Contacts of the strand formed by residues 93 - 102 (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 GLY 93 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  ILE      5.2     0.3    -      -       -      +
     23D  TRP*     6.0     0.3    -      -       -      +
     24D  SER*     3.3    13.6    -      -       -      -
     26D  GLY      3.9     3.8    -      -       -      -
     28D  VAL*     5.1     0.4    -      -       -      -
     51D  ILE*     4.7     0.9    -      -       -      -
     52D  PHE*     3.9    12.3    -      -       -      -
     92D  MET*     1.3    76.3    -      -       -      +
     94D  HIS*     1.3    58.7    +      -       -      +
    318D  PRO*     3.2     8.7    -      -       -      +
    319D  VAL*     2.4    44.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  ILE*     3.9    17.9    -      -       +      -
     21D  ARG*     4.6    14.2    -      -       +      +
     24D  SER*     2.9    31.2    +      -       -      -
     26D  GLY*     3.1    10.0    +      -       -      -
     27D  GLU*     3.1    38.0    +      -       +      +
     28D  VAL      3.0    24.5    +      -       -      +
     93D  GLY*     1.3    75.3    -      -       -      +
     95D  ILE*     1.3    79.7    +      -       -      +
     96D  GLU*     3.4    21.4    +      -       -      +
    316D  ALA*     4.2     8.1    -      -       +      -
    317D  VAL      3.3    11.9    -      -       -      +
    319D  VAL*     3.6     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  GLU*     4.0     3.1    -      -       -      +
     28D  VAL*     3.8    18.4    -      -       +      +
     94D  HIS*     1.3    83.3    -      -       -      +
     96D  GLU*     1.3    64.0    +      -       -      +
     97D  LEU*     3.6     1.6    +      -       +      -
    316D  ALA*     3.4     7.6    -      -       -      -
    317D  VAL*     2.8    47.0    +      -       +      +
    319D  VAL*     3.6    20.2    -      -       +      -
    344D  TYR*     4.4    14.4    -      -       +      -
    347D  VAL*     4.4    13.9    -      -       +      -
    348D  ILE*     3.6    35.7    -      -       +      -
    351D  ASN*     3.8    22.0    -      -       +      +
    381D  LEU*     6.0     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  ARG*     3.0    38.6    +      -       -      -
     27D  GLU*     3.2    31.8    +      -       +      +
     94D  HIS*     3.4    21.2    +      -       -      +
     95D  ILE*     1.3    71.8    -      -       -      +
     97D  LEU*     1.3    68.1    +      -       -      +
    315D  ASP*     3.0    18.2    -      -       -      +
    316D  ALA*     4.1     1.7    -      -       -      +
    351D  ASN*     2.8    19.5    +      -       -      -
    355D  LYS*     3.2    12.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  ILE*     5.0     0.9    -      -       +      -
     96D  GLU*     1.3    78.0    -      -       -      +
     98D  ALA*     1.3    58.8    +      -       -      +
     99D  ALA*     3.0    22.0    +      -       -      +
    100D  PRO*     5.5     0.3    -      -       -      +
    101D  VAL*     3.6    32.8    -      -       +      -
    314D  LEU      3.9     3.4    -      -       -      +
    315D  ASP*     3.2    40.6    +      -       -      +
    316D  ALA*     3.7     9.6    -      -       -      +
    317D  VAL*     4.0    24.2    -      -       +      +
    347D  VAL*     4.5     4.9    -      -       +      -
    351D  ASN*     3.3    10.1    -      -       -      +
    374D  LEU*     3.9    21.8    -      -       +      -
    378D  VAL*     4.0    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96D  GLU      3.5     2.0    +      -       -      -
     97D  LEU*     1.3    70.3    -      -       -      +
     99D  ALA*     1.3    61.5    +      -       -      +
    100D  PRO*     4.8     0.2    -      -       -      -
    351D  ASN*     3.0    10.7    +      -       -      +
    354D  LEU*     3.7    18.8    -      -       +      -
    355D  LYS*     3.7    34.5    -      -       +      +
    358D  ILE*     4.2    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  LEU*     3.0    19.4    -      -       -      +
     98D  ALA*     1.3    82.0    -      -       -      +
    100D  PRO*     1.3    81.2    -      -       +      +
    101D  VAL*     4.2     2.6    -      -       -      +
    259D  GLU*     4.6     4.5    -      -       +      +
    315D  ASP*     5.7     0.2    -      -       -      -
    354D  LEU*     3.6    19.5    -      -       +      +
    358D  ILE*     5.6     0.2    -      -       +      -
    371D  LYS*     4.2    28.0    -      -       +      -
    374D  LEU*     4.2     8.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  LEU      5.0     0.4    -      -       -      +
     98D  ALA      4.8     0.2    -      -       -      +
     99D  ALA*     1.3    94.6    -      -       +      +
    101D  VAL*     1.3    60.2    +      -       -      +
    258D  ALA*     3.4    13.3    -      -       -      +
    259D  GLU*     4.0    31.1    +      -       +      +
    262D  GLN*     3.2    21.3    -      -       -      +
    313D  VAL*     3.7    22.4    -      -       +      -
    314D  LEU      3.4    11.4    -      -       -      +
    315D  ASP*     3.4    19.5    -      -       -      +
    374D  LEU*     5.7     0.3    -      -       -      +
    375D  GLN*     4.5     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  LEU*     3.6    40.2    -      -       +      -
     99D  ALA      4.2     1.6    -      -       -      +
    100D  PRO*     1.3    77.9    -      -       -      +
    102D  THR*     1.3    69.8    +      -       -      +
    103D  HIS      3.7     0.7    +      -       -      -
    258D  ALA*     3.7     2.6    -      -       -      +
    313D  VAL*     4.3     1.7    -      -       -      +
    314D  LEU*     3.1    30.2    +      -       +      +
    374D  LEU*     5.2     3.4    -      -       +      +
    375D  GLN*     3.3    43.5    -      -       +      +
    378D  VAL*     3.9    28.0    -      -       +      -
    379D  ASP*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 102 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101D  VAL*     1.3    75.5    -      -       -      +
    103D  HIS*     1.3    67.3    +      -       -      +
    104D  ILE*     3.1     4.2    +      -       -      -
    107D  PHE*     4.7     5.7    -      -       -      +
    114D  LEU*     4.6    11.0    -      -       +      -
    129D  ILE*     3.5    32.6    -      -       +      +
    130D  TYR*     5.2     0.5    +      -       -      -
    258D  ALA*     3.9    22.7    -      -       +      +
    261D  ILE*     4.7     2.2    -      -       +      -
    312D  MET      3.7     8.7    -      -       -      -
    313D  VAL*     4.1    18.4    -      -       +      +
    314D  LEU*     5.3     0.4    -      -       -      -
    375D  GLN*     2.6    33.8    +      -       -      +
    378D  VAL*     5.6     0.7    -      -       -      +
    379D  ASP*     3.3     6.6    -      -       -      +
----------------------------------------------------------
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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