Contacts of the helix formed by residues 779 - 792 (chain V) in PDB entry 1I84
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 GLY 779 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723V ASN* 4.6 6.3 - - - +
777V ARG 3.3 0.8 + - - -
778V THR* 1.3 73.5 - - - +
780V VAL* 1.3 63.8 + - - +
781V LEU 3.2 2.9 - - - +
782V ALA* 3.0 25.3 + - - +
783V HIS* 3.2 15.1 + - - +
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Residues in contact with VAL 780 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762V LEU* 3.6 31.0 - - + -
766V LEU* 3.5 31.0 - - + -
776V PHE* 4.0 19.7 - - + -
777V ARG* 3.0 32.0 + - + +
778V THR 3.0 4.4 + - - +
779V GLY* 1.3 77.5 - - - +
781V LEU* 1.3 60.7 + - + +
783V HIS* 3.8 4.8 + - - +
784V LEU* 3.3 26.8 + - + +
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Residues in contact with LEU 781 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723V ASN* 4.1 28.5 - - + +
724V ARG 5.0 1.3 - - - +
725V ILE* 4.4 14.6 - - + -
730V PHE* 4.4 2.9 - - + -
734V TYR* 3.4 40.0 + - + +
776V PHE* 3.2 46.9 - - + -
777V ARG 4.2 2.0 + - - -
779V GLY 3.2 1.0 - - - +
780V VAL* 1.3 79.7 - - - +
782V ALA* 1.3 65.4 + - - +
784V LEU* 3.3 9.1 + - + +
785V GLU* 3.0 22.2 + - - +
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Residues in contact with ALA 782 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V LYS* 6.2 3.1 - - + -
147V HIS* 4.9 21.2 + - + +
723V ASN* 6.0 0.2 - - - +
779V GLY* 3.0 19.3 + - - +
781V LEU* 1.3 79.0 - - - +
783V HIS* 1.3 58.2 + - - +
785V GLU* 3.1 8.4 + - - +
786V GLU* 2.9 27.7 + - - +
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Residues in contact with HIS 783 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762V LEU* 5.9 3.4 - - + -
779V GLY 3.2 11.0 + - - +
780V VAL* 4.1 4.3 - - - +
782V ALA* 1.3 76.7 - - - +
784V LEU* 1.3 82.9 + - + +
786V GLU* 3.2 16.3 + - - +
787V GLU* 2.8 63.5 + - + +
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Residues in contact with LEU 784 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730V PHE* 5.1 4.7 - - + -
734V TYR* 4.0 35.1 - - + -
737V LEU* 3.5 33.1 - - + +
760V LEU* 3.7 20.2 - - + -
762V LEU* 4.4 22.2 - - + -
776V PHE* 6.2 1.8 - - + -
780V VAL* 3.3 25.5 + - + +
781V LEU* 3.3 14.8 + - + +
782V ALA 3.2 0.4 - - - -
783V HIS* 1.3 95.4 - - + +
785V GLU* 1.3 60.8 + - - +
787V GLU* 3.7 5.1 + - + +
788V ARG* 3.3 21.0 + - - +
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Residues in contact with GLU 785 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V LYS* 5.0 14.1 - - + +
733V ARG* 2.9 20.8 + - - -
734V TYR* 2.5 40.3 + - - -
781V LEU 3.0 11.2 + - - +
782V ALA* 3.1 11.9 + - - +
784V LEU* 1.3 74.9 - - - +
786V GLU* 1.3 68.3 + - - +
788V ARG* 2.7 35.2 + - - +
789V ASP* 2.9 29.8 + - - +
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Residues in contact with GLU 786 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V LYS* 6.4 0.2 - - - +
147V HIS* 3.8 26.1 + - - -
148V GLU* 4.5 4.5 - - - +
782V ALA 2.9 13.1 + - - +
783V HIS* 3.4 19.9 + - - +
785V GLU* 1.3 73.2 - - - +
787V GLU* 1.3 67.8 + - + +
789V ASP* 2.8 21.9 + - - +
790V LEU* 3.0 28.6 + - + +
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Residues in contact with GLU 787 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737V LEU* 3.8 18.2 - - + -
783V HIS* 2.8 51.5 + - + +
784V LEU* 3.7 7.4 - - + +
786V GLU* 1.3 78.9 - - + +
788V ARG* 1.3 51.4 + - - +
790V LEU* 2.7 16.9 + - - +
791V LYS* 2.7 34.5 + - + +
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Residues in contact with ARG 788 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733V ARG* 3.1 59.0 - - - +
734V TYR* 4.1 3.6 - - + -
736V ILE* 4.0 12.1 - - + -
737V LEU* 3.8 18.1 - - + +
784V LEU 3.3 10.1 + - - +
785V GLU* 2.7 37.8 + - - +
787V GLU* 1.3 79.1 - - - +
789V ASP* 1.3 93.8 + - - +
790V LEU 3.1 0.7 + - - -
791V LYS* 3.3 5.0 + - - +
792V ILE* 3.1 25.3 + - + +
94W VAL* 3.8 15.0 - - + +
95W PHE* 3.2 30.0 - - - -
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Residues in contact with ASP 789 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V LYS* 4.7 12.1 + - - -
785V GLU* 2.9 20.5 + - - +
786V GLU* 2.8 17.3 + - - +
788V ARG* 1.3 114.5 + - - +
790V LEU* 1.3 60.2 + - + +
792V ILE* 3.6 11.1 - - - +
793V THR* 3.1 28.8 + - - +
95W PHE* 5.6 0.9 - - - -
111W VAL* 5.9 0.9 - - - +
115W LEU* 4.2 26.1 - - + +
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Residues in contact with LEU 790 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786V GLU* 3.0 37.4 + - + +
787V GLU* 2.7 14.7 + - - +
789V ASP* 1.3 78.1 - - + +
791V LYS* 1.3 59.4 + - - +
792V ILE 2.8 8.8 + - - -
793V THR* 2.5 26.0 + - + +
794V ASP* 4.1 7.3 - - - +
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Residues in contact with LYS 791 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736V ILE* 3.8 36.3 - - + +
737V LEU* 4.0 16.6 - - + -
787V GLU 2.7 11.0 + - - +
788V ARG* 3.5 12.6 - - - +
790V LEU* 1.3 76.8 - - - +
792V ILE* 1.3 59.5 + - - +
794V ASP* 3.7 8.8 - - - +
795V VAL* 4.4 4.0 - - - +
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Residues in contact with ILE 792 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736V ILE* 3.3 32.1 - - + -
788V ARG* 3.1 17.7 - - - +
789V ASP* 3.6 9.0 - - - +
790V LEU 2.9 0.6 - - - -
791V LYS* 1.3 78.4 - - - +
793V THR* 1.3 66.7 + - - +
794V ASP* 3.4 5.2 - - - -
795V VAL* 3.3 14.2 - - + +
796V ILE* 2.9 40.2 + - + +
91W GLY* 4.8 9.9 - - - +
94W VAL* 4.7 15.0 - - + -
95W PHE* 3.4 28.3 - - + -
115W LEU* 3.4 31.2 - - + -
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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