Contacts of the helix formed by residues 164 - 176 (chain F) 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 ASN 164 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D GLN 5.7 4.7 - - - +
11D ASP* 4.6 10.0 + - - +
13D ASN* 5.1 1.0 - - - +
139F CYS* 3.2 30.0 + - + +
140F SER* 3.8 20.0 + - - +
142F LEU* 5.1 7.1 - - - +
163F ALA* 1.3 73.7 - - + +
165F THR* 1.3 63.5 + - - +
166F PHE 3.3 3.5 + - - -
167F ASN* 3.2 35.6 + - - +
168F ILE* 3.1 20.3 + - + +
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Residues in contact with THR 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F ASP* 3.3 21.8 + - - +
162F HIS* 3.0 35.7 + - - +
163F ALA 3.0 0.6 + - - -
164F ASN* 1.3 77.0 - - - +
166F PHE* 1.3 61.8 + - + +
168F ILE* 3.1 15.7 + - + +
169F MET* 3.0 25.1 + - - +
183F PHE* 4.1 9.9 - - + -
185F ILE* 3.6 27.8 - - + -
192F TRP* 3.9 12.2 - - + -
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Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 4.0 25.4 - + + -
10D GLN 5.3 2.9 - - - +
12D LEU* 4.5 21.1 - - + -
164F ASN 3.3 0.6 - - - -
165F THR* 1.3 84.1 - - + +
167F ASN* 1.3 61.7 + - - +
169F MET* 3.2 29.2 + - + +
170F LYS* 3.0 26.7 + - - +
185F ILE* 5.8 5.4 - - + -
189F ILE* 6.4 0.4 - - + -
192F TRP* 5.0 12.8 - + - -
200F PHE* 4.5 16.2 - + - -
203F TYR* 3.7 43.7 - + + -
204F LEU* 3.9 24.9 - - + -
207F PHE* 4.0 17.2 - + - -
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Residues in contact with ASN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASN* 4.2 16.0 + - - +
9D PHE* 3.4 32.7 + - - +
142F LEU* 4.0 11.4 - - + +
164F ASN* 3.2 33.5 + - - +
166F PHE* 1.3 75.1 - - - +
168F ILE* 1.3 58.9 + - - +
170F LYS* 3.8 13.1 + - - +
171F TRP* 3.0 30.7 + - - +
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Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 4.9 6.3 - - + -
139F CYS* 3.9 19.5 - - + +
142F LEU* 4.6 9.4 - - + -
145F PHE* 4.1 28.3 - - + -
157F PHE* 4.2 28.7 - - + -
159F ASP* 5.6 0.4 - - - +
163F ALA 3.4 18.6 - - - +
164F ASN* 3.1 28.0 + - + +
165F THR* 3.1 13.9 + - - +
167F ASN* 1.3 77.5 - - - +
169F MET* 1.3 55.4 + - - +
171F TRP* 3.9 6.9 - - + -
172F ALA* 2.9 26.9 + - + +
183F PHE* 4.3 6.5 - - + -
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Residues in contact with MET 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F THR 3.0 10.8 + - - +
166F PHE* 3.4 22.2 - - + +
168F ILE* 1.3 76.4 - - - +
170F LYS* 1.3 64.8 + - - +
171F TRP 3.3 0.2 - - - -
172F ALA* 3.3 5.8 - - + +
173F VAL* 3.0 27.7 + - - +
177F LEU* 6.3 0.2 - - + -
183F PHE* 3.4 38.1 - - + -
185F ILE* 4.5 7.9 - - - -
204F LEU* 3.9 22.7 - - + -
207F PHE* 3.4 49.3 - - + -
211F LEU* 3.8 18.6 - - + -
229F LEU* 4.5 5.4 - - + -
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Residues in contact with LYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.6 20.5 + - + +
5D SER* 3.9 21.8 + - - +
7D GLN 2.6 28.1 + - - -
8D ASN* 4.7 2.8 - - - +
9D PHE* 3.6 23.9 - - + -
166F PHE 3.0 17.0 + - - +
167F ASN* 3.5 13.6 + - - +
169F MET* 1.3 75.7 - - - +
171F TRP* 1.3 62.5 + - - +
173F VAL* 4.0 3.0 + - - +
174F ASP* 3.3 34.9 + - - +
207F PHE* 3.9 11.5 - - + -
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Residues in contact with TRP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F LEU* 3.7 37.5 + - + +
145F PHE* 3.7 38.6 - + + -
146F GLU* 3.8 35.9 + - - +
148F LEU 5.8 0.2 - - - -
149F ARG* 5.2 2.7 - - + -
167F ASN 3.0 18.3 + - - +
168F ILE* 4.0 9.9 - - + +
170F LYS* 1.3 75.4 - - - +
172F ALA* 1.3 74.2 + - + +
174F ASP* 3.3 4.0 + - - -
175F HIS* 2.9 56.6 + + + +
176F LEU* 4.0 30.5 - - + -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F PHE* 6.6 0.2 - - + -
168F ILE* 2.9 21.3 + - + +
169F MET* 3.1 10.1 + - + +
171F TRP* 1.3 85.4 - - + +
173F VAL* 1.3 61.7 + - - +
176F LEU* 2.8 37.9 + - + -
177F LEU* 3.4 30.8 + - + -
183F PHE* 4.5 9.9 - - + -
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Residues in contact with VAL 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.8 31.4 - - + +
169F MET 3.0 14.1 + - - +
170F LYS 4.0 2.2 - - - +
172F ALA* 1.3 77.4 - - - +
174F ASP* 1.3 62.9 + - - +
175F HIS 3.7 0.2 + - - -
176F LEU 4.9 0.7 + - - -
177F LEU* 4.1 10.8 - - + +
207F PHE* 4.3 5.2 - - + -
210F VAL* 3.3 39.3 - - + -
211F LEU* 4.0 23.1 - - + -
231F ARG* 3.2 30.2 + - - +
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Residues in contact with ASP 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.3 32.5 + - - -
5D SER* 4.3 11.6 - - - -
170F LYS* 3.3 22.8 + - - +
171F TRP* 4.5 0.7 - - - -
172F ALA 3.0 1.6 + - - -
173F VAL* 1.3 80.7 - - - +
175F HIS* 1.3 92.0 + - + +
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Residues in contact with HIS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU* 5.4 2.9 - - - +
149F ARG* 3.9 23.4 + - - +
171F TRP* 2.9 47.1 + + + +
172F ALA 3.5 0.4 - - - -
173F VAL 3.4 0.2 - - - -
174F ASP* 1.3 110.8 + - + +
176F LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LEU 4.4 15.0 - - - +
149F ARG* 2.7 46.3 + - - +
151F MET* 6.1 1.1 - - + -
153F HIS* 3.8 4.9 + - - +
155F LEU* 4.4 27.6 - - + -
157F PHE* 5.3 11.2 - - + -
171F TRP* 4.0 26.9 - - + -
172F ALA* 2.8 18.3 + - + +
173F VAL 4.8 0.8 + - - -
175F HIS* 1.3 76.1 - - - +
177F LEU* 1.3 87.1 + - + +
178F GLU* 3.2 4.2 + - - +
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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