Contacts of the helix formed by residues 768 - 777 (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 768 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A GLU* 1.3 76.3 - - - +
769A VAL* 1.3 55.8 + - - +
770A GLU* 3.1 18.9 + - - +
771A GLU* 3.3 30.4 + - - +
772A LEU* 2.7 34.8 + - - +
64B LYS* 3.9 23.2 - - - +
68B TYR* 5.3 0.4 - - - -
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Residues in contact with VAL 769 (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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760A TRP* 3.9 14.8 - - + -
768A SER* 1.3 73.5 - - - +
770A GLU* 1.3 80.5 + - + +
772A LEU* 3.9 4.8 - - - +
773A ARG* 2.9 32.2 + - - +
39B ARG* 4.9 7.4 - - - +
42B PRO* 3.9 34.3 - - + -
61B ILE* 5.5 15.3 - - + -
68B TYR* 3.7 24.0 + - + +
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Residues in contact with GLU 770 (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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768A SER* 3.1 15.8 + - - +
769A VAL* 1.3 91.6 + - + +
771A GLU* 1.3 59.1 + - + +
773A ARG* 3.8 5.5 - - - +
774A ASP* 2.9 29.3 + - - +
39B ARG* 5.9 4.5 - - - +
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Residues in contact with GLU 771 (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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767A GLU* 3.5 32.2 - - + +
768A SER* 3.1 28.6 + - - +
770A GLU* 1.3 76.2 - - + +
772A LEU* 1.3 59.0 + - - +
774A ASP* 3.2 8.4 + - - +
775A ARG* 2.8 28.4 + - - +
64B LYS* 4.3 13.9 + - - -
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Residues in contact with LEU 772 (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* 3.9 23.3 - - + +
760A TRP* 3.6 47.3 - - + +
763A ASN* 3.8 21.8 - - - +
764A PRO* 5.3 0.2 - - + -
767A GLU* 3.9 16.0 - - + +
768A SER 2.7 21.3 + - - +
769A VAL* 3.9 3.4 - - - +
771A GLU* 1.3 73.2 - - - +
773A ARG* 1.3 56.5 + - - +
775A ARG* 2.9 21.1 + - - +
776A VAL* 2.9 22.5 + - + +
68B TYR* 3.9 27.6 - - + -
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Residues in contact with ARG 773 (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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719A GLU* 2.4 44.9 + - - +
723A SER* 3.3 11.3 + - - +
724A VAL* 3.6 23.4 - - - +
725A TYR* 3.5 18.6 + - + +
760A TRP* 4.0 15.0 - - + -
769A VAL 2.9 19.7 + - - +
770A GLU* 3.8 5.6 - - - +
772A LEU* 1.3 72.8 - - - +
774A ASP* 1.3 66.8 + - - +
776A VAL* 4.0 7.9 - - - -
777A LYS 3.1 18.4 + - - -
778A GLY* 3.5 6.3 + - - +
780A SER* 5.2 1.1 - - - +
39B ARG* 3.0 49.7 - - - +
9I C 5.6 1.6 + - - -
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Residues in contact with ASP 774 (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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725A TYR* 3.5 13.0 + - - -
770A GLU 2.9 19.0 + - - +
771A GLU* 3.2 8.5 + - - +
773A ARG* 1.3 76.5 - - - +
775A ARG* 1.3 62.6 + - - +
777A LYS* 2.6 54.5 + - - +
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Residues in contact with ARG 775 (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* 4.6 5.2 + - - +
759A VAL* 3.6 29.6 - - + -
764A PRO* 5.6 0.2 - - - -
765A TYR* 3.6 36.7 - - - +
767A GLU* 2.7 43.6 + - - +
771A GLU 2.8 13.8 + - - +
772A LEU* 2.9 12.7 + - - +
774A ASP* 1.3 79.0 - - - +
776A VAL* 1.3 59.6 + - - +
777A LYS* 3.5 9.3 + - - +
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Residues in contact with VAL 776 (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* 3.3 50.1 - - + +
759A VAL* 3.8 18.6 - - + -
760A TRP* 3.6 33.9 - - + +
772A LEU* 2.9 23.2 + - + +
773A ARG* 3.7 7.4 - - - +
775A ARG* 1.3 73.4 - - + +
777A LYS* 1.3 69.9 + - - +
778A GLY 3.1 5.8 + - - +
779A VAL* 3.1 26.0 + - - +
780A SER* 4.6 1.1 - - - +
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Residues in contact with LYS 777 (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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718A LEU* 5.5 0.3 - - - +
725A TYR* 3.7 34.9 + - + +
731A ASP* 3.5 35.6 + - + +
733A THR* 6.2 0.2 - - - +
736A GLU* 5.8 1.8 + - - -
748A ARG* 2.5 32.3 + - - +
756A ARG* 3.3 23.8 - - - +
773A ARG 3.1 7.6 + - - -
774A ASP* 2.6 39.4 + - - +
775A ARG* 3.3 6.4 - - - +
776A VAL* 1.3 77.1 - - - +
778A GLY* 1.3 57.4 + - - +
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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