Contacts of the strand formed by residues 521 - 530 (chain A) in PDB entry 1K4T


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 521 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517A  GLU*     3.2     7.1    -      -       -      +
    518A  LEU*     2.8    41.2    +      -       -      +
    519A  ASP*     3.3    23.3    -      -       -      +
    520A  GLY*     1.3    81.1    -      -       -      +
    522A  GLU*     1.3    65.2    +      -       -      +
    524A  VAL*     3.7    17.5    -      -       +      +
    540A  LYS*     5.3     7.9    +      -       -      +
    542A  PRO*     3.4    30.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 522 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  PRO      3.6     7.9    -      -       -      +
    517A  GLU*     4.6     2.7    -      -       +      +
    520A  GLY      3.9    12.5    -      -       -      +
    521A  GLN*     1.3    78.0    -      -       -      +
    523A  TYR*     1.3    90.7    +      -       +      +
    524A  VAL      3.5     0.2    -      -       -      -
    542A  PRO*     4.1    16.1    -      -       -      +
    543A  VAL      4.3     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 523 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515A  HIS      3.6     4.0    -      -       -      -
    516A  PRO*     3.0    21.2    +      -       +      -
    522A  GLU*     1.3    85.5    -      -       +      +
    524A  VAL*     1.3    58.6    +      -       -      +
    543A  VAL*     2.9    41.7    +      -       -      +
    545A  LYS*     3.3    53.6    +      -       +      +
    548A  PHE*     3.6    46.4    -      +       +      -
    549A  LYS*     3.8    18.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  ASN      3.9     0.5    -      -       -      +
    514A  LEU      3.9     0.3    -      -       -      -
    515A  HIS*     2.8    46.3    +      -       +      +
    518A  LEU*     4.0    23.8    -      -       +      +
    521A  GLN*     3.7    41.5    -      -       +      +
    522A  GLU      4.4     1.3    -      -       -      +
    523A  TYR*     1.3    75.8    -      -       -      +
    525A  VAL*     1.3    66.8    +      -       -      +
    526A  GLU*     4.6     1.3    -      -       -      +
    540A  LYS*     3.9    30.3    -      -       +      -
    541A  VAL      3.6     6.5    -      -       -      +
    542A  PRO*     4.4    11.2    -      -       +      -
    548A  PHE*     3.6     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  PHE*     5.7     0.2    -      -       +      -
    512A  ILE*     4.3    17.0    -      -       +      -
    513A  ASN      3.8     2.5    -      -       -      -
    514A  LEU*     4.2    12.3    -      -       +      -
    524A  VAL*     1.3    77.5    -      -       -      +
    526A  GLU*     1.3    60.7    +      -       -      +
    527A  PHE*     3.6    32.4    +      -       +      -
    539A  ASN      3.4     4.2    -      -       -      +
    540A  LYS*     3.5     0.3    -      -       -      -
    541A  VAL*     2.9    35.7    +      -       -      +
    543A  VAL*     3.8    28.9    -      -       +      -
    548A  PHE*     4.3     3.4    -      -       +      -
    551A  LEU*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  HIS      3.7     0.5    -      -       -      +
    512A  ILE*     3.3     5.8    -      -       -      -
    513A  ASN*     2.8    56.8    +      -       +      +
    515A  HIS*     3.0    31.5    -      -       -      +
    524A  VAL*     4.1     1.1    -      -       +      -
    525A  VAL*     1.3    72.1    -      -       -      +
    527A  PHE*     1.3    61.5    -      -       -      +
    528A  ASP*     3.8     3.4    +      -       +      +
    538A  TYR*     2.8    42.9    +      -       +      +
    539A  ASN      3.6     2.5    -      -       -      +
    540A  LYS*     4.1    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 527 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  PHE*     3.7    37.0    -      +       -      -
    485A  LEU*     3.6    26.0    -      -       +      -
    487A  LEU*     4.4     5.6    -      -       +      -
    507A  LEU*     4.0    17.0    -      -       +      -
    511A  HIS      3.6     2.0    -      -       -      -
    512A  ILE*     3.7    22.2    -      -       +      -
    525A  VAL*     3.6    20.9    -      -       +      -
    526A  GLU*     1.3    71.5    -      -       -      +
    528A  ASP*     1.3    60.9    +      -       -      +
    529A  PHE*     4.0    18.2    -      +       +      -
    537A  TYR*     3.7    25.6    -      +       +      -
    538A  TYR*     3.2     9.4    -      -       -      -
    539A  ASN      2.8    36.8    +      -       -      +
    541A  VAL*     3.7    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 528 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510A  GLU      4.7     0.4    -      -       -      +
    511A  HIS*     3.1    28.2    +      -       -      +
    513A  ASN*     5.6     6.3    -      -       -      +
    526A  GLU*     3.8     5.8    +      -       +      +
    527A  PHE*     1.3    75.3    -      -       -      +
    529A  PHE*     1.3    68.1    +      -       -      +
    536A  ARG*     2.9    45.3    +      -       -      +
    537A  TYR      3.3     3.3    -      -       -      +
    538A  TYR*     3.6    15.9    -      -       +      -
    901A  PG4      3.7    32.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 529 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487A  LEU*     4.0    18.8    -      -       +      -
    502A  VAL*     3.5    36.6    -      -       +      -
    503A  GLY*     5.1     3.8    -      -       -      -
    507A  LEU*     3.8    22.0    -      -       +      -
    511A  HIS*     3.5    25.6    -      -       +      -
    527A  PHE*     4.0    14.4    -      +       -      -
    528A  ASP*     1.3    87.7    +      -       -      +
    530A  LEU*     1.3    65.9    +      -       -      +
    531A  GLY*     4.3     6.7    -      -       -      -
    536A  ARG*     3.5     2.7    -      -       -      -
    537A  TYR*     2.7    74.8    +      +       +      +
    901A  PG4      3.9     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 530 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    500A  ASP      4.2    15.9    -      -       -      +
    501A  THR*     3.4     2.8    -      -       +      -
    502A  VAL*     3.0    24.1    +      -       -      +
    529A  PHE*     1.3    80.0    -      -       -      +
    531A  GLY*     1.3    61.8    +      -       -      +
    534A  SER*     3.9    33.2    -      -       -      +
    535A  ILE      3.8     1.8    -      -       -      -
    536A  ARG*     3.9    30.1    -      -       +      -
    901A  PG4      3.2    22.6    +      -       -      +
----------------------------------------------------------
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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