Contacts of the strand formed by residues 214 - 224 (chain B) in PDB entry 1LHP


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 VAL 214 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  ARG*     3.6    42.6    -      -       +      +
    207B  THR      3.6     4.9    -      -       -      +
    208B  ARG*     4.0    30.1    -      -       +      +
    212B  GLY      3.9     8.7    -      -       -      +
    213B  SER*     1.3    81.1    -      -       -      +
    215B  VAL*     1.3    67.6    +      -       -      +
    216B  THR*     4.0     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  GLN      3.7     1.6    -      -       -      +
    206B  ARG*     3.6     0.9    -      -       -      -
    207B  THR*     2.7    49.9    +      -       +      +
    209B  ALA*     5.6     5.8    -      -       +      -
    213B  SER*     5.4     6.7    -      -       -      +
    214B  VAL*     1.3    76.1    -      -       -      +
    216B  THR*     1.3    69.6    +      -       -      +
    217B  GLN*     4.9     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  HIS*     4.5     2.2    -      -       -      +
    204B  SER*     3.5    25.1    -      -       -      +
    205B  GLN      3.4     9.2    -      -       -      +
    206B  ARG*     3.4    29.2    +      -       -      +
    214B  VAL*     4.0     5.8    +      -       -      +
    215B  VAL*     1.3    81.7    -      -       -      +
    217B  GLN*     1.3    61.9    +      -       -      +
    218B  ARG*     3.7    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  GLY      3.9     0.3    -      -       -      +
    204B  SER*     3.2     5.4    -      -       -      -
    205B  GLN*     2.9    43.4    +      -       +      +
    215B  VAL*     4.2     4.1    -      -       +      +
    216B  THR*     1.3    71.9    -      -       -      +
    218B  ARG*     1.3    62.7    +      -       -      +
    219B  ILE*     4.1    15.0    -      -       +      +
    250B  ASN      4.6     2.6    -      -       -      +
    251B  ASN*     3.9     7.8    +      -       -      -
    252B  LEU*     3.1    33.7    +      -       +      +
    253B  LYS*     3.5    27.7    +      -       -      +
    311B  VAL*     4.4    15.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  LEU*     4.1    36.0    +      -       +      +
    172B  MET*     6.0     0.6    -      -       -      +
    173B  ASP*     2.9    40.0    +      -       -      -
    203B  GLY      3.4     6.1    -      -       -      +
    204B  SER*     4.2     9.2    +      -       -      +
    206B  ARG*     3.9     8.3    -      -       -      +
    216B  THR*     3.7    31.4    +      -       +      +
    217B  GLN*     1.3    77.6    -      -       -      +
    219B  ILE*     1.3    67.1    +      -       -      +
    311B  VAL*     3.6     6.0    -      -       -      +
    312B  LEU*     2.8    49.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172B  MET*     5.3     0.2    -      -       -      +
    202B  LEU*     3.4     5.5    -      -       -      +
    203B  GLY*     2.9    45.0    +      -       -      +
    217B  GLN*     4.1    25.6    -      -       +      +
    218B  ARG*     1.3    79.3    -      -       -      +
    220B  ARG*     1.3    62.2    +      -       -      +
    221B  MET*     4.2     6.1    -      -       +      -
    252B  LEU*     4.0    17.5    -      -       +      +
    253B  LYS*     4.2     9.6    -      -       +      -
    256B  CYS*     3.9    36.8    -      -       +      -
    309B  ALA*     4.2    19.3    -      -       +      -
    310B  THR      3.2    11.7    -      -       -      +
    311B  VAL*     4.5     6.3    -      -       +      -
    312B  LEU*     3.8     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  GLN*     2.9    37.1    +      -       -      +
    193B  PRO*     4.0    23.4    -      -       -      +
    200B  MET*     3.9    28.5    -      -       +      -
    201B  ALA      3.6     4.7    -      -       -      -
    202B  LEU*     4.0     9.4    -      -       +      -
    219B  ILE*     1.3    75.1    -      -       -      +
    221B  MET*     1.3    67.9    +      -       -      +
    222B  GLU*     3.8    18.3    +      -       +      -
    308B  GLN      4.1     0.7    -      -       -      +
    309B  ALA*     3.4     3.8    -      -       -      -
    310B  THR*     2.8    63.9    +      -       -      +
    312B  LEU*     4.0    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  VAL*     5.1     8.1    -      -       +      -
    199B  LEU      3.5     0.9    -      -       -      +
    200B  MET*     3.4     4.3    -      -       -      +
    201B  ALA*     2.9    56.4    +      -       +      +
    202B  LEU      5.1     2.0    -      -       -      +
    219B  ILE*     4.2     9.2    -      -       +      -
    220B  ARG*     1.3    80.0    -      -       -      +
    222B  GLU*     1.3    65.3    +      -       -      +
    223B  MET      4.2     0.7    -      -       -      -
    237B  PHE*     5.6     1.3    -      -       +      -
    256B  CYS*     3.5    46.2    -      -       +      +
    257B  GLU*     4.5     2.0    -      -       -      -
    260B  VAL*     3.8    31.4    -      -       +      -
    307B  VAL*     5.2     5.6    -      -       +      -
    308B  GLN      4.6     6.1    -      -       -      +
    309B  ALA*     3.8    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  SER*     3.0    20.9    -      -       -      -
    193B  PRO*     2.9    33.7    -      -       -      +
    194B  ARG*     3.1    35.4    +      -       +      +
    198B  TYR*     4.3    16.3    -      -       +      -
    199B  LEU      3.2     6.3    -      -       -      +
    200B  MET*     4.4     7.0    -      -       +      -
    220B  ARG*     3.8    20.3    +      -       +      +
    221B  MET*     1.3    81.0    -      -       -      +
    223B  MET*     1.3    61.2    +      -       -      +
    224B  HIS      4.3     0.2    +      -       -      -
    260B  VAL*     6.0     0.2    -      -       -      -
    307B  VAL*     4.3    14.8    -      -       -      +
    308B  GLN      5.0     3.6    +      -       -      -
    310B  THR*     5.1     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  TYR*     3.7     2.5    -      -       -      -
    199B  LEU*     2.7    55.3    +      -       +      +
    221B  MET      4.2     0.4    -      -       -      -
    222B  GLU*     1.3    75.1    -      -       -      +
    224B  HIS*     1.3    76.8    +      -       -      +
    225B  LYS*     3.4     0.6    +      -       -      -
    226B  VAL*     5.2     5.4    -      -       +      -
    260B  VAL*     4.0    39.5    -      -       +      +
    263B  MET*     4.6     6.5    -      -       +      -
    264B  HIS*     4.2    27.6    -      -       +      -
    267B  LEU*     4.0    26.7    -      -       +      -
    307B  VAL*     4.8     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  ASP*     3.6    33.9    +      -       +      +
    198B  TYR*     3.6    36.0    -      +       +      -
    223B  MET*     1.3    90.9    -      -       -      +
    225B  LYS*     1.3    93.6    +      -       +      +
    226B  VAL*     4.3     4.5    -      -       -      +
    264B  HIS*     5.4     8.4    -      -       +      +
----------------------------------------------------------
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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