Contacts of the strand formed by residues 255 - 260 (chain E) in PDB entry 5TWV


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 LEU 255 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233C  LEU      4.1    17.5    -      -       -      +
    234C  HIS*     5.6     0.7    -      -       -      -
    235C  GLN*     3.5    38.4    -      -       +      +
    201E  ARG*     3.4     2.3    -      -       -      -
    202E  VAL*     3.2    28.4    +      -       +      +
    249E  ILE*     4.0    18.4    -      -       +      -
    250E  PHE      3.6    16.8    -      -       -      +
    251E  LEU*     3.7    17.7    -      -       +      +
    252E  VAL      5.4     0.4    -      -       -      +
    253E  ALA*     3.2    12.8    +      -       +      +
    254E  PRO*     1.3    77.0    -      -       -      +
    256E  ILE*     1.3    66.4    +      -       -      +
    257E  ILE*     3.5    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 256 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231C  VAL*     5.0    17.3    -      -       +      -
    199E  MET*     3.5    31.4    -      -       +      -
    200E  LEU      3.2     8.3    -      -       -      +
    201E  ARG*     3.8    23.8    -      -       -      +
    249E  ILE*     6.2     0.3    -      -       -      +
    254E  PRO      5.3     0.9    -      -       -      +
    255E  LEU*     1.3    80.9    -      -       -      +
    257E  ILE*     1.3    68.2    +      -       -      +
    258E  TYR*     4.0    12.8    +      -       +      -
    315E  PHE*     3.9    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 257 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198E  PHE*     3.1    12.3    -      -       -      +
    199E  MET*     3.2     3.1    -      -       -      -
    200E  LEU*     2.6    39.0    +      -       +      +
    202E  VAL*     4.2    17.5    -      -       +      -
    215E  ILE*     5.3    12.1    -      -       +      -
    217E  MET*     3.6    37.0    -      -       +      -
    240E  MET*     4.4    27.8    -      -       +      +
    249E  ILE*     6.2     4.5    -      -       +      -
    255E  LEU*     3.5    14.1    -      -       +      +
    256E  ILE*     1.3    80.3    -      -       -      +
    258E  TYR*     1.3    70.6    +      -       -      +
    259E  HIS*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 258 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234C  HIS*     5.1    14.4    -      +       -      -
    192E  ARG*     3.4    33.4    -      -       -      +
    197E  CYS*     4.3    15.3    -      -       +      -
    198E  PHE      3.2     4.5    -      -       -      +
    199E  MET*     5.4     3.4    -      -       +      -
    239E  PRO      4.1     1.2    -      -       -      +
    240E  MET      3.8    14.2    +      -       -      +
    241E  GLU*     3.2    54.7    +      -       +      +
    242E  ASN*     4.6     7.1    +      -       -      -
    249E  ILE*     6.4     2.5    -      -       +      -
    256E  ILE*     4.2    11.4    -      -       +      -
    257E  ILE*     1.3    83.5    -      -       -      +
    259E  HIS*     1.3    60.3    +      -       -      +
    260E  VAL*     4.3    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 259 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197E  CYS*     3.2     6.4    -      -       -      -
    198E  PHE*     2.8    53.1    +      -       +      +
    217E  MET*     6.1     1.1    -      -       -      -
    238E  ILE*     4.2    22.4    -      -       +      -
    239E  PRO*     4.5     9.9    -      -       +      +
    257E  ILE*     6.2     0.4    -      -       +      -
    258E  TYR*     1.3    71.6    -      -       -      +
    260E  VAL*     1.3    64.4    +      -       -      +
    261E  ILE*     3.3    14.2    +      -       +      +
    267E  LEU*     5.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 260 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195E  ARG*     4.3    34.5    -      -       +      +
    196E  LEU      3.6     5.6    -      -       -      -
    197E  CYS*     3.7    16.4    -      -       -      -
    239E  PRO*     4.8    12.2    +      -       +      +
    241E  GLU*     4.1    23.8    -      -       +      +
    258E  TYR*     3.9     7.5    +      -       +      -
    259E  HIS*     1.3    69.3    -      -       -      +
    261E  ILE*     1.3    68.7    +      -       -      +
    262E  ASP*     3.3    21.2    +      -       +      +
    265E  SER*     4.4     2.8    -      -       -      -
----------------------------------------------------------
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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