Contacts of the helix formed by residues 684 - 702 (chain A) in PDB entry 3CQC
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 GLN 684 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A LEU* 3.7 22.7 - - + +
681A ASP* 2.6 43.2 + - + +
683A ALA* 1.3 83.1 - - - +
685A ARG* 1.3 57.6 + - - -
686A ALA 3.4 2.0 - - - -
687A GLU* 3.4 29.8 + - + +
688A ALA* 2.9 27.4 + - - +
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Residues in contact with ARG 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL* 3.6 23.9 + - - +
681A ASP 3.9 1.2 + - - -
682A PRO* 2.9 43.4 + - - +
683A ALA 3.5 1.8 - - - -
684A GLN* 1.3 74.1 - - - +
686A ALA* 1.3 56.2 + - - +
688A ALA* 3.1 14.1 + - - +
689A LEU* 2.7 35.1 + - - +
715A ILE* 5.2 2.5 - - - -
716A PRO* 3.3 41.3 - - - +
718A ASP* 5.2 1.6 + - - -
719A SER* 3.3 39.0 + - - +
722A GLU* 5.7 4.7 - - + -
723A ILE* 4.1 12.1 - - + +
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Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A ALA 5.2 1.1 + - - +
684A GLN 3.4 0.4 - - - -
685A ARG* 1.3 76.3 - - - +
687A GLU* 1.3 63.3 + - - +
689A LEU* 3.3 4.2 + - - +
690A LYS* 3.0 33.1 + - - +
723A ILE* 3.8 24.8 - - + +
740A ASP* 3.9 31.0 - - + +
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Residues in contact with GLU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A LEU* 4.1 12.1 - - + -
684A GLN* 3.4 29.5 + - + +
685A ARG 3.3 0.6 - - - -
686A ALA* 1.3 79.5 - - - +
688A ALA* 1.3 57.7 + - - +
690A LYS* 3.4 22.2 + - - +
691A GLN* 2.7 68.3 + - - +
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Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A ILE* 3.5 11.5 - - + +
678A LEU* 3.8 30.7 - - + +
679A VAL* 4.0 13.5 - - + -
684A GLN 2.9 15.7 + - - +
685A ARG* 3.1 23.5 + - - +
687A GLU* 1.3 74.1 - - - +
689A LEU* 1.3 65.0 + - - +
692A GLY* 2.9 19.9 + - - -
715A ILE* 4.1 3.1 - - + +
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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
----------------------------------------------------------
685A ARG* 2.7 19.6 + - + +
686A ALA* 3.5 6.1 - - - +
688A ALA* 1.3 73.0 - - - +
690A LYS* 1.3 57.2 + - - +
692A GLY* 3.7 0.3 - - - -
693A ASN* 2.8 36.2 + - - +
715A ILE* 4.1 24.3 - - + +
719A SER* 4.9 2.7 - - - -
720A ILE* 4.9 7.2 - - + -
723A ILE* 4.0 18.2 - - + -
740A ASP* 4.7 1.3 - - + +
743A ALA* 3.6 39.5 - - + +
744A ILE* 3.7 20.4 - - + +
747A HIS* 3.7 31.2 - - + +
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Residues in contact with LYS 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA* 3.0 30.3 + - - +
687A GLU* 3.8 22.9 + - - +
689A LEU* 1.3 76.9 - - - +
691A GLN* 1.3 62.4 + - + +
693A ASN* 3.4 6.5 + - - +
694A ALA* 3.1 21.5 + - - +
697A ARG* 5.0 1.4 + - - -
739A GLU* 4.2 23.8 - - + +
740A ASP* 3.0 29.0 + - - +
743A ALA* 3.7 22.2 - - + -
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Residues in contact with GLN 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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671A LYS* 5.5 3.5 + - - -
674A VAL* 4.8 11.7 - - + +
675A ILE* 5.3 0.7 - - + -
678A LEU* 3.3 30.0 - - + +
687A GLU* 2.7 53.2 + - - +
688A ALA 4.3 0.4 - - - +
690A LYS* 1.3 75.3 - - + +
692A GLY* 1.3 60.9 + - - +
694A ALA* 3.3 7.6 + - + +
695A ILE* 3.0 38.5 + - + +
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Residues in contact with GLY 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A ILE* 3.9 20.5 - - - +
688A ALA 2.9 17.1 + - - -
689A LEU 3.7 0.9 - - - -
691A GLN* 1.3 74.7 - - - +
693A ASN* 1.3 60.5 + - - +
695A ILE* 3.3 3.2 + - - +
696A MET* 2.8 36.6 + - - +
711A VAL* 4.2 9.6 - - - -
715A ILE* 4.6 4.5 - - - -
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Residues in contact with ASN 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 21.1 + - - +
690A LYS* 3.6 6.5 - - - +
692A GLY* 1.3 72.1 - - - +
694A ALA* 1.3 57.3 + - - +
696A MET* 3.3 3.1 + - - +
697A ARG* 2.8 36.8 + - - +
743A ALA* 2.7 46.7 + - - +
746A GLU* 3.3 31.3 + - - +
747A HIS* 3.8 26.1 + - - +
750A ILE* 4.1 10.5 - - - +
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LYS 3.1 12.9 + - - +
691A GLN* 3.5 13.5 - - + +
692A GLY 3.1 0.2 - - - -
693A ASN* 1.3 73.8 - - - +
695A ILE* 1.3 67.4 + - + +
697A ARG* 3.1 30.2 + - - +
698A LYS* 2.8 38.8 - - - +
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Residues in contact with ILE 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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671A LYS* 3.2 50.9 - - + +
672A ILE* 4.9 0.4 - - - -
674A VAL* 4.0 9.6 - - + -
675A ILE* 3.8 22.4 - - + -
691A GLN* 3.0 25.0 + - + +
692A GLY* 3.7 4.7 - - - +
694A ALA* 1.3 76.0 - - + +
696A MET* 1.3 62.5 + - - +
698A LYS* 3.2 12.8 + - - +
699A PHE* 3.1 50.3 + - + -
711A VAL* 3.7 13.7 - - + -
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Residues in contact with MET 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A GLY 2.8 16.4 + - - +
693A ASN* 5.1 2.9 - - - +
695A ILE* 1.3 73.8 - - - +
697A ARG* 1.3 60.5 + - - +
699A PHE* 3.8 5.3 - - - +
700A LEU* 2.8 34.7 + - - +
708A ALA* 3.0 30.5 - - + +
711A VAL* 3.5 29.2 - - + -
712A PHE* 3.0 41.7 - - + -
715A ILE* 5.6 2.2 - - - -
747A HIS* 5.5 2.5 - - - -
750A ILE* 3.1 50.0 - - + -
754A LEU* 3.9 2.9 - - + -
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Residues in contact with ARG 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LYS 5.0 1.4 + - - -
693A ASN* 2.8 24.4 + - - +
694A ALA* 3.1 31.3 + - - +
696A MET* 1.3 76.9 - - - +
698A LYS* 1.3 63.2 + - - +
700A LEU* 3.9 2.5 - - - +
701A ALA* 3.1 23.2 + - - +
746A GLU* 2.6 55.9 + - - +
750A ILE* 4.9 3.1 - - + -
829A MET* 3.7 16.4 - - + -
839A ASP* 5.3 1.2 + - - -
842A ARG* 3.7 30.5 - - - +
845A GLN* 2.7 44.4 + - + +
846A MET* 3.8 11.9 - - - -
849A LEU* 3.8 23.7 - - + +
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Residues in contact with LYS 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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671A LYS* 6.3 4.3 - - + -
694A ALA* 2.8 49.0 + - - +
695A ILE* 3.2 10.6 + - - +
697A ARG* 1.3 80.2 - - - +
699A PHE* 1.3 71.2 + - + +
701A ALA* 3.1 17.2 + - - +
702A SER* 3.3 13.5 + - - -
704A LYS* 5.7 0.4 + - - -
845A GLN* 2.8 42.4 + - - +
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Residues in contact with PHE 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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668A ASP* 4.4 33.2 - - + -
671A LYS* 4.5 6.7 - - + -
672A ILE* 4.5 6.7 - - + -
695A ILE* 3.1 41.6 + - + +
696A MET 3.8 5.2 - - - +
698A LYS* 1.3 82.7 - - + +
700A LEU* 1.3 61.1 + - - +
702A SER* 3.0 9.4 + - - -
704A LYS* 2.8 65.4 + - + +
707A ALA* 3.4 26.7 - - + -
708A ALA* 3.7 14.8 - - + +
711A VAL* 4.0 11.2 - - + -
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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 MET 2.8 25.3 + - - +
697A ARG* 3.9 3.8 - - - +
699A PHE* 1.3 72.1 - - - +
701A ALA* 1.3 56.9 + - - +
703A LYS* 3.0 21.4 + - - +
704A LYS 5.3 0.2 - - - -
705A HIS* 4.1 8.5 - - + -
708A ALA* 3.8 22.4 - - + -
750A ILE* 4.0 33.7 - - + -
753A TYR* 3.7 42.0 + - + -
754A LEU* 4.0 9.0 - - + -
828A TRP* 5.1 6.3 - - + -
829A MET* 6.2 0.2 - - - -
849A LEU* 4.0 22.4 - - + +
852A LEU* 4.9 1.6 - - - +
853A CYS* 4.7 9.0 - - - -
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Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ARG 3.1 13.5 + - - +
698A LYS* 3.1 13.7 + - - +
700A LEU* 1.3 76.5 - - - +
702A SER* 1.3 60.6 + - - +
703A LYS* 3.4 4.1 + - - +
845A GLN* 6.5 1.3 - - + -
848A LEU* 4.5 13.9 - - + -
849A LEU* 3.8 8.0 - - + +
852A LEU* 3.5 31.4 - - + +
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Residues in contact with SER 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 LYS 3.3 8.8 + - - -
699A PHE 3.0 5.9 + - - -
701A ALA* 1.3 77.5 + - - +
703A LYS* 1.3 74.1 + - - +
704A LYS* 3.2 34.5 + - - +
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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