Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 1UFU


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 118 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ALA*     4.0    18.4    -      -       +      -
    107A  GLN      4.2     8.1    -      -       -      +
    108A  PRO*     6.1     0.9    -      -       +      -
    109A  SER      4.3     0.9    -      -       -      +
    112A  VAL*     3.4    25.6    -      -       +      -
    117A  ASN*     1.3    78.0    -      -       -      +
    119A  THR*     1.3    77.4    +      -       -      +
    120A  LEU*     4.1     5.6    -      -       +      -
    160A  SER*     3.1    18.4    +      -       -      -
    161A  VAL*     3.2    46.0    +      -       +      +
    164A  VAL*     4.2     4.5    -      -       +      -
    194A  LEU*     3.3    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ALA*     3.5     3.1    -      -       -      -
    107A  GLN*     2.6    57.1    +      -       +      +
    118A  VAL*     1.3    76.3    -      -       -      +
    120A  LEU*     1.3    63.1    +      -       -      +
    158A  ILE*     3.4    43.8    -      -       +      +
    159A  PHE      3.4     5.1    +      -       -      +
    160A  SER*     4.5     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     4.1     8.5    -      -       +      -
    105A  SER      3.7     0.7    -      -       -      -
    106A  ALA*     4.2     4.7    -      -       -      -
    118A  VAL*     4.1    14.8    -      -       +      -
    119A  THR*     1.3    79.1    -      -       -      +
    121A  GLN*     1.3    60.9    +      -       -      +
    122A  CYS      4.2     0.4    -      -       -      -
    133A  LEU*     3.6    18.6    -      -       +      -
    157A  ALA      3.8     0.3    -      -       -      +
    158A  ILE*     3.4    10.0    -      -       -      +
    159A  PHE*     2.7    44.7    +      -       +      +
    161A  VAL*     3.8    20.2    -      -       +      -
    172A  TYR*     3.5    40.6    -      -       +      -
    192A  LEU*     3.8    22.2    -      -       +      -
    194A  LEU*     4.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  THR      3.0     3.1    -      -       -      +
    104A  LEU*     2.9    10.6    -      -       -      +
    105A  SER*     2.8    50.5    +      -       -      +
    107A  GLN*     3.6    29.3    -      -       +      +
    120A  LEU*     1.3    73.7    -      -       -      +
    122A  CYS*     1.3    65.6    +      -       -      +
    123A  ASP*     3.8     7.2    +      -       +      +
    156A  ARG*     2.9    40.8    +      -       -      +
    157A  ALA      3.7     3.1    -      -       -      +
    158A  ILE*     3.0    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PRO*     4.0     7.6    -      -       -      -
    103A  THR      3.2     3.8    -      -       -      -
    104A  LEU*     3.9     2.0    -      -       +      +
    120A  LEU      4.2     0.4    -      -       -      -
    121A  GLN*     1.3    71.5    -      -       -      +
    123A  ASP*     1.3    59.9    +      -       -      +
    131A  PHE*     3.2    33.9    -      -       +      -
    156A  ARG*     3.3     4.3    -      -       -      +
    157A  ALA*     3.0    33.4    +      -       +      +
    159A  PHE*     4.2    13.6    -      -       +      -
    174A  CYS*     2.0    51.6    -      -       +      -
    175A  TYR      3.9     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PRO*     3.3     5.8    -      -       -      +
    103A  THR*     2.7    51.9    +      -       +      +
    121A  GLN*     5.0     9.9    -      -       +      +
    122A  CYS*     1.3    75.2    -      -       -      +
    124A  SER*     1.3    70.3    +      -       -      +
    125A  GLN*     5.6     1.4    -      -       -      +
    131A  PHE*     4.7     0.4    -      -       -      -
    155A  SER*     3.4    12.2    +      -       -      +
    156A  ARG*     3.7    19.3    +      -       +      +
----------------------------------------------------------
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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