Contacts of the helix formed by residues 165 - 176 (chain A) in PDB entry 2BM9
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ASP* 3.1 29.3 + - - +
162A HIS* 3.3 17.6 + - - -
163A ALA 3.5 3.0 + - - -
164A ASN* 1.3 73.4 - - - +
166A PHE* 1.3 67.3 + - + +
168A ILE* 3.1 10.0 + - - +
169A MET* 3.0 25.9 + - + +
183A PHE* 4.6 5.0 - - + -
185A ILE* 3.9 25.6 - - + -
192A TRP* 3.8 29.8 - - + -
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Residues in contact with PHE 166 (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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165A THR* 1.3 79.7 - - + +
167A ASN* 1.3 57.8 + - - +
168A ILE 3.1 0.4 - - - -
169A MET* 3.3 18.1 - - - +
170A LYS* 3.0 27.4 + - - +
185A ILE* 5.4 2.2 - - + -
192A TRP* 4.4 21.1 - + - -
200A PHE* 3.7 33.4 - + - -
203A TYR* 3.9 37.2 - + + -
204A LEU* 4.0 16.4 - - + -
207A PHE* 3.7 29.3 - + - -
9E PHE* 3.5 34.1 - + + -
10E GLN 5.3 4.3 - - - -
12E LEU* 4.5 8.1 - - + -
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Residues in contact with ASN 167 (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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142A LEU* 3.2 29.1 - - + +
164A ASN* 2.9 35.8 + - - +
165A THR 3.2 0.6 - - - -
166A PHE* 1.3 77.3 - - - +
168A ILE* 1.3 60.8 + - - +
170A LYS* 4.0 17.6 - - - +
171A TRP 3.9 6.4 + - - -
8E ASN* 3.4 20.6 + - - +
9E PHE* 4.2 30.9 + - - +
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Residues in contact with ILE 168 (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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88A LEU* 3.7 13.2 - - + -
139A CYS* 3.6 35.2 - - + +
142A LEU* 4.8 2.5 - - + -
145A PHE* 3.7 27.4 - - + -
157A PHE* 4.1 28.7 - - + -
163A ALA 3.7 3.8 - - - +
164A ASN* 3.4 20.4 - - - +
165A THR* 3.1 9.8 + - - +
166A PHE 3.1 0.6 - - - -
167A ASN* 1.3 78.3 - - - +
169A MET* 1.3 66.2 + - - +
170A LYS 3.0 1.1 - - - -
171A TRP* 2.9 10.9 + - + +
172A ALA* 2.8 22.3 + - + +
183A PHE* 4.1 11.0 - - + -
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Residues in contact with MET 169 (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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165A THR* 3.0 11.2 + - - +
166A PHE* 3.3 34.1 - - + +
168A ILE* 1.3 76.8 - - - +
170A LYS* 1.3 60.8 + - - +
172A ALA* 3.4 1.8 + - - +
173A VAL* 3.0 31.5 + - - +
183A PHE* 3.1 39.9 - - + -
185A ILE* 4.1 17.7 - - + -
204A LEU* 4.9 4.3 - - + -
207A PHE* 3.3 44.2 - - + -
211A LEU* 3.5 23.1 - - + -
229A LEU* 4.4 10.5 - - + -
38B LEU* 5.7 0.4 - - + -
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Residues in contact with LYS 170 (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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166A PHE 3.0 16.8 + - - +
167A ASN* 4.1 23.3 - - - +
168A ILE 3.0 0.2 - - - -
169A MET* 1.3 76.7 - - - +
171A TRP* 1.3 67.5 + - - +
173A VAL* 3.6 2.5 - - - +
174A ASP* 3.2 31.5 + - - +
207A PHE* 4.3 8.7 - - + -
4E TYR* 3.4 26.9 - - - +
5E SER* 4.2 14.6 + - - +
6E ARG 3.7 18.2 + - - -
7E GLN 4.0 5.8 + - - +
8E ASN* 3.6 20.8 + - - +
9E PHE* 4.6 6.1 - - + -
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Residues in contact with TRP 171 (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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142A LEU* 4.2 20.6 - - + -
145A PHE* 3.2 57.0 - + + -
146A GLU* 4.0 23.9 + - + +
148A LEU* 4.7 4.7 - - + -
150A GLU* 5.3 4.9 - - - -
157A PHE* 4.8 4.7 - + - -
167A ASN 3.9 9.7 + - - +
168A ILE* 2.9 11.5 + - + +
170A LYS* 1.3 80.0 - - - +
172A ALA* 1.3 75.8 - - + +
174A ASP* 3.0 4.9 + - - -
175A HIS* 2.8 71.2 + + + +
176A LEU* 3.8 37.5 - - + -
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Residues in contact with ALA 172 (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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157A PHE* 4.7 7.6 - - + -
168A ILE 2.8 17.9 + - - +
169A MET 3.7 4.3 - - - +
171A TRP* 1.3 87.1 - - + +
173A VAL* 1.3 59.5 + - - +
176A LEU* 2.8 29.9 + - + -
177A LEU* 3.0 31.4 + - + -
183A PHE* 4.0 21.3 - - + -
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Residues in contact with VAL 173 (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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169A MET* 3.0 22.4 + - - +
170A LYS* 3.6 4.7 - - - +
172A ALA* 1.3 78.3 - - - +
174A ASP* 1.3 71.4 + - - +
175A HIS 3.1 5.0 + - - -
176A LEU 4.3 1.0 + - - -
177A LEU* 3.9 20.7 + - + +
207A PHE* 4.5 6.3 - - + -
210A VAL* 4.0 43.5 - - + -
211A LEU* 4.1 20.2 - - + -
231A ARG* 4.2 22.7 + - - +
4E TYR* 4.2 7.2 - - + -
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Residues in contact with ASP 174 (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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170A LYS* 3.2 23.9 + - - +
171A TRP 3.0 2.0 + - - -
173A VAL* 1.3 93.7 - - - +
175A HIS* 1.3 82.7 + - + +
4E TYR* 3.7 15.7 - - - -
5E SER* 3.5 20.6 + - - -
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Residues in contact with HIS 175 (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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150A GLU* 3.9 18.9 - - - +
171A TRP* 2.8 63.3 + + + +
173A VAL 3.1 1.6 + - - -
174A ASP* 1.3 99.6 + - + +
176A LEU* 1.3 58.2 + - - +
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Residues in contact with LEU 176 (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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86A VAL* 5.4 1.1 - - + -
148A LEU* 3.3 39.3 - - + -
150A GLU* 3.8 13.7 - - + +
153A HIS* 3.1 31.5 + - + +
155A LEU* 4.1 26.2 - - + -
157A PHE* 4.1 25.4 - - + -
171A TRP* 3.8 29.8 - - + -
172A ALA* 2.8 17.5 + - + +
173A VAL 4.3 0.2 + - - -
175A HIS* 1.3 74.8 - - - +
177A LEU* 1.3 63.8 + - + +
178A GLU* 4.9 0.2 - - - -
181A ASP* 3.9 1.2 - - - +
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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