Contacts of the strand formed by residues 25 - 34 (chain Q) in PDB entry 5GAG


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 THR 25 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23Q  GLY      3.5     2.8    +      -       -      -
     24Q  ASP*     1.3    70.2    -      -       -      +
     26Q  VAL*     1.3    62.7    +      -       -      +
     44Q  GLU*     3.7    23.3    -      -       +      +
     45Q  GLY*     3.6    15.3    -      -       -      +
     46Q  VAL*     3.5    21.0    -      -       +      +
     86Q  VAL*     3.9     0.9    -      -       -      +
     87Q  LYS*     2.9    28.4    +      -       +      -
     88Q  ARG*     3.2    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 26 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20Q  PHE*     4.9     6.3    -      -       +      -
     24Q  ASP*     3.5    22.7    -      -       +      +
     25Q  THR*     1.3    80.5    -      -       -      +
     27Q  GLU*     1.3    73.7    +      -       -      +
     28Q  VAL*     3.7    16.8    -      -       +      -
     43Q  PHE      4.1     1.2    -      -       -      +
     44Q  GLU*     3.2     7.3    -      -       -      +
     45Q  GLY      2.8    37.4    +      -       -      +
     47Q  VAL*     3.7    21.1    -      -       +      -
     59Q  PHE*     5.0     2.5    -      -       +      -
     61Q  VAL*     4.6     3.5    -      -       +      +
     84Q  ILE*     3.9    13.0    -      -       +      -
     85Q  SER      3.4    12.1    -      -       -      +
     86Q  VAL*     4.2    12.3    -      -       +      -
     87Q  LYS*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 27 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26Q  VAL*     1.3    76.8    -      -       -      +
     28Q  VAL*     1.3    65.6    +      -       -      +
     29Q  LYS*     4.1    19.3    +      -       +      +
     42Q  ALA*     3.2    32.3    -      -       +      +
     43Q  PHE      3.9     2.5    -      -       -      +
     44Q  GLU*     3.7    23.4    -      -       +      +
     83Q  SER      3.8     1.0    -      -       -      +
     84Q  ILE*     3.6     1.2    -      -       -      -
     85Q  SER*     2.9    44.5    +      -       -      +
     87Q  LYS*     3.3    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26Q  VAL*     3.7    17.5    -      -       +      -
     27Q  GLU*     1.3    79.3    -      -       -      +
     29Q  LYS*     1.3    62.0    +      -       -      +
     30Q  VAL*     3.6    22.4    +      -       +      +
     41Q  GLN      3.6     1.9    -      -       -      +
     42Q  ALA*     4.4     0.2    -      -       -      -
     43Q  PHE*     2.9    43.3    +      -       -      +
     59Q  PHE*     3.8    24.7    -      -       +      -
     61Q  VAL*     4.9     2.5    -      -       +      -
     74Q  PHE*     4.2    15.0    -      -       +      -
     81Q  VAL*     3.7    28.9    -      -       +      -
     83Q  SER      3.4     2.9    -      -       -      +
     84Q  ILE*     4.1     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27Q  GLU*     4.1    22.9    +      -       -      -
     28Q  VAL*     1.3    71.7    -      -       -      +
     30Q  VAL*     1.3    55.0    +      -       -      +
     40Q  LEU*     4.2    23.3    -      -       +      -
     41Q  GLN      3.6     4.9    -      -       -      +
     42Q  ALA*     4.0    20.0    -      -       +      +
     81Q  VAL*     3.7     1.0    -      -       -      -
     82Q  ASP*     2.7    36.7    +      -       -      +
     83Q  SER*     2.9    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28Q  VAL*     3.7    25.6    -      -       +      +
     29Q  LYS*     1.3    76.2    -      -       -      +
     31Q  TRP*     1.3    78.1    +      -       -      +
     32Q  VAL*     3.3    17.0    +      -       +      +
     40Q  LEU*     3.6     3.5    -      -       -      -
     41Q  GLN*     2.9    37.1    +      -       +      +
     43Q  PHE*     5.3     2.0    -      -       +      -
     72Q  ARG*     4.4    16.4    -      -       -      +
     74Q  PHE*     4.1    20.9    -      -       +      -
     80Q  VAL*     3.6    20.4    -      -       +      -
     81Q  VAL*     4.2     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 31 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29Q  LYS      4.3     0.2    -      -       -      -
     30Q  VAL*     1.3    83.2    -      -       -      +
     32Q  VAL*     1.3    58.9    +      -       -      +
     38Q  LYS*     3.6    52.0    -      -       +      -
     39Q  ARG*     3.5    22.7    -      -       -      -
     40Q  LEU*     3.5    24.2    -      -       +      +
     79Q  PRO      3.8    13.0    -      -       -      +
     80Q  VAL*     3.0    29.9    +      -       -      +
     82Q  ASP*     3.2    36.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 32 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71L  ARG*     6.2     0.7    -      -       -      +
    105L  ARG*     3.8    26.2    -      -       -      +
    123L  LEU      5.4     1.8    -      -       -      +
     30Q  VAL*     3.4    20.9    -      -       +      +
     31Q  TRP*     1.3    81.4    -      -       -      +
     33Q  VAL*     1.3    64.0    +      -       -      +
     34Q  GLU*     3.6    32.1    -      -       +      +
     38Q  LYS*     3.6     4.9    -      -       -      +
     39Q  ARG      2.9    42.7    +      -       -      +
     41Q  GLN*     4.0    20.4    -      -       +      +
     72Q  ARG*     5.4     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ASP      6.2     0.7    -      -       -      +
    105L  ARG*     4.4    15.6    +      -       -      +
     32Q  VAL*     1.3    75.4    -      -       -      +
     34Q  GLU*     1.3    60.4    +      -       -      +
     35Q  GLY      3.3    23.4    +      -       -      +
     36Q  SER*     4.4     3.8    -      -       -      +
     37Q  LYS      3.2    17.9    -      -       -      +
     38Q  LYS*     3.8    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 34 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105L  ARG*     3.9    18.2    -      -       -      +
    108L  ARG*     4.3     3.6    -      -       -      +
     32Q  VAL*     3.6    26.8    +      -       +      +
     33Q  VAL*     1.3    68.9    -      -       -      +
     35Q  GLY*     1.3    58.8    +      -       -      +
     36Q  SER      3.2     0.2    +      -       -      -
     37Q  LYS*     2.9    40.2    +      -       +      +
     39Q  ARG*     3.2    31.9    -      -       +      +
     40Q  LEU      4.5     2.4    -      -       -      +
     41Q  GLN*     4.0    16.3    -      -       -      +
----------------------------------------------------------
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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