Contacts of the strand formed by residues 501 - 506 (chain X) in PDB entry 1T6B


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 VAL 501 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369X  THR*     4.2    20.4    -      -       +      +
    492X  ILE*     3.4     2.1    -      -       -      -
    493X  PHE*     2.8    43.1    +      -       +      +
    496X  LYS*     4.9    22.2    -      -       +      -
    499X  ASN*     3.6    16.4    -      -       +      +
    500X  LEU*     1.3    77.3    -      -       -      +
    502X  GLU*     1.3    61.9    +      -       -      +
    503X  ARG*     3.8    28.0    -      -       -      +
    531X  PHE*     3.6    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 502 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259X  TYR*     2.5    35.7    +      -       -      +
    261X  ILE*     3.5    20.7    -      -       +      +
    297X  ARG*     3.2    29.3    +      -       -      +
    326X  ASN*     4.8     3.6    -      -       -      +
    369X  THR*     5.0     3.0    +      -       -      -
    490X  ARG*     3.4    45.3    +      -       +      -
    491X  ILE      3.4     4.3    -      -       -      -
    492X  ILE*     4.1    10.9    -      -       +      +
    500X  LEU      4.4     0.2    +      -       -      -
    501X  VAL*     1.3    74.2    -      -       -      +
    503X  ARG*     1.3    90.2    +      -       -      +
    504X  ARG*     4.2     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 503 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248X  SER*     4.5     2.8    +      -       -      -
    250X  GLU*     2.7    32.9    +      -       -      -
    256X  VAL*     4.7     7.0    -      -       +      -
    257X  ALA      5.5     0.7    -      -       -      -
    259X  TYR*     4.3     3.4    -      -       -      -
    369X  THR      3.1    22.0    +      -       -      -
    370X  GLY*     3.8    10.3    +      -       -      -
    371X  THR*     3.2    29.8    -      -       -      +
    489X  ALA      3.7     0.2    -      -       -      +
    490X  ARG*     3.5     3.3    -      -       -      +
    491X  ILE*     2.9    33.2    +      -       -      +
    501X  VAL*     3.8    14.4    -      -       -      +
    502X  GLU*     1.3   102.6    +      -       -      +
    504X  ARG*     1.3    65.3    +      -       -      +
    505X  ILE*     4.2     1.6    -      -       +      +
    530X  ALA*     3.6    27.1    +      -       +      +
    531X  PHE*     3.5    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 504 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256X  VAL*     3.6     6.4    -      -       -      +
    257X  ALA*     2.9    39.4    +      -       +      +
    259X  TYR*     3.4    29.0    +      -       -      +
    324X  PHE      5.8     0.2    +      -       -      -
    326X  ASN*     2.8    35.3    +      -       -      +
    484X  ILE*     3.6    17.7    -      -       -      -
    485X  GLN*     3.5    29.3    +      -       -      +
    488X  THR*     2.9    41.0    +      -       -      +
    489X  ALA      3.2     4.7    -      -       -      +
    490X  ARG*     3.9    30.6    -      -       +      +
    502X  GLU*     4.2     4.9    +      -       -      -
    503X  ARG*     1.3    78.1    -      -       -      +
    505X  ILE*     1.3    65.1    +      -       -      +
    586X  LYS*     5.6     1.2    -      -       -      +
    587X  MET      5.3     0.4    +      -       -      -
    588X  ASN*     4.7     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 505 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255X  LEU*     3.2    14.4    -      -       +      +
    256X  VAL*     4.8     4.9    -      -       +      -
    488X  THR*     3.2     3.9    -      -       -      -
    489X  ALA*     2.9    34.3    +      -       -      +
    491X  ILE*     3.7    34.8    -      -       +      -
    503X  ARG      4.2     5.4    -      -       -      +
    504X  ARG*     1.3    80.7    -      -       -      +
    506X  ALA*     1.3    71.2    +      -       -      +
    507X  ALA*     3.9     1.6    -      -       -      +
    521X  MET*     3.6    34.1    -      -       +      -
    526X  ALA*     3.9    10.8    -      -       +      +
    529X  ILE*     4.2    10.3    -      -       +      -
    530X  ALA*     3.9    27.1    -      -       +      -
    583X  LEU*     5.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 506 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228X  THR*     3.7    41.5    -      -       +      +
    229X  ALA*     4.1     3.9    -      -       -      +
    255X  LEU*     2.6    32.1    +      -       +      +
    487X  THR      4.0     1.1    -      -       -      -
    488X  THR*     3.8    13.7    -      -       -      +
    504X  ARG      4.3     0.2    -      -       -      -
    505X  ILE*     1.3    81.9    -      -       -      +
    507X  ALA*     1.3    58.2    +      -       -      +
    518X  LYS*     4.2     5.6    -      -       +      +
    519X  PRO      5.1     2.0    -      -       -      +
    521X  MET*     3.9    10.4    -      -       -      +
----------------------------------------------------------
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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