Contacts of the strand formed by residues 346 - 350 (chain A) in PDB entry 7UUT


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 LYS 346 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ALA*     4.2     6.1    -      -       -      -
     36A  PRO      2.8    28.9    +      -       -      +
     37A  CYS*     3.6     9.1    -      -       -      +
     60A  GLU*     2.9    31.0    +      -       -      -
    147A  MET*     3.6    29.8    -      -       +      -
    151A  MET*     3.4    31.5    -      -       +      +
    177A  PRO*     4.2    11.8    -      -       +      +
    319A  LEU*     3.1    14.5    +      -       +      +
    320A  VAL*     3.5     6.1    -      -       -      +
    321A  THR*     3.2    22.4    +      -       -      -
    322A  HIS      3.9     0.3    +      -       -      -
    337A  MET*     4.3     6.6    -      -       +      +
    344A  LEU*     3.9     3.4    -      -       -      -
    345A  ILE*     1.3    83.3    -      -       +      +
    347A  PRO*     1.3    70.0    -      -       +      +
    348A  VAL*     4.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ALA*     3.5    21.8    -      -       -      +
     36A  PRO*     3.6    26.7    -      -       +      +
    322A  HIS*     3.4     8.5    -      -       +      +
    324A  PHE*     3.9    23.8    -      -       +      -
    333A  ALA*     3.9    13.7    -      -       +      +
    336A  LEU*     4.5     2.2    -      -       +      -
    337A  MET*     3.9    20.0    -      -       -      -
    344A  LEU*     3.7    22.0    -      -       +      -
    346A  LYS*     1.3    89.5    -      -       +      +
    348A  VAL*     1.3    61.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ALA*     4.2     3.4    -      -       +      -
     34A  VAL      3.6     7.6    -      -       -      +
     35A  ALA*     4.7     0.9    -      -       +      -
    143A  GLU*     4.3    10.8    -      -       +      +
    146A  VAL*     3.7    33.0    -      -       +      -
    147A  MET*     3.7    15.0    -      -       +      -
    320A  VAL*     3.7    28.0    -      -       +      -
    322A  HIS      2.9     6.8    +      -       -      +
    323A  VAL*     3.3     5.5    -      -       -      +
    324A  PHE*     2.8    32.6    +      -       -      +
    346A  LYS      4.7     0.2    -      -       -      +
    347A  PRO*     1.3    78.8    -      -       -      +
    349A  VAL*     1.3    59.9    +      -       -      +
    350A  ILE*     4.0    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ALA*     3.2     4.3    -      -       -      -
     34A  VAL*     2.9    45.4    +      -       +      +
     36A  PRO*     5.6     1.8    -      -       +      -
    324A  PHE*     3.7    16.4    -      -       +      -
    326A  GLY      3.4    26.2    -      -       -      +
    329A  ASN      3.8    11.4    -      -       -      +
    330A  ILE*     3.9    11.7    -      -       +      -
    333A  ALA*     3.6    30.7    -      -       +      -
    348A  VAL*     1.3    73.6    -      -       -      +
    350A  ILE*     1.3    65.5    +      -       -      +
    351A  LEU*     3.7    18.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU      3.6     6.1    -      -       -      +
     33A  ALA*     3.6    25.1    -      -       +      -
    142A  LEU*     3.9    21.8    -      -       +      -
    143A  GLU*     3.8    24.2    -      -       -      +
    323A  VAL*     4.0    11.7    -      -       +      -
    324A  PHE      2.9    15.5    +      -       -      +
    325A  ARG*     2.6    49.9    -      -       +      +
    348A  VAL*     4.0     9.6    -      -       +      -
    349A  VAL*     1.3    72.2    -      -       -      +
    351A  LEU*     1.3    55.9    +      -       -      +
    352A  ALA*     4.1    14.1    -      -       -      +
----------------------------------------------------------
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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