Contacts of the helix formed by residues 741 - 746 (chain C) in PDB entry 2C10
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 CYS 741 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734C CYS* 2.0 46.2 - - - -
738C PRO* 3.4 16.4 - - + +
739C LEU 3.1 0.8 - - - -
740C ALA* 1.3 79.1 - - - +
742C LEU* 1.3 60.8 + - - +
743C PRO 3.6 0.4 - - - -
744C GLN* 3.5 20.6 - - - +
745C ALA* 3.3 29.6 + - + +
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Residues in contact with LEU 742 (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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318C PRO* 4.8 4.3 - - + -
319C GLN* 6.0 0.9 - - - +
738C PRO 3.8 6.6 + - - +
739C LEU* 3.7 31.8 + - + +
741C CYS* 1.3 74.0 - - - +
743C PRO* 1.4 57.6 - - + +
744C GLN 2.6 20.3 + - - -
745C ALA* 5.0 2.2 - - + -
746C ALA* 2.9 47.1 + - + +
311D ALA* 4.4 21.5 - - + -
312D PRO* 5.6 4.9 - - + +
314D LEU* 3.9 28.3 - - + -
406D TYR* 4.3 10.5 - - + -
752D LEU* 3.6 6.8 - - + +
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Residues in contact with PRO 743 (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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739C LEU 3.5 12.6 - - - +
740C ALA 3.5 15.5 - - - +
742C LEU* 1.4 88.0 - - + +
744C GLN* 1.3 73.7 + - - +
747C ALA* 4.9 2.2 - - - -
406D TYR* 3.5 18.2 - - + +
752D LEU* 3.6 30.8 - - + +
753D PRO 3.5 20.2 - - - +
754D ALA* 4.7 2.7 - - - +
755D PHE 4.4 6.3 - - - +
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Residues in contact with GLN 744 (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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734C CYS* 5.3 3.2 - - - +
740C ALA 4.3 9.2 + - - +
741C CYS* 3.5 32.0 + - - +
742C LEU 2.6 8.3 + - - -
743C PRO* 1.3 82.3 - - - +
745C ALA* 1.3 68.7 - - + +
746C ALA 3.0 4.6 - - - +
747C ALA* 3.1 33.0 + - - +
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Residues in contact with ALA 745 (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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318C PRO* 4.4 10.7 - - - +
319C GLN* 4.2 23.0 + - - +
741C CYS* 3.3 21.8 - - + +
742C LEU* 3.4 4.5 + - + +
744C GLN* 1.3 80.7 - - + +
746C ALA* 1.3 57.6 + - - +
747C ALA 3.6 0.2 - - - -
748C CYS* 5.3 2.8 - - - -
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Residues in contact with ALA 746 (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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316C PHE* 4.3 2.8 - - + -
318C PRO* 3.8 20.4 - - + -
742C LEU* 2.9 41.7 + - + +
744C GLN 4.6 0.4 - - - -
745C ALA* 1.3 79.6 - - - +
747C ALA* 1.3 54.8 + - - +
748C CYS* 3.4 10.3 + - - +
314D LEU* 4.3 7.6 - - + -
750D PRO* 3.5 22.5 - - - +
752D LEU* 4.1 11.5 - - + +
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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