Contacts of the helix formed by residues 694 - 706 (chain C) in PDB entry 7AUD
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 694 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669C ARG* 3.9 10.3 - - - -
672C GLN* 2.9 23.9 - - - +
689C MET* 3.6 4.0 - - - +
692C GLY 3.2 6.2 - - - +
693C GLY* 1.3 79.5 - - - +
695C LYS* 1.3 65.6 + - - +
696C SER* 3.3 3.5 + - - -
697C LEU* 3.8 6.2 + - - -
698C CYS* 3.6 11.6 - - - -
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Residues in contact with LYS 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C ILE* 4.6 3.6 - - + -
689C MET* 2.9 55.0 + - + +
690C PRO 3.0 20.8 + - - -
691C THR* 3.3 14.8 - - - +
692C GLY 4.4 1.8 - - - +
694C GLY* 1.3 76.0 - - - +
696C SER* 1.3 67.1 + - - +
698C CYS* 3.2 18.2 + - - +
699C TYR* 3.6 0.2 - - - -
795C ASP* 5.6 3.4 - - - +
796C GLU* 4.9 13.5 - - - -
829C LEU* 3.5 30.0 - - + +
830C THR* 4.0 24.2 - - - +
831C ALA* 3.8 10.1 - - - +
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Residues in contact with SER 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694C GLY* 3.3 1.0 - - - -
695C LYS* 1.3 78.2 - - - +
697C LEU* 1.3 63.7 + - - +
698C CYS 3.2 0.3 + - - -
699C TYR* 3.2 18.7 + - - -
700C GLN* 2.9 49.3 + - - +
723C GLN* 3.9 15.5 + - - -
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Residues in contact with LEU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C PHE* 4.0 12.8 - - + -
663C PHE* 3.8 41.3 - - + -
665C LEU* 3.7 26.9 - - + -
668C PHE* 4.3 0.7 - - + -
672C GLN* 3.4 34.3 - - - +
676C ILE* 4.2 14.5 - - + +
694C GLY* 3.8 2.7 + - - -
695C LYS 3.3 0.4 - - - -
696C SER* 1.3 77.9 - - - +
698C CYS* 1.3 64.1 + - - +
699C TYR 2.9 0.2 + - - -
700C GLN* 4.1 6.2 + - - +
701C LEU* 2.9 39.2 + - + +
702C PRO* 3.5 3.1 - - - +
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Residues in contact with CYS 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C ASN 4.9 0.2 - - - -
672C GLN* 4.0 24.0 - - - -
675C ALA* 4.2 12.8 - - + -
676C ILE* 4.0 13.7 - - - +
679C ALA* 4.6 0.7 - - - +
687C ILE* 4.9 3.6 - - + -
689C MET* 3.7 20.6 - - - -
694C GLY 3.6 17.0 - - - -
695C LYS* 3.2 10.0 + - - +
696C SER 3.2 1.2 - - - -
697C LEU* 1.3 77.6 - - - +
699C TYR* 1.3 57.4 + - - +
702C PRO* 3.2 19.5 - - - +
827C MET* 3.5 30.2 - - + +
829C LEU* 4.8 2.5 - - + -
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Residues in contact with TYR 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C LYS 3.6 0.7 - - - -
696C SER* 3.2 34.1 + - - -
697C LEU 3.1 0.2 - - - -
698C CYS* 1.3 77.7 - - - +
700C GLN* 1.3 78.2 + - + +
701C LEU 3.5 0.9 - - - -
702C PRO* 3.7 5.1 - - - +
703C ALA* 3.2 26.3 + - - +
710C THR* 4.8 0.9 - - - +
712C VAL* 3.5 26.0 - - + +
723C GLN* 4.8 3.8 + - - +
762C LEU* 4.2 4.0 - - + -
764C TYR* 2.8 32.4 + - - -
791C ARG* 4.6 5.6 + - - +
793C VAL* 3.7 28.3 - - + -
795C ASP* 3.8 17.9 + - - -
827C MET* 3.7 19.1 - - - -
829C LEU* 3.3 28.0 - - + -
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Residues in contact with GLN 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C PHE* 3.9 20.7 - - + -
696C SER* 2.9 40.0 + - - +
697C LEU* 4.1 1.7 + - - +
699C TYR* 1.3 97.6 + - + +
701C LEU* 1.3 61.7 + - - +
703C ALA* 3.4 7.4 + - - +
704C CYS* 3.1 31.7 + - - -
723C GLN* 4.1 9.9 + - - -
727C LEU* 3.5 25.5 - - + +
730C LEU* 5.8 0.9 - - - +
762C LEU* 4.0 15.2 - - + +
764C TYR* 3.3 19.6 + - - -
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Residues in contact with LEU 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655C MET* 3.6 38.8 - - + +
658C ILE* 3.7 26.0 - - + -
659C PHE* 3.9 29.4 - - + +
663C PHE* 3.7 18.6 - - + -
668C PHE* 4.1 1.3 - - + -
676C ILE* 3.7 23.6 - - + -
697C LEU* 2.9 18.4 + - + +
700C GLN* 1.3 74.3 - - - +
702C PRO* 1.3 70.8 - - + +
704C CYS* 3.0 3.3 + - - +
705C VAL* 3.0 29.4 + - + +
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Residues in contact with PRO 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ILE* 3.8 20.6 - - + +
679C ALA* 4.1 12.8 - - + -
680C LEU* 3.7 24.2 - - + -
697C LEU 3.5 1.8 - - - +
698C CYS 3.2 27.6 - - - +
699C TYR* 3.7 5.6 - - - +
701C LEU* 1.3 95.6 - - + +
703C ALA* 1.3 51.9 + - - +
705C VAL* 3.6 1.3 - - + +
706C SER* 2.7 40.7 + - - -
791C ARG* 3.9 18.8 - - - +
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Residues in contact with ALA 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699C TYR 3.2 21.8 + - - +
700C GLN 3.5 6.7 - - - +
701C LEU 3.2 0.2 - - - -
702C PRO* 1.3 75.8 - - - +
704C CYS* 1.3 60.7 + - - +
706C SER* 3.5 9.7 - - - +
708C GLY 4.7 1.2 - - - +
710C THR* 3.5 27.7 + - - +
761C LYS* 3.2 24.9 + - - +
762C LEU* 3.6 28.3 - - + -
791C ARG* 4.0 1.7 - - - +
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Residues in contact with CYS 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658C ILE* 3.7 31.7 - - + +
662C LYS* 5.9 0.4 - - - -
663C PHE* 4.1 7.4 - - - -
700C GLN 3.1 21.9 + - - -
701C LEU 3.0 9.6 + - - +
703C ALA* 1.3 78.0 - - - +
705C VAL* 1.3 64.1 + - - +
706C SER 4.1 2.6 - - - +
732C ILE* 3.9 42.2 - - - -
761C LYS* 4.2 16.3 - - + +
762C LEU* 5.4 0.7 - - - -
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Residues in contact with VAL 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651C HIS* 4.4 13.2 - - + +
654C GLU* 4.5 13.7 - - + -
655C MET* 3.7 30.5 - - + +
658C ILE* 4.0 15.9 - - + -
680C LEU* 3.8 28.3 - - + -
701C LEU* 3.0 17.3 + - + +
702C PRO 3.7 4.7 - - - +
704C CYS* 1.3 78.4 - - - +
706C SER* 1.3 65.0 + - - +
707C PRO* 3.7 3.3 - - - +
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Residues in contact with SER 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C LEU* 3.4 10.3 - - - +
702C PRO 2.7 22.3 + - - -
703C ALA* 3.5 9.9 - - - +
704C CYS 4.1 0.7 - - - +
705C VAL* 1.3 77.8 - - - +
707C PRO* 1.3 75.4 - - - +
708C GLY 4.1 0.7 - - - +
761C LYS* 3.1 18.4 + - - +
790C ALA* 4.2 12.8 - - - -
791C ARG* 3.1 24.2 + - - -
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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