Contacts of the strand formed by residues 31 - 37 (chain F) 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 31 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  HIS*     4.4     0.3    -      -       -      +
     30F  ASN*     1.3    80.7    -      -       -      +
     32F  MET*     1.3    61.6    +      -       -      +
     33F  TYR*     3.4    29.9    +      -       +      -
     48F  TYR*     5.9     1.6    -      -       +      -
     49F  SER      2.6    23.8    -      -       -      +
     50F  TYR*     3.8    10.5    -      -       +      -
     69F  ARG*     3.7     0.2    -      -       -      +
     94F  SER*     3.3     3.1    -      -       -      -
     95F  GLY      2.8    43.6    +      -       -      +
     96F  ASP      3.7     3.9    +      -       -      -
     97F  ALA*     3.6    11.3    -      -       +      -
     98F  GLY      3.6     1.9    +      -       -      -
     61G  GLN*     3.3    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 32 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  CYS*     5.2     7.2    -      -       -      -
     25F  GLN*     3.5    31.0    -      -       +      -
     31F  ASN*     1.3    76.5    -      -       -      +
     33F  TYR*     1.3    66.1    +      -       -      +
     48F  TYR*     3.4     4.9    -      -       -      +
     49F  SER      2.9    28.6    +      -       -      +
     69F  ARG*     2.8    41.4    -      -       -      +
     72F  GLN      3.0    15.0    -      -       -      +
     73F  GLU      4.1     4.3    -      -       -      +
     74F  ASN      3.4    19.3    -      -       -      +
     75F  PHE*     3.4    41.1    -      -       +      -
     92F  CYS*     5.3     0.9    -      -       -      -
     93F  ALA      3.0    13.0    -      -       -      +
     94F  SER*     4.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  TYR*     4.4    18.5    -      -       +      +
     31F  ASN*     3.4    42.4    +      -       -      -
     32F  MET*     1.3    77.0    -      -       -      +
     34F  TRP*     1.3    72.8    +      -       -      +
     35F  TYR*     3.5    24.2    -      -       +      -
     45F  LEU*     3.9    11.0    -      -       +      -
     47F  TYR      3.9     3.6    -      -       -      -
     48F  TYR*     3.8    21.8    -      +       +      -
     75F  PHE*     3.3    13.6    -      -       -      -
     92F  CYS*     3.9     2.6    -      -       -      -
     93F  ALA*     2.7    35.8    +      -       +      -
     95F  GLY*     4.3     3.7    -      -       -      -
     96F  ASP      4.8     1.4    +      -       -      -
     98F  GLY      5.0     0.3    -      -       -      -
     99F  GLY*     4.5    14.2    +      -       -      -
    106F  GLN*     3.3    47.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 34 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  GLN*     3.8    18.2    -      -       +      -
     21F  LEU*     2.9    35.9    -      -       +      -
     22F  SER      4.0     3.1    -      -       -      -
     23F  CYS*     3.5    20.4    -      -       +      -
     33F  TYR*     1.3    77.6    -      -       -      +
     35F  TYR*     1.3    63.2    +      -       -      +
     45F  LEU*     4.0     1.2    -      -       -      +
     46F  ILE*     3.0    30.9    +      -       -      +
     47F  TYR      3.3    13.3    +      -       -      +
     75F  PHE*     2.8    45.4    +      +       -      -
     76F  SER      3.4    12.8    -      -       -      -
     77F  LEU*     3.7    37.5    -      -       +      -
     90F  TYR*     4.0    14.8    -      -       +      -
     91F  PHE      2.9    40.6    -      -       -      -
     92F  CYS*     3.6    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104E  GLN      4.7     4.6    +      -       -      -
    106E  PHE*     3.1    39.6    -      +       -      -
     33F  TYR*     3.5    25.2    -      -       +      -
     34F  TRP*     1.3    81.9    -      -       -      +
     36F  ARG*     1.3    64.7    +      -       -      +
     43F  LEU*     3.6    30.5    -      -       +      -
     44F  ARG      3.3     9.4    -      -       -      +
     45F  LEU*     3.8    33.0    -      -       +      +
     46F  ILE*     4.2     1.6    -      -       -      -
     90F  TYR*     3.4    13.3    -      -       -      +
     91F  PHE*     2.9    34.1    +      -       +      +
     93F  ALA*     4.2     2.2    -      -       +      -
    106F  GLN*     2.9    26.4    +      -       -      -
    108F  PHE*     3.7    22.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35F  TYR*     1.3    79.5    -      -       -      +
     37F  GLN*     1.3    62.0    +      -       -      +
     38F  ASP*     2.7    39.6    +      -       -      +
     41F  HIS      4.6     0.2    -      -       -      +
     42F  GLY      3.4     9.8    -      -       -      +
     43F  LEU*     4.7     0.7    -      -       -      -
     44F  ARG*     3.4    42.3    +      -       +      +
     46F  ILE*     3.5    28.9    -      -       +      -
     60F  ILE*     5.5     4.8    -      -       -      +
     65F  TYR*     3.0    24.4    +      -       -      -
     85F  SER      3.2    26.9    +      -       -      -
     86F  GLN*     3.9     3.4    -      -       -      +
     87F  THR      4.5     2.0    +      -       -      +
     88F  SER*     3.6    16.7    +      -       -      +
     89F  VAL      3.3     7.2    -      -       -      +
     90F  TYR*     3.9    13.9    -      -       +      -
     91F  PHE*     4.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  GLN*     2.8    33.1    -      -       -      +
     87E  THR*     5.4     0.7    -      -       -      +
     89E  PHE*     3.0    20.2    -      -       -      -
     36F  ARG*     1.3    69.6    -      -       -      +
     38F  ASP*     1.3    78.1    +      -       -      +
     42F  GLY*     3.3    17.5    -      -       -      +
     43F  LEU*     3.8    10.3    -      -       +      +
     88F  SER*     3.1    11.1    +      -       -      -
     89F  VAL*     2.9    16.2    +      -       +      +
     91F  PHE*     2.9    36.1    -      -       +      -
----------------------------------------------------------
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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