Contacts of the strand formed by residues 313 - 319 (chain D) in PDB entry 5UHG


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 VAL 313 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ALA*     5.2     3.8    -      -       -      +
    100D  PRO*     3.7    23.1    -      -       +      -
    101D  VAL      4.1     8.5    -      -       -      +
    102D  THR*     4.1    17.5    -      -       +      -
    114D  LEU*     5.1     1.6    -      -       +      -
    258D  ALA      4.4     3.6    -      -       -      +
    261D  ILE*     4.6     2.7    -      -       +      -
    262D  GLN*     3.6    43.1    +      -       +      +
    265D  ILE*     3.9    23.6    -      -       +      -
    310D  MET*     2.9    19.9    +      -       -      +
    311D  GLY*     4.1     2.6    -      -       -      +
    312D  MET*     1.3    83.8    -      -       +      +
    314D  LEU*     1.3    64.3    +      -       -      +
    315D  ASP*     4.0     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 314 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1132C  CYS*     3.7    37.7    -      -       +      -
     14D  LEU*     6.0     0.2    -      -       +      -
     15D  ALA      4.8     6.3    -      -       -      +
     17D  ALA*     5.2     6.1    -      -       -      +
     20D  ILE*     5.9     3.1    -      -       +      -
     97D  LEU*     4.3     1.1    -      -       +      -
    100D  PRO*     3.4     4.9    -      -       -      +
    101D  VAL*     3.1    42.2    +      -       +      +
    102D  THR      5.3     0.2    -      -       -      -
    103D  HIS*     4.2    17.5    -      -       +      -
    311D  GLY*     3.2    25.6    -      -       -      +
    312D  MET      4.8     0.4    -      -       -      -
    313D  VAL*     1.3    72.3    -      -       -      +
    315D  ASP*     1.3    62.8    +      -       -      +
    316D  ALA      3.8    16.4    -      -       -      +
    317D  VAL*     3.8    13.7    -      -       +      -
    378D  VAL*     5.1     1.8    -      -       +      -
    382D  PHE*     3.8    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 315 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ALA*     4.2    16.3    -      -       +      +
     21D  ARG*     4.1    16.4    -      -       -      +
     96D  GLU*     3.0    16.1    -      -       -      +
     97D  LEU*     3.2    28.7    +      -       -      +
    100D  PRO*     3.4    25.8    -      -       -      +
    262D  GLN*     3.1    25.2    +      -       -      +
    313D  VAL      4.0     4.0    -      -       -      +
    314D  LEU*     1.3    76.2    -      -       -      +
    316D  ALA*     1.3    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 316 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ALA*     4.2    17.4    -      -       +      +
     20D  ILE*     3.8    32.4    -      -       +      +
     21D  ARG*     4.5     5.2    -      -       +      +
     94D  HIS*     4.2     5.8    -      -       +      -
     95D  ILE      3.4    12.6    -      -       -      +
     96D  GLU*     4.1    14.1    -      -       -      +
     97D  LEU*     3.9     1.1    -      -       -      -
    314D  LEU*     3.4    14.3    -      -       -      +
    315D  ASP*     1.3    83.0    -      -       -      +
    317D  VAL*     1.3    64.5    +      -       -      +
    318D  PRO*     3.9     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 317 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  ILE*     4.1     2.2    -      -       -      -
     94D  HIS*     3.3     0.2    -      -       -      -
     95D  ILE*     2.8    62.7    +      -       +      +
     97D  LEU*     4.0    22.4    -      -       +      -
    101D  VAL*     5.3     0.2    -      -       +      -
    314D  LEU*     3.8    15.0    -      -       +      -
    316D  ALA*     1.3    72.4    -      -       -      +
    318D  PRO*     1.3    68.7    -      -       +      +
    344D  TYR*     6.2     0.2    -      -       +      -
    347D  VAL*     5.0     5.4    -      -       +      -
    378D  VAL*     3.8    18.8    -      -       +      -
    381D  LEU*     5.6     6.5    -      -       +      -
    382D  PHE*     3.8    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 318 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1129C  GLN      3.6    24.7    -      -       -      +
   1130C  SER*     3.7    20.3    -      -       -      +
   1132C  CYS*     3.7    15.7    -      -       -      -
     20D  ILE*     3.6    39.0    -      -       +      +
     23D  TRP*     4.3    10.5    -      -       +      -
     92D  MET*     4.7     4.9    -      -       +      -
     93D  GLY      3.2    10.8    -      -       -      +
     94D  HIS*     3.9     0.2    -      -       -      -
    317D  VAL*     1.3    89.5    -      -       +      +
    319D  VAL*     1.3    59.2    +      -       -      +
    344D  TYR*     3.6    14.9    +      -       -      -
    381D  LEU*     5.6     0.9    -      -       -      +
    382D  PHE*     5.1     1.0    -      -       +      -
    402D  LEU*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 319 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  VAL*     4.0    13.9    -      -       +      -
     46D  LEU*     4.1     8.3    -      -       +      -
     52D  PHE*     4.7     2.0    -      -       +      -
     92D  MET*     3.7     8.6    -      -       -      +
     93D  GLY*     2.4    49.5    +      -       -      -
     94D  HIS      3.6    16.4    -      -       -      +
     95D  ILE*     3.6    31.6    -      -       +      -
    318D  PRO*     1.3    70.0    -      -       -      +
    320D  ILE*     1.3    74.0    +      -       -      +
    321D  PRO      3.6     1.2    -      -       -      -
    325D  ARG*     4.0    14.8    -      -       -      +
    344D  TYR*     3.5    27.8    -      -       +      -
----------------------------------------------------------
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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