Contacts of the helix formed by residues 1073 - 1080 (chain B) in PDB entry 3B8R
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 ALA1073 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071B TRP 3.8 0.4 + - - -
1072B MET* 1.3 75.3 - - - +
1074B PRO* 1.3 77.7 - - + +
1075B GLU* 3.6 24.9 - - - +
1076B THR* 2.9 15.9 + - - +
1077B ILE* 3.1 11.1 + - - +
1086B SER* 3.9 16.5 + - - -
1089B TRP* 3.6 28.8 - - + +
1150B ARG* 3.9 2.0 - - - +
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Residues in contact with PRO1074 (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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1072B MET 3.9 0.4 - - - +
1073B ALA* 1.3 84.9 - - + +
1075B GLU* 1.3 64.1 + - - +
1077B ILE* 3.1 3.2 + - + +
1078B PHE* 2.9 52.9 + - + -
1089B TRP* 3.5 39.9 - - + -
1119B LEU* 4.0 26.0 - - + +
1120B LYS* 4.8 7.6 - - + -
1124B ARG* 5.2 1.8 - - - +
1145B GLY* 5.7 5.4 - - - +
1150B ARG* 4.3 2.5 - - - +
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Residues in contact with GLU1075 (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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1073B ALA* 3.6 12.4 - - - +
1074B PRO* 1.3 76.7 - - - +
1076B THR* 1.3 61.8 + - - +
1078B PHE* 5.1 0.9 - - - -
1079B ASP* 2.7 52.3 + - - +
1080B ARG 3.1 0.5 + - - -
1081B VAL* 3.6 21.6 + - + +
1083B THR* 4.6 3.1 + - + +
1086B SER* 3.9 8.2 + - - -
1145B GLY 4.7 1.4 - - - +
1147B PRO* 3.3 18.1 - - + +
1150B ARG* 2.7 45.5 + - - -
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Residues in contact with THR1076 (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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1072B MET* 4.0 18.5 - - + +
1073B ALA 2.9 17.5 + - - -
1075B GLU* 1.3 78.9 - - - +
1077B ILE* 1.3 61.0 + - - +
1080B ARG* 2.8 26.2 + - - +
1081B VAL 2.7 22.8 + - - +
1082B TYR* 3.6 42.0 - - + +
1086B SER* 3.4 22.0 + - - -
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Residues in contact with ILE1077 (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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1069B LEU* 3.9 41.5 - - + +
1072B MET* 3.8 20.4 - - + +
1073B ALA 3.1 8.3 + - - +
1074B PRO* 3.1 6.8 + - + +
1076B THR* 1.3 78.8 - - - +
1078B PHE* 1.3 75.6 + - + +
1080B ARG* 4.2 7.3 + - - +
1115B PHE* 5.0 3.1 - - + -
1116B CYS* 4.1 27.6 - - + -
1119B LEU* 3.7 29.2 - - + -
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Residues in contact with PHE1078 (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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1074B PRO* 2.9 41.3 + - + +
1075B GLU* 5.1 0.2 - - - -
1077B ILE* 1.3 84.3 - - + +
1079B ASP* 1.3 71.0 + - - +
1080B ARG* 4.9 2.5 - - - +
1116B CYS* 3.2 46.9 - - + -
1117B ARG* 4.4 1.3 - - - -
1119B LEU* 5.4 0.9 - - + -
1120B LYS* 3.2 39.9 - - + -
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Residues in contact with ASP1079 (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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1075B GLU* 2.7 35.6 + - - +
1078B PHE* 1.3 81.8 - - - +
1080B ARG* 1.3 73.4 + - - +
1081B VAL* 3.5 20.4 + - + +
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Residues in contact with ARG1080 (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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1075B GLU 3.1 0.4 + - - -
1076B THR 2.8 21.6 + - - +
1077B ILE 4.5 7.9 - - - +
1078B PHE 4.9 2.0 - - - +
1079B ASP* 1.3 83.0 - - - +
1081B VAL* 1.3 60.8 + - - +
1082B TYR* 3.6 21.2 + - + -
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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