Contacts of the strand formed by residues 102 - 106 (chain E) in PDB entry 3U8M


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 LEU 102 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  ASP*     3.6    37.2    -      -       +      +
    143D  TRP*     5.6     0.9    -      -       -      -
    144D  THR*     3.8    29.7    -      -       +      +
    145D  HIS*     4.9     3.6    -      -       -      +
     75E  SER*     4.4    10.1    -      -       -      -
     76E  VAL      3.5     3.8    -      -       -      +
     77E  PRO*     3.7    31.4    -      -       +      -
    100E  PRO*     2.9    17.4    +      -       +      +
    101E  GLN*     1.3    80.3    -      -       -      +
    103E  ALA*     1.3    63.8    +      -       -      +
    113E  TYR*     3.2    18.4    -      -       -      -
    114E  MET      5.0     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144D  THR*     5.4     2.2    -      -       -      -
     58E  TRP*     5.6     0.4    -      -       +      -
     75E  SER*     3.2     7.8    -      -       -      -
     76E  VAL      2.7    32.3    +      -       -      +
     78E  ILE*     3.8    13.8    -      -       +      +
     81E  LEU*     3.5    31.6    -      -       +      -
    102E  LEU*     1.3    75.6    -      -       -      +
    104E  ARG*     1.3    61.5    +      -       -      +
    105E  VAL*     4.1     0.9    -      -       -      -
    111E  VAL*     3.9     8.3    -      -       +      -
    112E  LEU      3.3    12.8    -      -       -      +
    113E  TYR*     4.1     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 104 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144D  THR*     3.7    22.4    +      -       +      -
    145D  HIS*     3.6     6.1    +      -       -      -
    146D  HIS*     3.7    15.7    +      -       -      -
    149D  GLU*     2.9    43.5    +      -       -      -
    192D  TYR*     5.6     2.5    +      -       -      +
     73E  GLN*     2.8    45.6    +      -       -      +
     74E  VAL*     3.5    10.4    -      -       -      +
     75E  SER*     2.7    40.4    +      -       -      +
    103E  ALA*     1.3    74.1    -      -       -      +
    105E  VAL*     1.3    61.2    +      -       -      +
    106E  VAL*     4.1     3.8    +      -       +      +
    110E  GLU      3.8     0.7    -      -       -      +
    111E  VAL*     3.4     4.7    -      -       -      -
    112E  LEU*     2.7    52.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 105 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  ILE*     4.7     3.4    -      -       +      -
     63E  LEU*     4.0    25.8    -      -       +      -
     65E  TRP*     3.5    16.5    -      -       +      -
     73E  GLN*     3.2     6.5    -      -       -      -
     74E  VAL*     2.8    43.9    +      -       +      +
     76E  VAL*     3.8    21.8    -      -       +      -
     81E  LEU*     3.9    28.0    -      -       +      -
    104E  ARG*     1.3    78.1    -      -       -      +
    106E  VAL*     1.3    72.8    +      -       -      +
    109E  GLY*     4.8     1.3    -      -       -      -
    110E  GLU      3.5     7.9    -      -       -      +
    111E  VAL*     4.4     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 106 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65E  TRP*     3.8     2.6    -      -       -      -
     72E  ASP*     3.4    27.8    -      -       -      +
     73E  GLN*     4.0    21.1    -      -       +      +
    104E  ARG*     5.0     4.5    -      -       +      +
    105E  VAL*     1.3    80.8    -      -       -      +
    107E  SER*     1.3    61.7    +      -       -      +
    108E  ASP*     3.5    22.9    -      -       -      +
    109E  GLY*     2.7    29.5    +      -       -      -
    110E  GLU*     3.0    22.1    +      -       +      +
    112E  LEU      6.1     0.7    -      -       -      +
----------------------------------------------------------
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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