +      +
    718N  PRO*     4.2     0.8    +      -       +      -
    719N  VAL*     1.3    73.2    -      -       -      +
    721N  VAL*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 721 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185L  ARG*     4.7     9.0    -      -       -      +
    190L  THR*     5.1     0.9    -      -       +      -
    643N  GLY*     4.1     4.9    -      -       -      -
    644N  LEU      2.9    28.1    +      -       -      +
    645N  PRO*     3.4     5.3    -      -       +      +
    646N  LYS*     3.0    31.1    +      -       -      +
    719N  VAL*     3.3    22.2    -      -       +      +
    720N  LEU*     1.3    75.3    -      -       -      +
    722N  GLU*     1.3    71.7    +      -       -      +
    725N  SER      4.3     7.9    -      -       -      +
    727N  GLN*     3.3    35.7    -      -       -      +
----------------------------------------------------------
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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