Contacts of the strand formed by residues 195 - 204 (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 ARG 195 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191E  PRO*     3.7     4.5    -      -       -      +
    192E  ARG      2.7    38.5    +      -       -      +
    193E  HIS*     4.7     6.1    -      -       -      +
    194E  GLY*     1.3    86.9    -      -       -      +
    196E  LEU*     1.3    61.0    -      -       -      +
    197E  CYS*     3.5     5.4    +      -       -      -
    260E  VAL*     4.3    29.7    -      -       +      +
    261E  ILE      6.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 196 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189E  ILE*     3.9    17.3    -      -       +      +
    190E  THR*     4.6     0.2    -      -       -      -
    191E  PRO*     3.7    31.6    -      -       +      +
    195E  ARG*     1.3    71.6    -      -       -      +
    197E  CYS*     1.3    64.3    +      -       -      +
    260E  VAL*     3.6     1.2    -      -       -      +
    261E  ILE*     3.0    44.9    +      -       +      +
    267E  LEU      5.3     3.6    -      -       -      +
    270E  LEU      5.8     0.4    -      -       -      +
    311E  TRP*     3.7    39.9    -      -       +      -
    342E  PRO*     6.3     1.3    -      -       +      -
    346E  ALA*     4.1    25.8    -      -       +      +
    349E  LEU*     4.5    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 197 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189E  ILE*     3.2     9.1    -      -       -      +
    190E  THR      3.0    39.0    +      -       -      +
    192E  ARG*     4.5    17.0    -      -       +      +
    195E  ARG*     3.6    13.5    -      -       -      -
    196E  LEU*     1.3    82.5    -      -       -      +
    198E  PHE*     1.3    60.6    +      -       -      +
    199E  MET*     4.0     2.0    +      -       +      +
    258E  TYR*     4.3    17.3    -      -       +      -
    259E  HIS      3.2    11.9    -      -       -      +
    260E  VAL*     3.7    29.4    -      -       -      -
    261E  ILE*     5.3     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 198 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  ALA*     3.4    25.1    -      -       +      -
    188E  VAL      3.5     4.9    -      -       -      -
    189E  ILE*     3.5    28.7    -      -       +      -
    197E  CYS*     1.3    73.4    -      -       -      +
    199E  MET*     1.3    59.1    +      -       -      +
    200E  LEU*     3.4    43.5    -      -       +      -
    217E  MET*     4.9     8.3    -      -       -      -
    238E  ILE*     5.1     6.3    -      -       +      -
    257E  ILE*     3.1     7.6    -      -       +      +
    258E  TYR*     3.2     2.0    -      -       -      -
    259E  HIS*     2.8    51.0    +      -       +      +
    261E  ILE*     5.2     2.0    -      -       +      -
    267E  LEU*     5.2    11.4    -      -       +      -
    283E  ILE*     5.1    21.8    -      -       +      -
    304E  TYR*     5.6     4.0    -      -       +      -
    309E  ILE*     4.4    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 199 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  ALA*     3.8     1.2    -      -       -      +
    188E  VAL*     2.6    47.2    +      -       +      +
    190E  THR*     6.1     4.3    -      -       +      +
    197E  CYS*     4.0     2.6    +      -       +      +
    198E  PHE*     1.3    74.3    -      -       -      +
    200E  LEU*     1.3    67.4    +      -       -      +
    256E  ILE*     3.5    21.8    -      -       +      -
    257E  ILE      3.2     3.6    -      -       -      +
    258E  TYR*     5.3     3.4    -      -       +      -
    315E  PHE*     3.2    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184E  SER*     4.3     7.0    -      -       -      +
    187E  ALA*     3.5    28.0    -      -       +      -
    198E  PHE*     3.4    31.4    +      -       +      -
    199E  MET*     1.3    72.6    -      -       -      +
    201E  ARG*     1.3    59.9    +      -       -      +
    217E  MET*     4.0    26.0    -      -       +      -
    256E  ILE*     3.2     1.6    -      -       -      -
    257E  ILE*     2.6    42.4    +      -       +      +
    283E  ILE*     5.9     3.1    -      -       +      -
    285E  VAL*     4.0    27.8    -      -       +      -
    304E  TYR*     3.9    27.4    -      -       +      +
    315E  PHE*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 201 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183E  PHE*     4.0     4.8    -      -       -      -
    184E  SER*     3.5    28.2    +      -       -      +
    200E  LEU*     1.3    76.5    -      -       -      +
    202E  VAL*     1.3    62.9    +      -       -      +
    254E  PRO*     4.2    15.5    -      -       +      -
    255E  LEU      3.4    13.5    -      -       -      +
    256E  ILE*     3.8    20.5    -      -       +      +
    315E  PHE*     3.2    51.0    +      -       +      +
    316E  VAL      2.9    32.1    +      -       -      +
    317E  PRO*     4.8     0.8    -      -       -      +
    318E  ILE*     3.5    17.8    -      -       -      +
    332E  LYS      3.5    12.9    +      -       -      -
    333E  PHE*     3.5    45.6    +      -       +      +
    335E  ASN      4.3     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181E  LEU*     5.3     2.5    -      -       +      -
    182E  ILE      3.5    14.8    -      -       -      +
    183E  PHE*     3.8    25.6    -      -       +      -
    201E  ARG*     1.3    75.8    -      -       -      +
    203E  GLY*     1.3    68.3    +      -       -      +
    215E  ILE*     6.2     3.6    -      -       +      -
    251E  LEU*     4.0    23.4    -      -       +      +
    254E  PRO*     3.1    21.0    -      -       -      +
    255E  LEU*     3.2    14.2    +      -       +      +
    257E  ILE*     4.2    15.0    -      -       +      -
    287E  LEU*     4.2    17.9    -      -       +      -
    333E  PHE*     4.0     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180E  THR      4.5     0.2    -      -       -      -
    181E  LEU*     3.7     5.9    -      -       -      +
    182E  ILE*     3.0    37.7    +      -       -      +
    202E  VAL*     1.3    77.7    -      -       -      +
    204E  ASP*     1.3    60.3    +      -       -      -
    205E  LEU*     5.8     0.2    -      -       -      -
    251E  LEU*     4.2     7.0    -      -       -      -
    254E  PRO*     4.1    19.5    -      -       -      -
    330E  TYR*     4.7     6.1    -      -       -      -
    333E  PHE*     3.9     5.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 204 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  HIS*     3.7    11.4    +      -       -      -
    177E  ARG*     4.7     3.1    +      -       -      -
    180E  THR*     3.7    17.3    +      -       -      +
    181E  LEU*     3.8    17.6    -      -       +      +
    203E  GLY*     1.3    74.8    -      -       -      -
    205E  LEU*     1.3    64.0    +      -       -      +
    206E  ARG*     3.2    27.8    +      -       -      +
    208E  SER      3.3    17.1    -      -       -      +
    209E  MET*     5.1     2.5    -      -       -      +
    210E  ILE*     5.7     4.6    -      -       +      +
    251E  LEU*     3.9    25.2    -      -       +      +
    252E  VAL*     4.6     9.6    +      -       -      +
    254E  PRO*     5.2     0.6    -      -       -      +
    330E  TYR*     3.0    21.7    +      -       -      -
----------------------------------------------------------
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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