Contacts of the helix formed by residues 684 - 705 (chain A) in PDB entry 2RC4
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 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A LEU* 5.4 2.2 - - - -
602A ASP 6.4 0.7 - - - -
682A PRO 3.9 1.6 + - - -
683A LEU* 1.3 75.7 - - - +
685A ASP* 1.3 58.0 + - - +
686A LEU* 3.3 2.1 + - - -
687A GLY 2.8 17.5 + - - -
688A ARG* 2.8 28.2 + - - +
900A ACO 2.7 46.9 + - - +
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Residues in contact with ASP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A LEU 3.9 0.4 + - - +
684A SER* 1.3 73.8 - - - +
686A LEU* 1.3 71.5 + - + +
688A ARG* 3.3 27.2 + - - +
689A LEU* 3.4 20.1 + - + +
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A TRP* 4.8 18.6 - - + -
654A GLN* 5.8 1.3 - - - +
684A SER* 3.3 1.6 + - - -
685A ASP* 1.3 83.1 - - + +
687A GLY* 1.3 66.2 + - - +
689A LEU* 3.4 9.9 + - + +
690A SER* 3.2 22.5 + - - -
900A ACO 3.2 80.6 + - + +
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ILE* 5.7 1.8 - - - -
683A LEU* 4.6 2.5 - - - -
684A SER* 2.8 21.9 + - - -
686A LEU* 1.3 70.3 - - - +
688A ARG* 1.3 65.1 + - - +
690A SER* 3.0 15.2 + - - -
691A TYR* 3.0 25.3 + - - -
900A ACO 3.7 27.9 - - - +
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Residues in contact with ARG 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU* 3.7 26.0 - - + +
684A SER 2.8 17.9 + - - +
685A ASP* 3.3 18.4 + - - +
686A LEU 3.3 0.2 - - - -
687A GLY* 1.3 75.2 - - - +
689A LEU* 1.3 64.0 + - + +
691A TYR* 3.3 1.7 + - - +
692A MET* 2.9 35.3 + - + +
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Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A ASP* 3.5 20.0 - - + +
686A LEU* 3.9 8.1 - - + +
687A GLY 3.3 0.6 - - - -
688A ARG* 1.3 81.9 - - + +
690A SER* 1.3 60.7 + - - +
692A MET* 4.3 5.8 - - - -
693A ALA* 2.8 36.2 + - + +
900A ACO 3.1 44.2 - - - +
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Residues in contact with SER 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A GLY 6.0 2.2 - - - -
660A ARG* 5.9 2.2 - - - +
663A ILE* 5.1 14.0 - - - +
686A LEU 3.2 6.3 + - - -
687A GLY* 3.0 16.3 + - - -
689A LEU* 1.3 78.4 - - - +
691A TYR* 1.3 58.6 + - - +
693A ALA* 4.0 1.7 - - - +
694A TYR* 3.1 26.5 + - - +
900A ACO 3.2 57.6 + - - +
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Residues in contact with TYR 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A VAL* 3.4 24.3 - - - +
647A ILE* 4.8 6.5 - - + -
663A ILE* 3.1 47.6 - - + +
666A SER* 4.6 0.6 + - - -
667A TYR* 3.8 12.6 - + - -
679A PRO* 3.1 36.1 - - + +
683A LEU* 4.3 17.5 - - + -
687A GLY* 3.0 22.0 + - - +
688A ARG 3.8 5.2 - - - +
690A SER* 1.3 75.6 - - - +
692A MET* 1.3 68.8 + - - +
693A ALA 3.0 1.6 - - - -
694A TYR* 2.7 13.6 + + - +
695A TRP* 2.7 58.3 + + + -
900A ACO 4.7 4.7 - - + -
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Residues in contact with MET 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ARG* 2.9 23.6 + - + +
689A LEU* 3.9 6.5 - - - +
691A TYR* 1.3 77.1 - - - +
693A ALA* 1.3 60.6 + - - +
695A TRP* 3.7 12.8 + - + +
696A LYS* 3.3 15.5 + - + +
728A THR* 5.0 2.9 - - - +
729A SER* 3.7 37.5 - - - -
732A HIS* 4.1 38.6 - - + +
733A HIS* 3.7 16.2 - - + +
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Residues in contact with ALA 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A LEU* 2.8 20.3 + - + +
690A SER* 4.4 2.2 - - - +
692A MET* 1.3 73.9 - - - +
694A TYR* 1.3 63.5 + - - +
696A LYS* 3.8 6.9 - - - +
697A SER* 3.2 22.3 + - - -
900A ACO 4.1 48.2 + - + +
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Residues in contact with TYR 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A ARG* 3.4 48.7 - - + +
663A ILE* 3.5 17.9 - - + -
664A ASP* 2.8 38.1 + - + -
667A TYR* 3.1 37.8 - + - +
690A SER 3.1 20.9 + - - +
691A TYR* 2.7 13.6 + + - +
693A ALA* 1.3 70.1 - - - +
695A TRP* 1.3 80.1 - + - +
697A SER* 2.5 20.7 + - - -
698A VAL* 3.0 31.4 + - + +
719A LEU* 5.6 1.6 + - - +
900A ACO 6.2 1.1 - - - -
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Residues in contact with TRP 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A TYR* 2.8 27.4 + + - -
679A PRO* 4.4 8.5 - - + -
681A LYS* 5.8 0.7 - - + -
683A LEU* 5.3 7.6 - - + -
691A TYR* 2.7 57.7 + + + +
692A MET* 4.0 15.5 - - + +
694A TYR* 1.3 84.1 - + - +
696A LYS* 1.3 54.7 - - - +
698A VAL* 3.1 10.7 + - + +
699A ILE* 2.7 42.5 + - + +
721A GLY* 4.7 11.0 - - - -
725A GLN* 3.8 46.3 - - + +
726A ASP* 4.8 7.6 - - + -
728A THR* 4.8 5.4 - - - -
729A SER* 3.5 29.2 - - - +
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Residues in contact with LYS 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A MET* 3.3 16.4 + - + +
693A ALA* 3.8 9.0 - - - +
694A TYR 3.3 0.2 - - - -
695A TRP* 1.3 75.5 - - - +
697A SER* 1.3 66.0 + - - +
699A ILE* 2.8 4.7 + - - -
700A LEU* 2.7 37.8 + - + +
733A HIS* 4.2 29.7 + - + +
900A ACO 6.3 0.7 - - - +
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Residues in contact with SER 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ARG* 3.6 29.5 + - - -
693A ALA 3.2 12.4 + - - -
694A TYR* 2.5 26.7 + - - -
696A LYS* 1.3 77.2 - - - +
698A VAL* 1.3 53.5 + - - +
701A GLU* 2.8 28.4 + - - +
757A MET* 3.3 27.7 - - - +
761A GLN* 4.7 2.6 + - - -
900A ACO 5.2 11.8 + - - -
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Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A ARG* 4.7 7.6 - - - +
664A ASP* 5.7 0.9 - - - +
694A TYR* 3.0 42.3 + - + +
695A TRP* 3.2 24.9 - - + +
697A SER* 1.3 79.4 + - - +
699A ILE* 1.3 62.9 + - + +
701A GLU* 3.2 19.3 - - + +
702A CYS* 3.8 3.3 + - - -
715A LYS* 4.4 1.6 - - - -
719A LEU* 3.3 50.1 - - + +
721A GLY* 6.2 0.2 - - - -
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Residues in contact with ILE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A TRP* 2.7 27.5 + - + +
696A LYS* 2.8 5.3 + - - +
698A VAL* 1.3 71.0 - - + +
700A LEU* 1.3 65.9 - - + +
701A GLU 2.8 9.9 + - - -
702A CYS* 3.0 15.9 + - - +
703A LEU* 3.4 20.0 + - + +
715A LYS* 4.1 25.5 - - + +
719A LEU* 3.7 21.5 - - + -
726A ASP* 3.6 37.0 - - + +
729A SER* 5.2 2.5 - - - -
730A THR* 4.4 20.4 - - + -
733A HIS* 5.0 3.8 - - + -
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A LYS* 2.7 31.0 + - + +
697A SER 3.7 0.4 - - - -
699A ILE* 1.3 75.2 - - + +
701A GLU* 1.3 62.6 + - - +
703A LEU* 3.8 30.5 + - + +
704A TYR* 3.9 7.4 + - - +
733A HIS* 4.8 16.4 - - + +
750A GLU* 6.4 1.3 - - + -
753A ILE* 4.5 15.9 - - + +
754A GLN* 4.2 18.7 - - - +
757A MET* 3.6 40.8 - - + +
758A ALA* 5.4 0.2 - - - +
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Residues in contact with GLU 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A ARG* 5.9 1.8 - - - +
697A SER 2.8 20.1 + - - +
698A VAL* 3.2 19.3 - - + +
699A ILE 2.8 1.0 + - - -
700A LEU* 1.3 80.5 - - - +
702A CYS* 1.3 65.8 + - + +
704A TYR* 3.3 11.1 + - - +
705A HIS* 3.3 23.8 + - + -
757A MET* 3.9 7.9 - - + -
758A ALA* 5.8 1.1 - - - +
761A GLN* 4.9 6.1 - - - +
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Residues in contact with CYS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A VAL 4.4 1.1 - - - -
699A ILE 3.0 6.1 + - - +
701A GLU* 1.3 78.9 - - - +
703A LEU* 1.3 67.1 + - + +
705A HIS* 2.8 28.6 + - - +
706A GLN* 3.4 11.0 + - - +
715A LYS* 2.9 47.6 - - + +
718A LYS* 3.9 25.4 - - - +
719A LEU* 4.4 9.6 - - - -
749A ARG* 4.9 1.6 + - - -
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Residues in contact with LEU 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A ILE* 3.4 21.5 + - + +
700A LEU* 4.0 21.3 - - + +
701A GLU 3.3 0.8 - - - -
702A CYS* 1.3 80.7 - - + +
704A TYR* 1.3 59.8 + - - +
706A GLN 3.4 15.4 - - - +
707A ASN* 4.6 1.7 + - - -
715A LYS* 6.2 2.9 - - + -
748A ARG 5.1 3.1 - - - +
749A ARG* 3.6 47.5 + - + +
750A GLU* 4.4 18.4 - - + +
754A GLN* 3.6 30.3 - - + +
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Residues in contact with TYR 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A LEU 3.9 2.5 + - - +
701A GLU 3.3 9.3 + - - +
702A CYS 3.2 0.4 - - - -
703A LEU* 1.3 77.5 - - - +
705A HIS* 1.3 66.5 + - + +
706A GLN 3.5 3.0 + - - -
707A ASN* 4.5 7.8 + - - -
754A GLN* 3.9 13.2 - - - +
755A ASP* 5.7 0.9 - - - -
758A ALA* 3.8 29.4 - - + -
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Residues in contact with HIS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A GLU* 3.3 24.1 + - + +
702A CYS* 2.8 14.1 + - - +
704A TYR* 1.3 84.9 + - + +
706A GLN* 1.3 64.2 + - - +
707A ASN* 5.4 0.2 - - - +
718A LYS* 3.9 12.7 + - - +
758A ALA* 6.1 2.7 - - + +
761A GLN* 5.4 6.3 + - - -
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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
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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