Contacts of the strand formed by residues 263 - 271 (chain E) in PDB entry 3IT8


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 TYR 263 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  ASP*     2.5    38.6    +      -       +      +
    206E  SER*     2.8    21.5    +      -       -      -
    207E  PHE*     2.8    34.4    +      -       +      -
    208E  TYR*     3.8     9.0    -      +       -      -
    210E  PRO*     3.8    26.7    -      -       +      -
    254E  ILE*     3.9    17.0    -      -       +      -
    255E  LYS*     3.7     3.4    -      -       -      -
    256E  LYS*     3.6    45.7    +      -       +      +
    257E  ASP*     3.4     4.9    -      -       -      -
    261E  ASN      3.3    15.3    -      -       -      -
    262E  THR*     1.3    81.8    +      -       -      +
    264E  SER*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 264 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204E  VAL      3.5     8.3    -      -       -      -
    205E  ASN*     3.8    11.5    +      -       -      +
    206E  SER*     3.0    13.2    +      -       -      -
    207E  PHE*     3.7     2.9    -      -       -      -
    253E  ASN      3.7     0.5    -      -       -      +
    254E  ILE*     3.2     5.7    -      -       -      +
    255E  LYS*     3.0    36.7    +      -       -      +
    257E  ASP*     2.8    27.9    +      -       -      +
    258E  LYS*     5.3     0.9    +      -       -      -
    263E  TYR*     1.3    71.6    -      -       -      +
    265E  LEU*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 265 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202E  CYS      5.1     0.2    -      -       -      +
    203E  THR*     3.3     2.8    -      -       -      -
    204E  VAL*     2.8    50.1    +      -       +      +
    205E  ASN*     5.2     0.5    -      -       -      +
    207E  PHE*     3.7    15.2    -      -       +      -
    212E  VAL*     3.5    32.8    -      -       +      +
    214E  THR*     5.1     6.5    -      -       -      -
    252E  TRP*     4.3    20.0    -      -       +      -
    253E  ASN      3.3    29.2    -      -       -      +
    254E  ILE*     4.0    10.5    -      -       +      -
    264E  SER*     1.3    75.8    -      -       -      +
    266E  THR*     1.3    88.6    +      -       -      +
    267E  ASP*     4.2     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 266 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201E  GLU*     3.9    32.1    +      -       +      +
    202E  CYS      3.6     4.3    -      -       -      +
    203E  THR*     4.2     8.1    -      -       +      +
    253E  ASN*     3.1    37.0    +      -       +      +
    265E  LEU*     1.3    83.2    +      -       -      +
    267E  ASP*     1.3    62.6    +      -       -      +
    268E  LEU*     4.1     4.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 267 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201E  GLU*     3.4     1.9    -      -       -      -
    202E  CYS*     2.7    49.0    +      -       +      +
    214E  THR*     2.9    27.4    -      -       +      +
    216E  TRP*     2.7    32.6    +      -       -      -
    239E  ARG*     3.4    31.2    +      -       -      -
    252E  TRP*     3.7     8.1    -      -       -      -
    253E  ASN      5.9     0.7    +      -       -      -
    265E  LEU*     4.2    12.2    -      -       +      +
    266E  THR*     1.3    74.8    -      -       -      +
    268E  LEU*     1.3    64.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 268 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191E  ASN*     5.2     0.2    -      -       -      +
    193E  LEU*     4.1    22.2    -      -       +      -
    199E  THR*     3.8    24.5    -      -       +      +
    200E  LEU      3.3    14.4    -      -       -      +
    201E  GLU*     3.4    32.1    -      -       +      +
    239E  ARG*     4.8     7.3    +      -       -      -
    266E  THR*     4.1     5.0    +      -       +      -
    267E  ASP*     1.3    79.8    +      -       -      +
    269E  VAL*     1.3    73.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 269 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199E  THR*     3.3     7.5    +      -       -      -
    200E  LEU*     2.7    40.3    +      -       +      +
    216E  TRP*     3.0    55.9    -      -       +      +
    237E  TRP*     5.3     8.5    -      -       +      -
    239E  ARG*     5.3     5.4    -      -       -      -
    267E  ASP*     4.4     0.2    -      -       -      +
    268E  LEU*     1.3    81.2    -      -       -      +
    270E  ARG*     1.3    70.6    +      -       -      +
    271E  THR*     3.2     6.9    +      -       -      +
    275E  MET*     5.3     0.7    -      -       +      -
    279E  PRO*     4.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 270 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193E  LEU*     6.1     6.1    -      -       +      +
    195E  ASP*     3.2    22.6    +      -       -      -
    196E  GLY*     2.9    38.0    -      -       -      +
    197E  ASN*     3.5    17.2    +      -       -      +
    198E  MET      4.3     6.0    +      -       -      -
    199E  THR*     4.6     4.7    -      -       -      +
    269E  VAL*     1.3    77.3    -      -       -      +
    271E  THR*     1.3    53.5    +      -       -      +
    272E  THR*     2.7    42.6    +      -       -      +
    275E  MET*     4.4     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 271 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197E  ASN*     2.5    32.0    +      -       -      +
    198E  MET*     2.9    44.5    +      -       +      +
    200E  LEU*     3.6    34.2    +      -       +      +
    269E  VAL*     3.2     3.1    +      -       -      +
    270E  ARG*     1.3    67.9    -      -       -      +
    272E  THR*     1.3    53.8    +      -       -      +
    275E  MET*     3.8    28.9    -      -       -      -
    278E  GLN*     5.2     4.7    -      -       +      -
    279E  PRO*     4.8     4.0    -      -       +      +
----------------------------------------------------------
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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