Contacts of the helix formed by residues 960 - 966 (chain A) in PDB entry 1M8X
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 HIS 960 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926A LEU* 3.4 45.9 - - + +
956A GLU 3.8 15.8 + - - -
957A LEU 2.9 9.3 + - - +
958A ASP 3.5 16.1 + - - -
959A GLY* 1.3 84.3 + - - +
961A VAL* 1.3 67.0 + - - +
962A LEU 3.5 2.0 - - - -
963A LYS* 3.3 19.3 + - + +
964A CYS* 3.1 23.6 + - - -
840B ARG* 6.3 1.1 - - - -
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Residues in contact with VAL 961 (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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957A LEU* 4.0 6.1 - - + +
959A GLY 3.7 4.6 - - - +
960A HIS* 1.3 76.9 - - - +
962A LEU* 1.3 65.3 + - + +
964A CYS* 3.1 7.1 + - - +
965A VAL* 2.9 36.8 + - + +
974A VAL* 5.5 2.9 - - + -
988A PHE* 3.7 46.2 - - + +
989A ILE* 3.9 29.8 - - + -
992A ALA* 3.8 20.4 - - + -
993A PHE* 4.1 4.9 - - + -
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Residues in contact with LEU 962 (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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960A HIS 3.5 0.6 - - - -
961A VAL* 1.3 78.1 - - + +
963A LYS* 1.3 62.4 + - - +
965A VAL* 3.3 3.3 + - + -
966A LYS* 3.0 50.5 + - - +
992A ALA* 4.1 24.5 - - + +
993A PHE* 4.6 10.5 - - + -
996A GLN* 4.9 16.4 - - + +
1000A LEU* 4.1 34.8 - - + -
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Residues in contact with LYS 963 (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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926A LEU* 5.5 5.2 - - + +
930A LEU* 3.7 33.8 - - + +
960A HIS* 3.3 25.1 + - + +
961A VAL 3.2 1.0 - - - -
962A LEU* 1.3 79.2 - - - +
964A CYS* 1.3 63.0 + - - +
966A LYS* 3.6 5.0 + - - +
967A ASP* 3.3 22.6 + - + +
835B ASP* 5.5 4.0 + - - -
840B ARG* 3.3 29.7 - - - +
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Residues in contact with CYS 964 (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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926A LEU* 3.7 28.7 - - - -
929A ALA* 4.9 7.4 - - - -
930A LEU* 4.2 11.2 - - - -
957A LEU* 4.2 20.0 - - + -
960A HIS* 3.1 18.2 + - - +
961A VAL* 3.6 7.0 - - - +
963A LYS* 1.3 74.1 - - - +
965A VAL* 1.3 64.4 + - - +
967A ASP* 3.1 10.9 + - - -
970A GLY* 3.0 7.5 - - - +
971A ASN 2.9 25.1 + - - -
973A VAL* 6.3 0.2 - - + -
974A VAL* 3.7 17.9 - - + -
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Residues in contact with VAL 965 (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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961A VAL* 2.9 26.2 + - + +
962A LEU* 3.3 8.3 + - + +
964A CYS* 1.3 77.6 - - - +
966A LYS* 1.3 58.7 + - + +
967A ASP 3.3 0.2 - - - -
971A ASN* 3.2 13.3 - - - +
974A VAL* 4.2 18.4 - - + -
993A PHE* 3.8 29.6 - - + -
1000A LEU* 4.2 17.5 - - + -
1003A HIS* 5.4 0.2 - - - +
1005A TYR* 3.2 22.9 - - - +
1006A GLY* 4.0 24.9 - - - +
1009A VAL* 4.2 8.5 - - + -
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Residues in contact with LYS 966 (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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962A LEU* 3.0 38.9 + - - +
963A LYS* 3.9 5.2 - - - +
965A VAL* 1.3 80.8 - - + +
967A ASP* 1.3 58.2 + - - +
968A GLN 4.0 0.2 + - - -
996A GLN* 5.5 4.2 + - - -
1000A LEU* 4.3 20.0 - - + -
1003A HIS* 3.9 32.7 + - + +
1005A TYR* 3.4 15.1 - - - -
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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