Contacts of the strand formed by residues 174 - 184 (chain D) in PDB entry 1CT8


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 174 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  THR*     3.8    33.2    -      -       +      +
    144D  GLY*     3.9    21.5    -      -       -      +
    145D  TYR      3.6    12.8    -      -       -      +
    146D  PHE*     3.9     4.3    -      -       +      -
    170D  LEU*     3.5     2.1    -      -       -      +
    171D  GLN*     2.6    61.3    +      -       -      +
    173D  ASP*     1.3    99.7    -      -       -      +
    175D  TYR*     1.3    56.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 175 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110D  THR*     5.6     4.7    -      -       -      +
    144D  GLY      2.8    22.5    +      -       -      -
    145D  TYR*     2.9    51.3    +      +       +      +
    146D  PHE*     3.9    27.7    -      +       -      -
    147D  PRO*     5.1     0.2    -      -       +      -
    148D  GLU*     3.4    42.2    -      -       +      +
    168D  ALA*     4.0    13.9    -      -       +      -
    169D  VAL      3.3     7.0    -      -       -      +
    170D  LEU*     3.6    47.1    -      -       +      +
    171D  GLN*     3.1     6.1    -      -       -      -
    174D  LEU*     1.3    71.0    -      -       -      +
    176D  THR*     1.3    58.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 176 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160C  LEU*     4.1    28.3    -      -       +      +
    178C  THR*     5.6     4.9    -      -       +      +
    141D  LEU*     3.7    28.5    -      -       +      -
    142D  VAL      3.3     7.6    -      -       -      +
    143D  LYS*     3.7    15.8    -      -       +      +
    144D  GLY      3.5     7.4    +      -       -      -
    145D  TYR*     4.4     0.7    -      -       -      -
    167D  PRO      4.3     1.0    -      -       -      +
    168D  ALA*     3.3     1.0    -      -       -      -
    169D  VAL*     2.9    32.6    +      -       -      +
    171D  GLN*     2.7    23.8    +      -       -      +
    175D  TYR*     1.3    73.4    +      -       -      +
    177D  LEU*     1.3    65.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 177 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160C  LEU*     6.3     0.2    -      -       -      -
    141D  LEU*     3.6     4.3    -      -       -      +
    142D  VAL*     2.8    44.4    +      -       +      +
    145D  TYR*     3.9    15.0    -      -       +      +
    148D  GLU*     5.2     1.3    -      -       -      +
    150D  VAL*     3.8    23.1    -      -       +      +
    152D  VAL*     3.8    26.7    -      -       +      -
    165D  THR*     4.2    11.2    -      -       +      -
    166D  PHE*     3.2    25.4    -      -       -      +
    167D  PRO*     4.8     2.0    -      -       +      -
    168D  ALA*     3.9    11.4    -      -       +      +
    176D  THR*     1.3    78.3    -      -       -      +
    178D  SER*     1.3    71.8    +      -       -      +
    179D  SER      4.8     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 178 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  VAL*     4.9     6.2    -      -       -      +
    135C  PHE*     3.7    13.1    -      -       -      -
    176C  SER*     3.2    29.6    +      -       -      -
    178C  THR*     4.9     2.9    +      -       -      -
    124D  LEU*     5.2     0.4    -      -       -      -
    140D  CYS      3.2    13.2    -      -       -      -
    141D  LEU*     4.3    13.9    -      -       -      -
    165D  THR*     3.7     0.5    -      -       -      -
    166D  PHE*     2.8    32.5    +      -       -      +
    177D  LEU*     1.3    82.3    -      -       -      +
    179D  SER*     1.3    64.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 179 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  PHE*     3.5     6.7    -      -       -      -
    139D  GLY*     3.2     3.8    -      -       -      -
    140D  CYS*     3.0    31.5    +      -       -      -
    142D  VAL*     6.3     0.2    -      -       -      -
    152D  VAL*     3.9    23.0    -      -       -      +
    154D  TRP*     3.0    29.3    +      -       -      -
    163D  VAL*     3.9     1.9    -      -       -      +
    164D  HIS      3.2     7.8    +      -       -      -
    165D  THR*     3.0    25.5    +      -       -      -
    166D  PHE*     4.4     0.2    -      -       -      -
    177D  LEU*     5.1     0.2    -      -       -      -
    178D  SER*     1.3    76.2    -      -       -      +
    180D  SER*     1.3    61.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 180 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  PHE*     3.4    35.2    -      -       -      -
    137C  ASN*     3.6    13.0    +      -       -      -
    137D  THR*     4.0     7.6    -      -       -      -
    138D  LEU      3.4     7.0    -      -       -      -
    139D  GLY*     4.3     0.2    -      -       -      -
    154D  TRP*     4.3     2.5    -      -       -      -
    162D  GLY      4.1     1.3    +      -       -      -
    163D  VAL*     3.2     7.1    -      -       -      +
    164D  HIS*     2.8    52.0    +      -       -      +
    166D  PHE*     3.9     3.5    -      -       -      -
    179D  SER*     1.3    73.2    -      -       -      +
    181D  VAL*     1.3    62.7    +      -       -      +
    182D  THR*     5.6     0.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 181 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  VAL      3.7     1.0    -      -       -      +
    137D  THR*     3.3     2.4    -      -       -      -
    138D  LEU*     2.9    51.1    +      -       +      +
    154D  TRP*     3.7    39.5    -      -       +      +
    159D  LEU*     3.7    25.8    -      -       +      -
    161D  SER      4.1     6.7    -      -       -      +
    162D  GLY      3.4     2.5    -      -       -      -
    163D  VAL*     3.6    24.2    -      -       +      -
    180D  SER*     1.3    75.9    -      -       -      +
    182D  THR*     1.3    63.8    +      -       -      +
    183D  VAL*     4.3     4.3    -      -       +      -
    193D  VAL*     4.2     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 182 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  ASN*     4.6     8.0    +      -       -      -
    135D  MET*     3.7    45.3    -      -       +      +
    136D  VAL      3.3     8.3    -      -       -      +
    137D  THR*     3.2    22.5    +      -       -      +
    161D  SER      4.1    11.8    -      -       -      +
    162D  GLY*     3.2    20.9    +      -       -      -
    164D  HIS*     5.7     0.9    +      -       -      -
    180D  SER*     5.6     0.5    +      -       -      -
    181D  VAL*     1.3    73.8    -      -       -      +
    183D  VAL*     1.3    67.5    +      -       -      +
    184D  PRO*     4.8     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 183 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  MET*     3.4     7.4    -      -       -      -
    136D  VAL*     2.8    54.2    +      -       +      +
    138D  LEU*     3.9    15.9    -      -       +      -
    159D  LEU*     3.8    39.3    -      -       +      -
    181D  VAL*     4.3     7.6    -      -       +      -
    182D  THR*     1.3    80.4    -      -       -      +
    184D  PRO*     1.3    79.3    -      -       +      +
    187D  THR*     4.1    19.5    -      -       +      +
    188D  TRP*     4.2     5.2    -      -       +      -
    193D  VAL*     4.9     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 184 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134D  SER*     3.2    13.2    -      -       -      +
    135D  MET*     3.8    13.4    -      -       +      -
    136D  VAL*     4.4     0.4    -      -       -      -
    182D  THR      4.8     0.4    -      -       -      +
    183D  VAL*     1.3    90.3    -      -       +      +
    185D  SER*     1.3    53.1    +      -       -      +
    186D  SER*     2.7    17.8    +      -       -      +
    187D  THR*     2.7    46.6    +      -       -      +
    188D  TRP      3.7     2.1    +      -       -      -
----------------------------------------------------------
 Back to top of page


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