Contacts of the strand formed by residues 382 - 388 (chain B) in PDB entry 3U1K


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 GLY 382 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380B  LEU*     3.1     6.1    -      -       -      +
    381B  HIS*     1.3    80.4    -      -       -      +
    383B  SER*     1.3    63.7    +      -       -      -
    396B  THR*     3.4     5.2    -      -       -      -
    397B  VAL      2.9    27.8    +      -       -      +
    494B  ALA*     3.9     6.7    -      -       -      -
    497B  ASP*     3.4    11.7    -      -       -      -
    498B  SER*     3.9    15.2    -      -       -      -
    601B  LYS*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 383 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374B  VAL*     3.1     7.1    -      -       -      +
    375B  ASP*     3.1    22.5    +      -       -      -
    376B  MET*     2.9    35.3    +      -       -      +
    377B  PHE      3.9     4.0    +      -       -      -
    380B  LEU*     3.8    23.8    -      -       -      +
    382B  GLY*     1.3    76.3    -      -       -      -
    384B  ALA*     1.3    63.7    -      -       -      +
    394B  LEU*     5.3     2.5    -      -       -      -
    395B  CYS      3.2    12.1    -      -       -      -
    396B  THR*     4.6     1.6    -      -       -      -
    494B  ALA*     3.8     7.5    -      -       -      +
    497B  ASP*     2.9    10.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 384 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373B  GLU      3.0    13.7    -      -       -      +
    374B  VAL*     3.8     1.3    -      -       +      -
    376B  MET*     3.9     5.6    -      -       -      -
    383B  SER*     1.3    78.3    -      -       -      +
    385B  LEU*     1.3    60.7    +      -       -      +
    386B  PHE      4.1     0.2    -      -       -      -
    393B  VAL      3.9     0.3    -      -       -      +
    394B  LEU*     3.5     6.0    -      -       -      +
    395B  CYS*     2.9    32.5    +      -       -      +
    490B  GLY*     3.7    15.0    -      -       -      +
    493B  LEU*     3.6    34.5    -      -       +      -
    494B  ALA*     3.8     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371B  SER      3.9     0.9    -      -       -      +
    372B  CYS*     3.2     7.1    -      -       -      +
    373B  GLU*     2.8    50.3    +      -       +      +
    376B  MET*     3.7    15.5    -      -       +      -
    384B  ALA*     1.3    74.5    -      -       -      +
    386B  PHE*     1.3    63.5    +      -       -      +
    387B  GLN*     5.0     5.6    -      -       +      +
    392B  GLN*     3.9    30.5    -      -       +      +
    393B  VAL      3.6    13.2    -      -       -      +
    394B  LEU*     4.1    22.0    -      -       +      -
    477B  LEU*     4.5     0.9    -      -       +      -
    493B  LEU*     4.7     0.3    -      -       -      +
     62C  LYS*     5.5     0.9    -      -       +      +
     63C  LEU*     3.9    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370B  VAL*     4.1    26.5    -      -       +      -
    371B  SER      3.8     0.9    -      -       -      -
    372B  CYS*     3.9     6.7    -      -       -      -
    384B  ALA      4.1     0.6    -      -       -      -
    385B  LEU*     1.3    75.4    -      -       -      +
    387B  GLN*     1.3    61.9    +      -       -      +
    388B  ARG*     3.8    30.3    -      -       +      -
    391B  THR      3.7     1.0    -      -       -      +
    392B  GLN*     3.6     1.7    -      -       -      +
    393B  VAL*     2.9    36.6    +      -       +      +
    486B  ALA*     3.7    30.7    -      -       +      +
    489B  CYS*     3.6    35.4    -      -       +      -
    490B  GLY*     4.1    17.9    -      -       -      -
    493B  LEU*     3.9    15.9    -      -       +      -
    585B  ILE*     4.1    10.3    -      -       +      -
    589B  MET*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369B  ASN      5.3     0.9    -      -       -      +
    370B  VAL*     3.0     9.7    -      -       -      +
    371B  SER*     2.9    48.9    +      -       -      +
    385B  LEU*     5.0     6.2    -      -       +      +
    386B  PHE*     1.3    76.4    -      -       -      +
    388B  ARG*     1.3    59.3    +      -       -      +
    389B  GLY      2.7    27.7    +      -       -      +
    390B  GLN*     3.8     3.0    -      -       -      +
    391B  THR      3.2    15.7    +      -       -      -
    392B  GLN*     3.1    30.8    +      -       -      +
    478B  GLU*     3.2    19.8    +      -       -      -
     65C  ARG*     3.4    14.7    +      -       -      +
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Residues in contact with ARG 388 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  LEU*     4.5    10.1    -      -       -      -
    368B  ARG*     3.1    25.9    -      -       +      +
    369B  ASN      3.4     3.8    -      -       -      -
    370B  VAL*     4.2    17.0    -      -       +      -
    386B  PHE*     3.8    19.1    -      -       +      -
    387B  GLN*     1.3    73.7    -      -       -      +
    389B  GLY*     1.3    65.0    +      -       -      +
    390B  GLN      3.3     0.2    +      -       -      -
    391B  THR*     2.9    31.1    +      -       +      +
    481B  GLY      3.3     4.0    +      -       -      -
    482B  SER*     3.0    42.9    +      -       -      -
    485B  MET*     4.1     3.8    -      -       -      +
    486B  ALA*     3.6    21.5    -      -       -      +
    508B  GLY      4.6     3.0    +      -       -      -
    509B  VAL*     5.2     1.5    -      -       -      +
    532B  ASP*     2.9    44.7    +      -       -      +
    585B  ILE*     4.5    11.4    -      -       -      +
----------------------------------------------------------
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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