Contacts of the strand formed by residues 272 - 281 (chain B) in PDB entry 5DVX


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 272 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  TYR*     4.0     3.1    -      -       -      -
    223B  LEU*     4.8     3.4    -      -       +      -
    253B  VAL*     5.4     3.8    -      -       +      -
    254B  HIS      3.3    17.3    -      -       -      +
    255B  LEU*     3.9    20.6    -      -       +      -
    262B  VAL*     4.6    17.3    -      -       +      -
    265B  ALA*     4.1    11.0    +      -       +      +
    266B  LEU*     4.0    30.3    -      -       +      -
    267B  GLY      5.7     0.4    -      -       -      +
    268B  ARG      4.8     0.4    +      -       -      -
    270B  GLY      4.1     4.2    -      -       -      +
    271B  GLY*     1.3    83.7    -      -       -      +
    273B  ALA*     1.3    62.8    +      -       -      +
    331B  LEU*     4.1    23.3    -      -       +      -
    337B  ALA*     5.8     0.4    -      -       +      -
    339B  GLY      4.1     3.2    +      -       -      +
    340B  VAL*     3.5    21.2    -      -       +      -
    341B  ILE*     3.0    22.2    +      -       -      +
    402B  GOL      4.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  MET*     4.2    11.9    -      -       +      -
    214B  LEU*     4.4     3.1    -      -       +      -
    220B  TYR*     3.6    37.2    -      -       +      -
    253B  VAL*     4.5     0.2    -      -       -      +
    254B  HIS*     2.7    41.4    +      -       +      -
    272B  LEU*     1.3    76.0    -      -       -      +
    274B  VAL*     1.3    65.5    +      -       -      +
    340B  VAL*     4.3     0.4    -      -       -      -
    341B  ILE*     3.2    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  MET*     5.8     1.6    -      -       -      -
    251B  HIS*     3.8    17.5    -      -       +      +
    252B  VAL      3.4     9.9    -      -       -      +
    253B  VAL*     4.3    20.0    -      -       +      -
    254B  HIS*     4.9     0.2    -      -       -      -
    272B  LEU*     5.9     0.4    -      -       +      -
    273B  ALA*     1.3    80.4    -      -       -      +
    275B  LEU*     1.3    71.3    +      -       -      +
    276B  ALA      4.1     0.2    +      -       -      -
    331B  LEU*     4.9     6.7    -      -       +      -
    340B  VAL*     3.8    18.1    -      -       +      +
    341B  ILE      3.0     8.3    +      -       -      +
    342B  TRP*     3.4    45.3    -      -       +      -
    343B  THR*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  LEU*     3.7    20.4    -      -       +      -
    182B  LEU*     4.4    22.2    -      -       +      -
    185B  PHE*     5.6     0.9    -      -       +      -
    212B  MET*     4.5    15.3    -      -       +      -
    250B  ILE      3.6     0.7    -      -       -      +
    251B  HIS*     3.4     3.8    -      -       -      -
    252B  VAL*     2.9    43.4    +      -       +      +
    254B  HIS*     4.1    12.2    +      -       +      +
    273B  ALA      4.2     0.2    -      -       -      -
    274B  VAL*     1.3    72.9    -      -       -      +
    276B  ALA*     1.3    59.3    +      -       -      +
    317B  LEU*     3.8    27.9    -      -       +      +
    343B  THR*     3.6    22.2    -      -       +      +
    345B  PHE*     3.4    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 276 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  GLU*     3.8    12.1    -      -       -      +
    250B  ILE      3.2     4.3    -      -       -      -
    251B  HIS*     3.7    22.9    -      -       +      -
    275B  LEU*     1.3    75.9    -      -       -      +
    277B  ALA*     1.3    60.9    +      -       -      +
    317B  LEU*     5.9     0.7    -      -       -      -
    342B  TRP*     4.1    11.7    -      -       +      -
    343B  THR      2.8    14.5    +      -       -      +
    344B  VAL*     3.3    17.5    -      -       +      +
    345B  PHE*     2.9    31.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 277 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  GLU*     3.3     6.3    -      -       -      +
    250B  ILE*     2.9    46.9    +      -       +      +
    276B  ALA*     1.3    74.8    -      -       -      +
    278B  PHE*     1.3    67.3    -      -       -      +
    279B  LEU*     5.2     0.2    -      -       +      -
    317B  LEU*     4.7     1.3    -      -       +      +
    318B  PRO*     3.6    37.0    -      -       +      -
    344B  VAL*     5.3     1.6    -      -       -      -
    345B  PHE*     3.8    10.1    -      -       +      +
    347B  GLN      4.7     0.2    -      -       -      +
    349B  VAL*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 278 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ILE*     4.6     2.2    -      -       +      -
    237B  SER*     3.9     8.3    -      -       -      -
    239B  HIS*     3.3    43.1    -      -       +      -
    241B  VAL*     3.8    24.7    -      -       +      -
    246B  PHE*     3.6    52.0    -      +       +      -
    248B  ALA      3.6     2.2    -      -       -      -
    249B  GLU*     3.5    18.2    -      -       -      -
    277B  ALA*     1.3    75.4    -      -       -      +
    279B  LEU*     1.3    59.9    +      -       -      +
    280B  GLU      4.2     0.2    -      -       -      -
    344B  VAL*     4.1    19.7    -      -       +      -
    345B  PHE      4.7    10.9    +      -       -      -
    346B  ASN      5.7     0.9    -      -       -      -
    347B  GLN      5.1     0.8    +      -       -      -
    348B  THR*     3.5    19.1    -      -       +      +
    349B  VAL*     3.0    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  LEU*     4.3    12.1    -      -       +      -
    246B  PHE*     4.2     0.9    -      -       -      +
    247B  PRO*     3.3    12.5    -      -       -      +
    248B  ALA*     2.9    55.0    +      -       +      +
    249B  GLU      3.9     0.9    -      -       -      +
    250B  ILE*     3.8    11.9    -      -       +      +
    277B  ALA      3.7    11.7    -      -       -      +
    278B  PHE*     1.3    77.9    -      -       -      +
    280B  GLU*     1.3    61.1    +      -       -      +
    289B  TYR*     3.6    32.5    -      -       +      +
    349B  VAL*     3.3    27.6    -      -       +      +
    351B  LEU*     4.0    22.9    -      -       +      -
    356B  LEU*     4.7     4.7    -      -       +      -
    359B  LEU*     4.6     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 280 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  PHE*     3.5    40.4    -      -       +      -
    247B  PRO*     4.1    10.6    -      -       +      +
    279B  LEU*     1.3    73.4    -      -       -      +
    281B  GLU*     1.3    65.6    +      -       -      +
    348B  THR*     2.9    30.0    +      -       -      +
    349B  VAL      2.8    10.5    +      -       -      +
    350B  SER*     3.2     8.0    +      -       -      +
    351B  LEU*     2.8    25.6    +      -       -      +
    356B  LEU*     4.1     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  PRO*     4.3     6.4    -      -       +      +
    280B  GLU*     1.3    78.8    -      -       -      +
    282B  GLY*     1.3    72.4    +      -       -      +
    350B  SER*     4.4     3.1    +      -       -      -
    351B  LEU      3.3     8.3    -      -       -      +
    353B  ALA*     3.7    32.6    +      -       -      +
    356B  LEU*     3.8    14.2    -      -       +      +
----------------------------------------------------------
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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