Contacts of the helix formed by residues 936 - 944 (chain B) in PDB entry 2B7A
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 936 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B TYR 4.0 0.5 + - - +
935B GLY* 1.3 74.5 - - - -
937B LEU* 1.3 60.2 + - - +
938B ARG* 3.8 4.2 + - - +
939B ASP* 2.8 38.4 + - - +
940B TYR* 2.9 25.5 + - - +
979B THR 4.0 4.5 - - - -
980B ARG* 3.8 21.8 - - - +
982B ILE 3.2 13.0 - - - -
983B LEU* 4.0 8.8 - - - +
984B VAL* 4.2 0.4 - - - -
2002B IZA 4.6 7.9 - - - -
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Residues in contact with LEU 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B GLY 3.8 1.0 + - - -
936B SER* 1.3 68.8 - - - +
938B ARG* 1.3 60.2 + - - +
940B TYR* 4.1 8.5 - - + -
941B LEU* 2.9 45.2 + - + +
956B TYR* 4.2 26.7 - - + -
960B ILE* 5.3 2.2 - - + -
979B THR* 3.9 9.0 - - + +
982B ILE* 2.7 47.5 + - + +
984B VAL* 3.7 22.1 - - + +
990B VAL* 4.0 17.5 - - + -
1047B LEU* 3.6 30.1 - - + -
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Residues in contact with ARG 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B SER* 3.2 7.4 - - - +
937B LEU* 1.3 80.6 - - - +
939B ASP* 1.3 70.9 + - - +
942B GLN* 3.3 29.4 + - - +
979B THR* 3.3 37.3 + - - +
980B ARG* 3.2 56.6 - - - +
1020B TRP* 6.4 0.4 - - - -
1046B GLU* 4.5 5.2 - - - -
1051B ILE* 3.5 30.2 - - + +
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Residues in contact with ASP 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B TYR 5.8 1.8 - - - +
936B SER* 2.8 25.5 + - - +
938B ARG* 1.3 85.8 + - - +
940B TYR* 1.3 67.2 + - - +
941B LEU 3.5 0.3 + - - -
942B GLN* 3.5 24.7 + - - +
943B LYS* 3.4 32.3 + - - +
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Residues in contact with TYR 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B TYR* 4.0 39.0 + + + +
936B SER 2.9 16.7 + - - +
937B LEU* 3.9 8.7 - - + +
939B ASP* 1.3 77.6 - - - +
941B LEU* 1.3 62.2 + - - +
942B GLN 3.5 0.2 + - - -
943B LYS* 3.5 7.9 - - + +
944B HIS* 3.2 59.7 + + - +
947B ARG* 4.5 9.5 + - - -
948B ILE* 3.9 24.8 - - + +
956B TYR* 3.9 12.8 - - - -
984B VAL* 3.7 38.1 - - + -
987B GLU* 3.4 27.8 + - - +
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Residues in contact with LEU 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B LEU* 2.9 26.5 + - + +
940B TYR* 1.3 79.1 - - - +
942B GLN* 1.3 61.3 + - - +
944B HIS 3.4 0.7 + - - -
945B LYS* 3.1 27.0 + - - +
948B ILE* 3.8 21.5 - - + -
953B LEU* 3.6 23.1 - - + -
956B TYR* 5.2 0.4 - - + -
1047B LEU* 3.4 48.0 - - + +
1050B TYR* 3.7 31.8 - - + -
1051B ILE* 3.9 16.2 - - + -
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Residues in contact with GLN 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B ARG* 3.3 25.3 + - - +
939B ASP* 3.7 24.4 + - - +
940B TYR 3.3 0.2 - - - -
941B LEU* 1.3 79.5 - - - +
943B LYS* 1.3 62.9 + - + +
944B HIS 3.5 0.2 + - - -
945B LYS* 3.6 22.4 - - - +
1050B TYR 3.9 8.3 - - - +
1051B ILE* 3.5 40.1 - - + +
1053B LYS* 3.8 21.5 + - - +
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Residues in contact with LYS 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B ASP* 3.4 30.8 - - - +
940B TYR* 3.5 12.3 - - + +
942B GLN* 1.3 78.8 - - + +
944B HIS* 1.3 78.9 + - + +
945B LYS* 3.6 1.9 + - - +
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Residues in contact with HIS 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B TYR* 5.7 2.7 - + - -
940B TYR* 3.2 57.8 + + + +
941B LEU 3.7 2.2 - - - -
943B LYS* 1.3 98.2 + - + +
945B LYS* 1.3 58.3 + - - +
946B GLU 3.3 2.9 - - - -
947B ARG* 2.9 50.9 + - + +
948B ILE* 3.0 29.9 + - + +
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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