Contacts of the helix formed by residues 961 - 969 (chain C) in PDB entry 6GHM
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 THR 961 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C LEU* 3.6 7.4 - - - -
952C PRO 5.0 0.7 - - - -
953C SER* 3.3 33.7 - - - +
954C LEU 4.4 1.1 - - - -
955C PRO* 4.0 15.3 - - + -
959C GLY 4.2 1.3 - - - +
960C ILE* 1.3 79.6 - - - +
962C ALA* 1.3 65.1 + - - +
963C LEU* 3.4 10.1 + - - +
964C HIS* 2.8 46.0 + - + +
965C ASN* 3.2 11.4 + - - -
983C VAL* 5.3 3.0 - - + +
984C ASN 5.2 0.9 + - - -
987C ALA* 3.8 21.5 - - + +
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Residues in contact with ALA 962 (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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930C LEU* 3.8 31.2 - - + +
931C LEU* 3.3 16.6 - - + +
934C SER* 3.4 30.1 - - - +
952C PRO 4.5 7.5 + - - +
954C LEU 5.1 0.2 + - - -
961C THR* 1.3 73.7 - - - +
963C LEU* 1.3 58.4 + - - +
965C ASN* 3.2 3.9 + - - +
966C ALA* 2.9 26.0 + - - +
978C LEU* 3.7 10.3 - - + -
983C VAL* 6.3 0.2 - - + -
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Residues in contact with LEU 963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961C THR* 3.2 8.7 + - - +
962C ALA* 1.3 75.3 - - - +
964C HIS* 1.3 66.9 + - - +
966C ALA* 4.4 0.4 - - - -
967C VAL* 3.0 32.5 + - + +
975C VAL* 3.9 45.3 - - + +
978C LEU* 3.6 14.9 - - + +
979C VAL* 3.9 18.2 - - + -
983C VAL* 4.0 20.9 - - + +
984C ASN 4.1 4.3 - - - +
985C VAL* 4.0 21.1 - - + -
995C PRO* 3.8 27.6 - - + -
1011C LEU* 4.5 2.0 - - + -
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Residues in contact with HIS 964 (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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959C GLY 3.7 15.2 + - - -
960C ILE* 3.7 24.0 - - + -
961C THR* 2.8 38.8 + - - +
963C LEU* 1.3 77.8 - - - +
965C ASN* 1.3 61.6 + - - +
967C VAL* 3.7 4.3 - - - +
968C CYS* 3.0 30.9 + - - -
987C ALA* 2.9 31.8 + - + -
989C ASP* 4.2 2.5 + - + -
993C TRP* 2.9 27.1 + - + -
995C PRO* 3.6 15.5 - - + +
998C CYS* 3.9 23.8 - - - -
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Residues in contact with ASN 965 (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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931C LEU* 3.0 40.3 + - - +
934C SER* 4.1 2.2 - - - -
935C LEU* 3.8 39.8 - - + +
956C ASN* 6.2 0.2 - - - +
960C ILE* 3.3 20.8 - - - +
961C THR 3.2 8.4 + - - -
962C ALA 3.2 8.8 + - - +
964C HIS* 1.3 78.2 - - - +
966C ALA* 1.3 63.2 + - - +
968C CYS* 3.4 4.9 + - - +
969C ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 966 (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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934C SER 3.6 12.7 + - - +
962C ALA 2.9 16.0 + - - +
963C LEU 3.9 3.4 - - - +
965C ASN* 1.3 76.2 - - - +
967C VAL* 1.3 63.0 + - - +
969C ALA 3.5 0.3 + - - -
970C GLY 3.1 2.9 + - - -
971C HIS* 3.0 30.1 + - - +
974C ILE* 3.9 27.6 - - + -
975C VAL* 3.6 21.9 - - + +
978C LEU* 4.2 5.6 - - + -
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Residues in contact with VAL 967 (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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963C LEU* 3.0 27.9 + - + +
964C HIS* 3.7 4.3 - - - +
966C ALA* 1.3 76.2 - - - +
968C CYS* 1.3 64.2 + - - +
970C GLY* 3.1 13.7 + - - -
975C VAL* 3.8 20.0 - - + -
995C PRO* 3.5 24.7 - - + +
998C CYS* 3.7 6.3 - - + -
999C ALA* 3.3 40.6 - - + +
1002C CYS* 4.5 6.1 - - - +
1004C ASN* 5.0 5.9 + - - +
1007C VAL* 4.2 15.3 - - + +
1011C LEU* 4.3 2.7 - - + -
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Residues in contact with CYS 968 (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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935C LEU* 5.6 4.3 - - + -
964C HIS* 3.0 22.8 + - - +
965C ASN* 4.0 5.6 - - - +
967C VAL* 1.3 76.8 - - - +
969C ALA* 1.3 60.3 + - - +
970C GLY 3.6 0.3 + - - -
998C CYS* 3.5 33.0 - - - -
1001C SER* 5.7 1.3 - - - -
1002C CYS* 4.0 22.3 - - - -
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Residues in contact with ALA 969 (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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935C LEU* 3.2 34.1 - - + +
965C ASN 3.0 16.4 + - - +
966C ALA 4.2 0.2 - - - +
967C VAL 3.2 0.2 - - - -
968C CYS* 1.3 76.7 - - - +
970C GLY* 1.3 63.1 + - - +
971C HIS* 3.4 23.8 + - + +
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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