Contacts of the helix formed by residues 787 - 792 (chain B) in PDB entry 1JQO
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 HIS 787 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778B ILE* 6.4 0.4 - - - -
781B TRP* 2.9 16.0 + - - -
782B THR* 3.5 46.2 + - + +
785B ARG* 3.9 7.7 - - - -
786B PHE* 1.3 77.5 - - - +
788B LEU* 1.3 64.4 + - - +
789B PRO* 3.3 5.2 - - - -
790B VAL* 2.9 24.1 + - + +
791B TRP* 3.1 9.7 - - + -
832B VAL* 3.6 33.4 - - + -
833B PHE* 5.4 0.4 - - - -
835B LYS* 3.5 10.7 + - + +
836B GLY* 3.3 40.5 + - - -
864B TYR* 5.8 0.9 - + - -
966B MET* 4.2 9.9 - - - -
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Residues in contact with LEU 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B VAL* 5.8 0.9 - - + -
732B VAL* 5.4 0.7 - - + -
738B PHE* 4.3 15.7 - - + -
777B TRP* 5.3 2.2 - - + -
781B TRP* 3.5 46.9 - - + +
786B PHE* 2.9 17.0 + - + -
787B HIS* 1.3 75.5 - - - +
789B PRO* 1.3 66.3 - - + +
790B VAL 3.2 0.2 + - - -
791B TRP* 3.4 33.3 - - + +
792B LEU* 3.1 60.4 + - + +
860B LEU* 3.8 15.5 - - + -
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Residues in contact with PRO 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B GLY 4.9 7.1 - - - +
610B ARG* 4.1 15.1 + - - +
646B GLY* 5.8 0.5 - - - -
728B TYR* 5.0 11.2 - - + +
777B TRP* 3.8 31.9 - - + +
778B ILE* 3.6 28.0 - - + -
781B TRP* 3.3 32.8 - - + +
787B HIS* 3.3 5.4 - - - -
788B LEU* 1.3 96.9 - - + +
790B VAL* 1.3 59.8 + - + +
791B TRP 3.6 0.2 - - - -
792B LEU* 4.6 7.4 + - + +
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Residues in contact with VAL 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B ARG* 3.2 34.5 - - + +
645B VAL* 4.2 8.7 - - + -
646B GLY* 4.1 33.4 - - - +
778B ILE* 4.4 13.0 - - + -
787B HIS* 2.9 28.4 + - + +
789B PRO* 1.3 79.9 - - - +
791B TRP* 1.3 59.7 + - - +
794B VAL* 4.5 0.9 - - - +
829B LEU* 3.4 13.0 - - + +
832B VAL* 4.1 29.8 - - + -
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Residues in contact with TRP 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ARG* 5.8 0.4 - - - -
786B PHE* 2.8 30.1 + + - -
787B HIS* 3.1 25.2 + - + -
788B LEU* 3.4 32.5 - - + +
790B VAL* 1.3 79.2 - - + +
792B LEU* 1.3 90.4 + - + +
793B GLY 3.6 1.6 - - - -
794B VAL* 3.4 24.3 + - + +
795B GLY 4.0 1.6 + - - -
829B LEU* 4.3 6.7 - - + -
832B VAL* 5.0 3.8 - - + -
833B PHE* 3.6 38.1 - + + -
860B LEU* 3.9 8.3 - - + -
863B LYS* 4.0 11.7 - - + -
864B TYR* 3.5 49.9 - + + -
867B THR* 4.0 15.6 - - + +
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Residues in contact with LEU 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ARG* 5.9 0.6 - - - +
727B GLU* 4.1 14.5 - - + +
728B TYR* 3.1 40.8 - - + -
731B VAL* 3.2 31.4 - - + -
732B VAL* 4.1 6.7 - - + -
777B TRP* 6.5 0.2 - - + -
788B LEU* 3.1 48.1 + - + +
789B PRO* 4.6 3.6 - - + +
790B VAL 3.8 1.0 - - - -
791B TRP* 1.3 97.0 - - + +
793B GLY* 1.3 65.8 + - - +
795B GLY* 3.9 5.5 + - - -
860B LEU* 4.4 7.2 - - + -
863B LYS* 5.6 4.5 - - + -
867B THR* 4.9 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
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Atomic class I II III IV V VI VII VIII
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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