Contacts of the strand formed by residues 113 - 122 (chain H) in PDB entry 1U3H


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 ASN 113 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  LEU*     3.9    17.2    -      -       +      +
    105H  ARG*     3.0    39.2    -      -       +      +
    106H  THR*     3.9    13.3    +      -       -      +
    111H  HIS*     3.4    28.1    -      -       -      +
    112H  HIS*     1.3    81.4    +      -       -      +
    114H  THR*     1.3    69.9    +      -       -      +
    162H  GLU*     3.5     6.1    -      -       -      +
    163H  MET*     3.0    31.1    +      -       -      +
    165H  PRO*     3.4    26.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 114 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  LEU*     3.6     5.8    -      -       -      -
    104H  SER*     2.9    41.5    +      -       -      +
    105H  ARG*     4.3     4.5    -      -       -      +
    113H  ASN*     1.3    79.8    +      -       -      +
    115H  LEU*     1.3    76.5    +      -       -      +
    116H  VAL*     4.1     4.5    -      -       +      -
    160H  MET*     3.7    27.4    -      -       +      -
    161H  LEU      3.5     8.1    -      -       -      +
    162H  GLU*     2.8    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101H  ILE*     4.5     1.3    -      -       +      -
    102H  SER      3.4     8.3    -      -       -      +
    103H  LEU*     3.4    26.0    -      -       +      -
    114H  THR*     1.3    79.9    -      -       -      +
    116H  VAL*     1.3    61.3    +      -       -      +
    131H  TRP*     3.7    23.2    -      -       +      -
    159H  VAL      3.9     0.7    -      -       -      +
    160H  MET*     3.4     1.0    -      -       -      -
    161H  LEU*     3.0    36.7    +      -       +      +
    163H  MET*     3.6    21.1    -      -       +      +
    171H  TYR*     3.6    43.1    -      -       +      -
    188H  TRP*     3.9    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 116 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100H  VAL      3.5     2.3    -      -       -      +
    101H  ILE*     3.4     3.8    -      -       -      -
    102H  SER*     2.7    44.0    +      -       -      +
    104H  SER*     3.9    21.1    -      -       -      +
    114H  THR*     4.1     4.5    -      -       +      +
    115H  LEU*     1.3    79.0    -      -       -      +
    117H  CYS*     1.3    65.3    -      -       -      +
    118H  SER*     3.6    17.4    +      -       -      +
    131H  TRP*     4.0     3.1    -      -       -      -
    158H  LEU*     4.4    19.3    -      -       +      -
    159H  VAL      3.5     6.3    -      -       -      +
    160H  MET*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 117 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  VAL*     3.6    20.4    -      -       -      -
    100H  VAL      3.6     4.7    -      -       -      -
    101H  ILE*     4.5     2.9    -      -       +      +
    116H  VAL*     1.3    73.4    -      -       -      +
    118H  SER*     1.3    59.0    +      -       -      +
    119H  VAL*     3.6    12.4    +      -       -      +
    129H  VAL*     4.8     0.2    -      -       +      -
    131H  TRP*     3.5    19.2    -      -       +      +
    157H  VAL      3.8     0.9    -      -       -      +
    158H  LEU*     3.7     1.0    -      -       -      -
    159H  VAL*     2.7    38.4    +      -       +      +
    173H  CYS*     2.0    49.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  PRO*     3.7    31.4    -      -       -      +
     98H  ASN      3.0    12.0    -      -       -      +
     99H  VAL*     3.4     1.6    -      -       -      -
    100H  VAL*     2.9    29.8    +      -       -      +
    102H  SER*     5.0     3.6    +      -       -      -
    116H  VAL*     3.6    11.3    +      -       -      +
    117H  CYS*     1.3    70.8    -      -       -      +
    119H  VAL*     1.3    60.3    +      -       -      +
    120H  THR*     3.8     5.4    -      -       -      +
    158H  LEU*     3.7    24.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97H  PRO*     3.8    19.1    -      -       +      -
     98H  ASN      3.2     4.7    -      -       -      +
     99H  VAL*     4.4     3.1    -      -       +      -
    117H  CYS*     3.9    19.7    -      -       -      +
    118H  SER*     1.3    76.1    -      -       -      +
    120H  THR*     1.3    60.9    +      -       -      +
    122H  PHE*     3.0    19.1    -      -       +      -
    127H  ILE*     3.3    33.2    -      -       +      -
    129H  VAL*     4.0    12.6    -      -       +      -
    157H  VAL*     3.0    31.3    +      -       +      +
    175H  VAL*     3.8    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94G  LYS      3.8    20.8    +      -       -      +
     95G  SER*     4.4     0.7    -      -       -      -
     96G  PRO*     3.8    25.6    -      -       +      +
     97H  PRO*     3.6     1.7    -      -       -      +
     98H  ASN*     2.7    50.5    +      -       -      +
    118H  SER*     4.2     8.7    -      -       -      -
    119H  VAL*     1.3    84.6    -      -       -      +
    121H  ASP*     1.3    76.5    +      -       -      +
    122H  PHE*     3.3     3.8    +      -       -      -
    155H  PHE      3.6     4.0    -      -       -      -
    156H  GLN*     3.7    19.5    -      -       +      +
    158H  LEU*     5.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94G  LYS*     2.8    44.0    +      -       -      +
     95G  SER*     3.6    12.0    +      -       -      -
     95H  GLU*     3.3    20.1    -      -       -      +
     96H  GLN      3.8     8.9    -      -       -      +
     98H  ASN*     4.1    14.6    +      -       +      +
    120H  THR*     1.3    86.4    +      -       -      +
    122H  PHE*     1.3    60.2    +      -       -      +
    150H  ASN*     4.6     1.9    +      -       -      +
    154H  THR*     3.7    17.4    +      -       +      +
    155H  PHE      2.9    10.2    +      -       -      -
    156H  GLN*     4.6     0.4    -      -       -      +
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Residues in contact with PHE 122 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95H  GLU      3.3     4.7    -      -       -      -
     97H  PRO*     3.3    31.0    -      -       +      -
    119H  VAL*     3.0    32.3    -      -       +      -
    120H  THR      4.0     4.5    -      -       -      -
    121H  ASP*     1.3    80.0    -      -       -      +
    123H  TYR*     1.3    64.9    +      -       -      +
    124H  PRO      3.4    14.1    -      -       -      -
    125H  ALA      3.5    21.5    -      -       -      -
    127H  ILE*     3.7    33.7    -      -       +      -
    147H  LEU*     3.8    15.0    -      -       +      -
    154H  THR*     3.3     2.8    -      -       -      -
    155H  PHE*     2.9    48.7    +      -       +      -
    156H  GLN*     3.6     4.5    -      -       -      -
    157H  VAL*     4.0     5.6    -      -       +      -
    177H  HIS*     3.7     8.3    -      +       +      -
----------------------------------------------------------
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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