Contacts of the helix formed by residues 749 - 763 (chain A) in PDB entry 6CIM
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 749 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716A GLU* 5.1 2.2 - - - -
747A THR 3.7 2.4 + - - -
748A ARG* 1.3 78.2 - - - +
750A HIS* 1.3 65.0 + - - +
751A ALA* 3.3 7.9 + - - +
752A GLU* 3.1 24.5 + - - +
753A ASN* 2.9 29.4 + - - -
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Residues in contact with HIS 750 (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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716A GLU* 2.9 29.3 + - - +
749A SER* 1.3 74.7 - - - +
751A ALA* 1.3 58.7 + - - +
753A ASN* 3.8 1.6 - - - +
754A LEU* 2.9 57.5 + - + +
783A PRO* 3.5 29.9 + - + +
784A PHE* 4.4 2.8 - - - -
785A ILE 3.7 23.7 + - - -
786A GLU* 3.7 40.1 + - + +
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Residues in contact with ALA 751 (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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749A SER* 3.2 6.8 + - - +
750A HIS* 1.3 77.1 - - - +
752A GLU* 1.3 66.7 + - - +
754A LEU* 3.1 12.9 + - - +
755A GLN* 2.8 23.4 + - - +
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Residues in contact with GLU 752 (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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731A ASP* 3.9 3.3 - - - +
747A THR* 3.3 16.0 + - - +
748A ARG* 3.3 24.8 - - - +
749A SER* 3.1 18.1 + - - +
751A ALA* 1.3 76.9 - - - +
753A ASN* 1.3 55.9 + - - +
755A GLN* 3.0 10.5 + - - +
756A ARG* 2.8 79.9 + - + +
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Residues in contact with ASN 753 (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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716A GLU* 3.6 32.6 + - - +
718A LEU* 4.3 10.7 - - - +
748A ARG* 4.0 17.8 + - - +
749A SER 2.9 22.2 + - - +
750A HIS* 3.8 4.7 - - - +
752A GLU* 1.3 83.9 - - - +
754A LEU* 1.3 65.0 + - - +
756A ARG* 4.4 1.4 - - - -
757A TYR* 3.0 21.7 + - - +
779A VAL* 3.2 33.3 - - + +
783A PRO* 3.6 18.5 - - + +
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Residues in contact with LEU 754 (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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750A HIS* 2.9 52.2 + - + +
751A ALA* 3.5 9.2 - - - +
753A ASN* 1.3 74.6 - - - +
755A GLN* 1.3 63.3 + - - +
757A TYR* 3.3 5.9 + - - +
758A GLU* 3.1 21.5 + - - +
782A LYS* 4.1 26.5 - - + -
783A PRO* 3.9 21.5 - - + +
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Residues in contact with GLN 755 (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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751A ALA 2.8 12.7 + - - +
752A GLU* 3.2 13.0 - - - +
754A LEU* 1.3 78.0 - - - +
756A ARG* 1.3 60.6 + - + +
758A GLU* 3.0 14.0 + - - +
759A VAL* 2.8 46.3 + - + +
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Residues in contact with ARG 756 (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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731A ASP* 2.5 44.6 + - - -
748A ARG* 3.6 8.9 - - - +
752A GLU* 2.8 54.7 + - + +
753A ASN* 3.9 0.9 + - - +
754A LEU 3.3 0.2 - - - -
755A GLN* 1.3 72.0 - - + +
757A TYR* 1.3 61.9 + - - +
759A VAL* 3.2 9.1 + - + -
760A TRP* 2.8 26.0 + - - +
775A ARG 4.6 3.4 + - - -
776A VAL* 3.3 32.8 + - + +
777A LYS* 3.3 23.6 - - - +
779A VAL* 3.7 24.2 - - + -
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Residues in contact with TYR 757 (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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753A ASN 3.0 12.9 + - - +
754A LEU 3.7 8.3 - - - +
755A GLN 3.2 0.2 - - - -
756A ARG* 1.3 78.1 - - - +
758A GLU* 1.3 65.6 + - - +
760A TRP* 3.2 9.6 + + - +
761A ARG* 2.8 55.7 + - + +
779A VAL* 3.8 8.3 - - + +
780A SER 4.2 6.7 - - - -
781A ALA* 3.5 36.8 - - - +
782A LYS* 3.6 42.8 - - + -
783A PRO* 4.2 1.1 - - + -
36B TRP* 3.7 12.5 - + - -
68B TYR 5.1 1.4 + - - -
70B PRO* 3.4 31.4 - - - +
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Residues in contact with GLU 758 (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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754A LEU 3.1 11.7 + - - +
755A GLN* 3.0 21.7 + - - +
757A TYR* 1.3 83.6 - - + +
759A VAL* 1.3 63.7 + - - +
761A ARG* 2.6 46.3 + - - -
762A SER* 3.0 32.4 + - - +
106B LYS* 5.9 0.2 - - - -
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Residues in contact with VAL 759 (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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755A GLN* 2.8 40.6 + - + +
756A ARG* 3.5 9.6 - - + +
758A GLU* 1.3 75.7 - - - +
760A TRP* 1.3 63.3 + - - +
762A SER* 4.1 4.7 - - - -
763A ASN* 3.0 22.5 + - - -
764A PRO* 3.3 20.3 - - + +
765A TYR* 5.6 0.9 - - + -
772A LEU* 3.9 2.8 - - + +
775A ARG* 3.6 31.6 - - + -
776A VAL* 3.8 10.5 - - + -
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Residues in contact with TRP 760 (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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756A ARG 2.8 17.0 + - - +
757A TYR* 3.5 15.7 - + - +
759A VAL* 1.3 73.6 - - - +
761A ARG* 1.3 69.6 + - - +
763A ASN 4.0 1.6 + - - -
769A VAL* 3.9 21.5 - - + -
772A LEU* 3.6 44.2 - - + +
773A ARG* 4.0 22.4 - - + -
776A VAL* 3.6 13.1 - - + +
779A VAL 3.8 10.5 - - - +
780A SER* 3.7 45.7 + - - -
39B ARG* 5.8 0.9 - - - -
42B PRO* 4.0 21.3 + - + -
68B TYR* 3.5 44.8 + + + +
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Residues in contact with ARG 761 (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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757A TYR* 2.8 44.6 + - + +
758A GLU* 2.6 42.1 + - - +
759A VAL 3.2 0.2 - - - -
760A TRP* 1.3 79.4 - - - +
762A SER* 1.3 75.9 + - - +
67B CYS* 3.6 6.8 - - - +
68B TYR 3.1 41.4 + - - +
69B LEU* 5.0 0.2 - - - -
70B PRO* 4.7 3.6 - - + -
106B LYS* 3.3 24.9 - - - +
108B TYR* 3.1 26.0 + - + +
126B GLU* 2.8 42.9 + - - +
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Residues in contact with SER 762 (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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758A GLU* 3.0 21.3 + - - +
759A VAL* 4.1 0.5 - - - -
761A ARG* 1.3 95.4 - - - +
763A ASN* 1.3 72.8 + - - +
764A PRO* 3.4 21.1 - - - +
766A HIS* 5.4 0.3 + - - -
66B SER 4.5 0.5 - - - +
67B CYS* 4.2 16.7 - - - -
126B GLU* 4.8 4.5 - - - -
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Residues in contact with ASN 763 (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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759A VAL 3.0 13.2 + - - -
761A ARG 3.4 1.4 - - - -
762A SER* 1.3 75.9 - - - +
764A PRO* 1.3 66.0 - - - +
765A TYR 3.3 0.5 + - - -
766A HIS* 3.3 16.8 + - - +
767A GLU* 3.1 39.7 + - - +
772A LEU* 3.8 23.2 - - + +
64B LYS 2.9 28.3 + - - -
66B SER 3.2 26.4 + - - +
68B TYR* 4.3 10.0 - - + -
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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