Contacts of the strand formed by residues 10 - 17 (chain A) in PDB entry 5UWS


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 GLN 10 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     1.3    83.8    -      -       -      +
     11A  PHE*     1.3    71.0    +      -       -      +
     60A  LYS*     3.2    39.8    +      -       +      +
     62A  ASN*     2.6    29.7    +      -       -      +
     84A  GLN*     3.9     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     4.8    13.0    -      -       +      -
     10A  GLN*     1.3    80.6    -      -       -      +
     12A  LYS*     1.3    63.4    +      -       -      +
     13A  LEU      3.6     0.2    +      -       -      -
     59A  ILE*     3.6    39.7    -      -       +      -
     60A  LYS      2.9     8.1    +      -       -      +
     61A  PHE*     3.4    10.8    -      +       +      +
     62A  ASN*     2.8    29.8    +      -       -      -
     84A  GLN*     3.2    31.0    -      -       +      +
     85A  CYS*     4.8     0.7    -      -       -      -
    168A  LEU*     3.8    48.2    -      -       +      -
    169A  ILE*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLN      4.5     0.2    +      -       -      -
     11A  PHE*     1.3    70.9    -      -       -      +
     13A  LEU*     1.3    62.5    +      -       -      +
     14A  VAL*     3.9     9.6    -      -       -      -
     62A  ASN*     3.7     8.9    -      -       +      +
     64A  TRP*     3.5    51.6    -      -       +      +
     79A  TYR      2.8    28.3    +      -       -      -
     81A  ILE      2.6    24.6    +      -       -      +
     82A  GLN*     3.6    26.2    -      -       +      +
     83A  ALA*     3.7     5.6    -      -       +      -
     84A  GLN*     2.8    36.2    +      -       -      +
     85A  CYS*     3.2    10.3    +      -       -      +
     24C  TYR*     4.5     4.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE      3.6     0.8    +      -       -      -
     12A  LYS*     1.3    74.3    -      -       -      +
     14A  VAL*     1.3    75.0    +      -       -      +
     15A  LEU*     4.1     5.6    -      -       +      +
     61A  PHE*     3.7    17.9    -      -       +      -
     62A  ASN      3.0     9.4    +      -       -      +
     63A  VAL*     3.4    21.5    -      -       +      -
     64A  TRP*     2.6    34.7    +      -       -      +
     85A  CYS*     3.4    18.8    -      -       -      +
     86A  ALA*     4.4     1.6    -      -       -      -
     87A  ILE*     4.2    17.7    -      -       +      -
    161A  PHE*     3.6    29.6    -      -       +      -
    164A  LEU*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LYS*     3.9     8.3    -      -       -      -
     13A  LEU*     1.3    78.6    -      -       -      +
     15A  LEU*     1.3    60.5    +      -       -      +
     16A  VAL*     4.1     4.8    -      -       +      +
     64A  TRP*     3.7    10.5    -      -       +      +
     66A  THR*     5.3     1.1    -      -       +      -
     79A  TYR*     3.4    27.6    -      -       +      +
     80A  TYR*     4.1    12.1    -      -       +      -
     83A  ALA*     3.7    21.8    -      -       +      -
     85A  CYS      3.1     6.4    +      -       -      +
     86A  ALA*     3.0    26.3    -      -       +      +
     87A  ILE      2.9    24.6    +      -       -      +
    108A  LEU*     3.7    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     4.2    10.5    -      -       +      -
     14A  VAL*     1.3    74.1    -      -       -      +
     16A  VAL*     1.3    56.2    +      -       -      +
     23A  LYS*     3.6    39.3    -      -       +      +
     26A  PHE*     4.8     5.8    -      -       +      -
     27A  VAL*     3.3    34.3    -      -       +      -
     63A  VAL*     4.4     6.1    -      -       +      -
     64A  TRP      3.1    13.1    +      -       -      +
     65A  ASP*     4.0     9.0    -      -       -      +
     66A  THR*     2.8    32.2    +      -       -      -
     87A  ILE*     3.4    35.0    -      -       +      +
     89A  MET*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     4.7     5.8    -      -       +      +
     15A  LEU*     1.3    80.3    -      -       -      +
     17A  GLY*     1.3    60.0    +      -       -      +
     23A  LYS*     3.4     9.8    -      -       -      +
     66A  THR*     3.5    14.6    -      -       +      +
     80A  TYR*     3.4    38.4    -      -       +      +
     87A  ILE      3.0    13.4    +      -       -      +
     88A  ILE*     3.4    19.1    -      -       +      -
     89A  MET*     2.9    24.1    +      -       -      +
    104A  TRP*     3.8    31.2    -      -       +      +
    108A  LEU*     4.8     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL*     1.3    78.9    -      -       -      +
     18A  ASP*     1.3    66.3    +      -       -      -
     21A  THR*     4.3     0.2    -      -       -      -
     23A  LYS*     2.8    21.1    +      -       -      +
     68A  GLY*     3.1    13.0    -      -       -      -
     88A  ILE*     5.2     0.7    -      -       -      -
     89A  MET      3.4    15.9    -      -       -      -
    104A  TRP*     3.5    23.4    -      -       -      -
----------------------------------------------------------
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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