Contacts of the strand formed by residues 10 - 16 (chain L) in PDB entry 5X22


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 10 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229K  GLN*     4.8    16.6    -      -       +      +
      9L  PRO*     1.3    75.2    -      -       -      +
     11L  PHE*     1.3    65.5    +      -       -      +
     12L  THR*     4.1    15.9    +      -       -      +
     24L  VAL      3.6     1.6    -      -       -      +
     25L  LEU*     3.4     5.4    -      -       -      +
     26L  GLU*     2.8    59.1    +      -       +      +
     27L  PRO*     4.7     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 11 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224K  TYR      3.9     5.6    -      -       -      +
    225K  PHE*     3.2    59.2    -      +       +      -
    227K  ASN      3.6    20.3    +      -       -      +
    228K  PRO*     3.6    11.0    -      -       +      -
    229K  GLN*     3.1    29.8    +      -       -      +
      9L  PRO      4.2     1.0    +      -       -      -
     10L  VAL*     1.3    74.4    -      -       -      +
     12L  THR*     1.3    66.1    +      -       -      +
     13L  VAL*     4.1     8.1    -      -       +      -
     23L  PHE*     3.7    43.1    -      +       +      -
     24L  VAL      3.2    12.8    -      -       -      -
     25L  LEU*     3.9    16.4    -      -       +      -
    208L  LEU*     5.2     4.9    -      -       +      -
    211L  LEU*     3.9     7.4    -      -       +      -
    212L  ASN*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 12 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229K  GLN*     3.8     7.5    -      -       +      +
    230K  ALA      4.8     0.9    -      -       -      +
    231K  ALA*     3.7    31.6    -      -       +      -
     10L  VAL*     4.3    17.7    -      -       -      +
     11L  PHE*     1.3    74.3    -      -       -      +
     13L  VAL*     1.3    66.2    +      -       -      +
     14L  ARG*     4.3     6.1    -      -       +      +
     22L  GLU      3.9     0.5    -      -       -      +
     23L  PHE*     3.4     5.5    -      -       -      -
     24L  VAL*     2.9    52.2    +      -       +      +
     26L  GLU*     5.6     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 13 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228K  PRO*     3.7    30.3    -      -       +      -
    229K  GLN      3.0    12.7    +      -       -      +
    230K  ALA*     4.3     1.9    -      -       -      -
    231K  ALA*     3.4    21.6    +      -       -      -
     11L  PHE*     4.1    11.4    -      -       +      -
     12L  THR*     1.3    78.8    -      -       -      +
     14L  ARG*     1.3    63.5    +      -       -      +
     15L  THR*     3.7    24.0    -      -       +      -
     22L  GLU      3.7     2.2    -      -       -      -
     23L  PHE*     3.8    29.6    -      -       +      -
    208L  LEU*     4.9    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 14 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231K  ALA*     3.6    17.3    -      -       +      +
    233K  VAL*     3.5    33.6    -      -       -      +
    234K  ALA*     6.5     1.1    -      -       -      -
     12L  THR*     5.1     4.3    -      -       +      +
     13L  VAL*     1.3    75.4    -      -       -      +
     15L  THR*     1.3    64.9    +      -       -      +
     16L  GLN*     5.8     7.2    -      -       +      +
     20L  TYR*     5.5     1.0    -      -       -      -
     21L  GLY*     3.6     0.5    -      -       -      -
     22L  GLU*     2.9    75.9    +      -       +      +
     24L  VAL*     4.4    17.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 15 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13L  VAL*     3.7    22.9    -      -       +      -
     14L  ARG*     1.3    82.2    -      -       -      +
     16L  GLN*     1.3    69.1    +      -       -      +
     17L  GLY      4.2    11.9    +      -       -      -
     20L  TYR*     3.7    10.3    -      -       -      -
     21L  GLY*     4.5     8.5    -      -       -      -
     23L  PHE*     4.9     6.5    -      -       +      -
    207L  PRO*     5.7     4.3    -      -       +      -
    208L  LEU*     5.6     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 16 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  ARG*     5.8     8.7    -      -       +      +
     15L  THR*     1.3    78.3    -      -       -      +
     17L  GLY*     1.3    66.2    +      -       -      +
     19L  GLU*     3.8     5.7    +      -       -      +
     20L  TYR*     3.2    44.8    +      -       +      +
     21L  GLY*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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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