Contacts of the helix formed by residues 164 - 176 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B GLN 6.6 0.2 - - - -
11B ASP* 3.2 20.4 + - - -
139C CYS 3.3 29.4 + - - +
140C SER* 3.5 18.4 + - - +
142C LEU* 3.9 18.4 - - - +
163C ALA* 1.3 72.0 - - + +
165C THR* 1.3 54.0 + - - +
166C PHE 3.3 2.2 - - - -
167C ASN* 2.6 42.8 + - - +
168C ILE* 2.8 39.0 + - + +
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Residues in contact with THR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASP* 2.5 34.6 + - + +
162C HIS* 3.1 21.5 - - - -
163C ALA 3.4 4.2 + - - -
164C ASN* 1.3 76.5 - - - +
166C PHE* 1.3 61.2 + - + +
168C ILE* 3.6 8.0 - - - +
169C MET* 3.3 18.9 + - - +
183C PHE* 4.1 4.4 - - + -
185C ILE* 3.7 30.3 - - + -
192C TRP* 3.6 23.2 - - + -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.6 26.2 - + + -
10B GLN 5.4 2.7 - - - +
12B LEU* 3.7 28.7 - - + -
164C ASN 3.3 0.6 - - - -
165C THR* 1.3 75.5 - - + +
167C ASN* 1.3 65.4 + - - +
168C ILE 3.0 1.6 - - - -
169C MET* 2.9 33.6 + - + +
170C LYS* 3.0 11.1 + - - +
185C ILE* 5.5 5.8 - - + -
189C ILE* 5.9 0.4 - - + -
192C TRP* 4.3 17.0 - + - -
200C PHE* 4.3 13.7 - + - -
203C TYR* 3.7 42.2 - + + -
204C LEU* 3.8 21.5 - - + -
207C PHE* 3.7 22.9 - + - -
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Residues in contact with ASN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN 4.6 2.3 - - - +
8B ASN* 3.4 18.0 + - - +
9B PHE* 2.8 53.6 + - - +
10B GLN 5.2 0.2 + - - -
142C LEU* 4.8 12.0 - - + +
164C ASN* 2.6 40.1 + - - +
166C PHE* 1.3 78.3 - - - +
168C ILE* 1.3 60.6 + - - +
170C LYS* 3.4 13.9 + - - +
171C TRP* 3.4 19.6 + - - +
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 4.4 6.1 - - + -
139C CYS* 4.0 26.7 - - + +
142C LEU* 5.3 4.3 - - + -
145C PHE* 3.2 54.5 - - + -
157C PHE* 4.1 20.0 - - + -
163C ALA 4.0 3.6 - - - +
164C ASN* 2.8 33.2 + - + +
165C THR* 3.6 8.3 - - - +
166C PHE 3.0 0.2 - - - -
167C ASN* 1.3 73.8 - - - +
169C MET* 1.3 55.7 + - - +
171C TRP* 3.2 11.3 + - + +
172C ALA* 2.8 31.6 + - - +
183C PHE* 4.6 3.1 - - + -
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C THR 3.3 8.8 + - - +
166C PHE* 2.9 30.0 + - + +
168C ILE* 1.3 79.4 - - - +
170C LYS* 1.3 58.9 + - - +
172C ALA* 3.2 1.7 + - - +
173C VAL* 3.0 29.9 + - + +
183C PHE* 3.5 36.3 - - + -
185C ILE* 4.3 11.9 - - - -
204C LEU* 4.4 4.0 - - + -
207C PHE* 3.2 50.7 - - + -
211C LEU* 3.9 17.0 - - + -
229C LEU* 3.7 25.4 - - + -
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 4.0 30.7 + - + +
5B SER* 3.0 30.5 + - - +
6B ARG* 4.2 2.2 - - - +
7B GLN 3.1 26.4 + - - +
9B PHE* 4.5 8.1 - - + -
142C LEU* 5.8 8.5 - - - -
166C PHE 3.0 10.3 + - - +
167C ASN* 3.5 18.8 - - - +
168C ILE 3.2 0.2 - - - -
169C MET* 1.3 76.8 - - - +
171C TRP* 1.3 59.9 + - - +
173C VAL* 3.3 2.9 + - - +
174C ASP* 3.1 36.2 + - - +
207C PHE* 3.9 13.0 - - + -
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Residues in contact with TRP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.8 18.4 - - + -
145C PHE* 3.5 63.5 - + + -
146C GLU* 3.9 30.6 - - - +
148C LEU* 5.0 8.1 - - + -
157C PHE* 4.8 3.6 - + - -
167C ASN 3.4 8.6 + - - +
168C ILE* 3.2 14.2 + - + +
170C LYS* 1.3 80.0 - - + +
172C ALA* 1.3 73.4 + - + +
173C VAL 3.2 0.2 - - - -
174C ASP* 4.4 0.4 - - - -
175C HIS* 3.0 70.6 + + + +
176C LEU* 3.9 28.9 + - + -
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE* 5.3 1.8 - - + -
168C ILE* 2.8 18.0 + - + +
169C MET 3.4 6.3 - - - +
170C LYS 3.2 0.4 - - - -
171C TRP* 1.3 93.8 - - + +
173C VAL* 1.3 53.8 + - - +
176C LEU* 3.1 11.3 + - + -
177C LEU* 2.7 47.6 + - + +
183C PHE* 3.5 24.5 - - + -
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.3 24.5 - - - +
169C MET 3.0 18.3 + - - +
170C LYS* 3.8 4.3 - - - +
172C ALA* 1.3 77.0 - - - +
174C ASP* 1.3 65.6 + - - +
177C LEU* 3.7 31.1 - - + +
207C PHE* 4.5 4.5 - - + -
210C VAL* 3.8 36.3 - - + -
211C LEU* 4.1 15.9 - - + -
231C ARG* 3.8 25.3 + - - +
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Residues in contact with ASP 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.3 23.4 + - - -
5B SER* 4.3 17.6 - - - +
170C LYS* 3.1 22.1 + - - +
171C TRP* 5.0 0.4 - - - -
173C VAL* 1.3 81.3 - - - +
175C HIS* 1.3 84.1 + - + +
176C LEU 3.8 0.2 - - - -
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Residues in contact with HIS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLU* 5.7 3.9 + - + +
150C GLU* 5.4 3.6 - - - +
171C TRP* 3.0 56.5 + + + +
174C ASP* 1.3 107.0 + - + +
176C LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 6.0 1.1 - - + -
149C ARG 5.6 1.3 - - - +
150C GLU* 6.3 0.7 - - - -
151C MET* 3.5 37.2 - - + +
153C HIS* 3.1 29.5 + - + -
155C LEU* 3.6 20.2 - - + -
157C PHE* 3.7 33.7 - - + -
171C TRP* 4.2 26.2 - - + -
172C ALA* 3.1 13.9 + - + +
174C ASP 3.8 0.4 - - - -
175C HIS* 1.3 80.2 - - - +
177C LEU* 1.3 70.0 + - + +
178C GLU* 4.4 0.7 - - - +
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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