Contacts of the helix formed by residues 789 - 794 (chain Z) in PDB entry 5GJQ
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.
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 SER 789 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780Z PRO* 2.9 35.3 + - - +
781Z TYR* 4.9 1.1 - - - -
782Z HIS 5.8 0.4 - - - -
787Z LEU 3.6 2.7 + - - -
788Z MET* 1.3 72.7 - - - +
790Z GLN* 1.3 58.2 + - - +
791Z VAL* 3.1 14.3 + - - -
792Z ALA* 3.9 7.6 + - - +
793Z VAL* 3.7 16.0 + - - +
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Residues in contact with GLN 790 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527Z VAL* 3.9 18.8 - - + +
528Z GLY* 5.0 12.6 - - - +
564Z LEU 6.0 0.2 - - - +
567Z LEU* 5.6 6.1 - - + -
788Z MET 3.9 3.8 + - - -
789Z SER* 1.3 69.7 - - - +
791Z VAL* 1.3 61.2 + - - +
792Z ALA 3.5 0.2 - - - -
793Z VAL* 3.9 12.8 - - + +
794Z ALA* 3.4 19.6 + - - +
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Residues in contact with VAL 791 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Z GLU* 5.3 14.6 - - + -
490Z ALA* 4.9 19.4 - - + +
527Z VAL* 5.5 2.5 - - - -
789Z SER* 3.1 7.8 - - - -
790Z GLN* 1.3 77.3 - - - +
792Z ALA* 1.3 65.7 + - - +
794Z ALA* 3.4 13.8 + - - +
795Z GLY* 3.5 7.3 + - - -
823Z ALA* 4.4 16.1 - - + +
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Residues in contact with ALA 792 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780Z PRO* 5.2 11.9 - - + +
789Z SER* 3.9 8.4 + - - +
791Z VAL* 1.3 75.7 - - - +
793Z VAL* 1.3 59.2 + - - +
794Z ALA 2.9 2.2 - - - -
795Z GLY* 2.4 30.3 + - - +
796Z LEU* 3.5 6.8 + - - +
821Z LEU 5.5 0.7 - - - +
823Z ALA 4.7 0.9 + - - -
824Z ALA* 2.5 46.7 - - + +
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Residues in contact with VAL 793 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780Z PRO* 6.0 2.4 - - + +
789Z SER 3.7 17.4 + - - +
790Z GLN* 3.9 13.2 - - + +
791Z VAL 3.3 0.2 - - - -
792Z ALA* 1.3 78.1 - - - +
794Z ALA* 1.3 59.4 + - - +
795Z GLY 3.5 0.2 + - - -
796Z LEU* 3.7 16.8 + - - +
797Z LEU* 4.4 4.5 + - - +
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Residues in contact with ALA 794 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490Z ALA* 5.9 1.1 - - + -
520Z LEU 5.6 0.3 - - - +
523Z GLY 4.4 3.6 - - - +
524Z MET* 4.2 34.0 - - + +
527Z VAL* 4.3 11.7 - - + -
564Z LEU* 4.7 11.7 - - + -
790Z GLN 3.4 11.7 + - - +
791Z VAL 3.4 11.6 + - - +
792Z ALA 2.9 0.8 - - - -
793Z VAL* 1.3 77.2 - - - +
795Z GLY* 1.3 55.7 + - - +
796Z LEU 3.2 7.1 + - - -
797Z LEU 5.2 0.2 - - - -
798Z THR* 3.5 16.6 + - - -
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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
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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) + - + + + + + -
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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