Contacts of the helix formed by residues 169 - 186 (chain F) in PDB entry 2B05
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 HIS 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118F GLU* 3.5 32.0 + - - -
165F MET* 3.3 37.8 - - + +
166F GLN* 2.9 23.4 + - + +
167F PRO 3.4 0.6 - - - -
168F THR* 1.3 78.1 + - - +
170F PRO* 1.4 83.3 - - + +
171F ILE* 3.2 20.5 + - + -
172F ARG* 3.0 11.5 + - + +
173F LEU* 2.9 20.9 + - - +
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Residues in contact with PRO 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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168F THR 3.3 1.3 - - - +
169F HIS* 1.4 97.2 - - + +
171F ILE* 1.3 55.7 + - + +
173F LEU* 3.2 3.4 + - + -
174F GLY* 2.7 32.1 + - - -
215F SER* 3.9 24.2 - - - +
218F ASP* 3.9 28.3 - - + +
219F SER* 3.2 20.9 - - - +
222F ILE* 3.3 19.2 - - + +
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Residues in contact with ILE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ASN* 5.4 2.7 - - - +
42F ARG* 4.1 8.1 - - - +
118F GLU* 3.7 35.0 - - + +
121F VAL* 3.8 24.0 - - + +
122F PHE* 3.9 42.4 - - + +
125F LYS* 4.6 6.1 - - + +
165F MET* 3.7 14.4 - - + -
169F HIS* 3.1 6.7 + - + +
170F PRO* 1.3 83.6 - - + +
172F ARG* 1.3 58.2 + - - +
174F GLY* 4.0 1.2 - - - -
175F LEU* 3.1 27.9 + - - +
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Residues in contact with ARG 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 5.2 0.2 - - - -
158F HIS* 6.2 1.0 + - + -
161F SER* 3.6 43.1 + - - +
162F LYS* 4.1 25.2 + - - +
165F MET* 2.8 36.7 + - + +
166F GLN 3.6 11.4 - - - +
167F PRO* 3.4 37.5 + - - +
169F HIS* 3.0 18.8 + - + +
171F ILE* 1.3 76.0 - - - +
173F LEU* 1.3 65.2 + - + +
175F LEU* 3.3 8.2 + - - +
176F ALA* 3.0 21.9 + - + +
200F ALA* 6.1 3.2 - - - +
203F ASP* 4.2 16.0 + - - +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F PRO 3.4 20.2 - - - +
168F THR* 3.4 29.4 - - - +
169F HIS 2.9 8.9 + - - +
170F PRO 3.6 5.2 - - - +
172F ARG* 1.3 76.3 - - + +
174F GLY* 1.3 57.0 + - - +
176F ALA* 3.1 8.9 + - - +
177F LEU* 2.9 27.5 + - - +
200F ALA* 4.1 10.8 - - + +
204F ALA* 3.9 15.0 - - + -
219F SER* 3.7 30.3 - - - +
222F ILE* 3.6 17.2 - - + +
223F MET* 4.3 9.9 - - + -
226F LEU* 4.1 21.9 - - + +
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Residues in contact with GLY 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LYS* 3.6 15.8 - - - -
170F PRO 2.7 19.4 + - - -
171F ILE* 4.0 1.8 - - - -
173F LEU* 1.3 72.8 - - - +
175F LEU* 1.3 61.1 + - - +
177F LEU* 3.4 4.6 + - - +
178F ASN* 3.1 21.7 + - - +
222F ILE* 3.8 16.3 - - - +
506L LEU* 4.3 15.7 - - - -
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 4.0 9.0 - - + -
125F LYS* 3.7 27.9 - - + +
154F TYR* 3.6 31.4 - - + +
157F ALA* 3.5 44.0 - - + +
158F HIS* 3.6 16.8 - - + +
161F SER* 3.8 10.3 - - - +
171F ILE 3.1 18.1 + - - +
172F ARG 3.5 4.5 - - - +
174F GLY* 1.3 74.1 - - - +
176F ALA* 1.3 61.1 + - - +
178F ASN* 3.3 0.5 + - - +
179F TYR* 2.8 39.4 + - + +
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Residues in contact with ALA 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F HIS* 5.6 5.6 - - + +
172F ARG* 3.0 15.7 + - + +
173F LEU* 3.1 10.3 + - - +
175F LEU* 1.3 76.2 - - - +
177F LEU* 1.3 58.7 + - - +
179F TYR* 4.5 4.3 - - - -
180F SER* 3.0 29.8 + - - -
196F LEU* 3.9 18.2 - - + +
197F ALA 5.1 0.2 + - - -
200F ALA* 3.5 31.4 - - + -
226F LEU* 4.2 5.4 - - + +
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Residues in contact with LEU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU 2.9 12.5 + - - +
174F GLY 3.5 7.4 - - - +
176F ALA* 1.3 75.4 - - - +
178F ASN* 1.3 63.1 + - - +
180F SER* 2.7 21.3 + - - +
181F VAL* 3.1 13.7 + - - +
222F ILE* 4.2 12.1 - - + -
225F LEU* 3.7 23.1 - - + -
226F LEU* 3.6 38.3 - - + +
229F ASN* 3.4 27.1 - - - +
504L ILE 3.9 6.1 - - - +
505L SEP 3.9 3.8 - - - -
506L LEU* 3.6 34.8 - - + +
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Residues in contact with ASN 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LYS* 3.4 14.8 - - - +
129F ASP* 2.8 40.6 + - - +
132F ARG* 3.5 16.5 + - - +
154F TYR* 4.0 7.0 - - + +
174F GLY 3.1 13.0 + - - +
175F LEU* 4.0 2.5 - - - +
177F LEU* 1.3 81.0 - - - +
179F TYR* 1.3 57.0 + - - +
181F VAL* 3.4 8.9 + - - +
182F PHE* 3.0 26.5 + - - +
505L SEP 3.5 8.2 + - - +
506L LEU* 2.8 35.7 + - - +
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Residues in contact with TYR 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F GLU* 3.0 28.2 + - - -
154F TYR* 3.4 44.3 - + + -
155F SER* 3.8 11.2 + - - -
158F HIS* 4.0 36.3 - + + -
175F LEU* 2.8 23.0 + - + +
176F ALA* 4.5 0.2 - - - -
178F ASN* 1.3 77.1 - - - +
180F SER* 1.3 57.4 + - - +
182F PHE* 3.2 13.6 + + - +
183F TYR* 2.9 59.7 + + - -
196F LEU* 3.6 20.0 - - + -
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Residues in contact with SER 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176F ALA 3.0 15.8 + - - -
177F LEU* 2.7 24.9 + - - +
179F TYR* 1.3 73.4 - - - +
181F VAL* 1.3 63.9 + - - +
183F TYR* 3.2 7.3 + - - -
184F TYR* 3.0 19.8 + - - +
193F ALA* 3.3 32.3 - - - +
196F LEU* 3.7 11.1 - - - +
197F ALA* 4.1 11.3 - - - +
226F LEU* 4.7 0.9 - - - +
233F TRP* 3.7 16.9 - - - -
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Residues in contact with VAL 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ARG* 4.1 21.3 - - - +
177F LEU 3.1 16.5 + - - +
178F ASN* 3.4 9.0 - - - +
180F SER* 1.3 74.8 + - - +
182F PHE* 1.3 57.4 + - - +
184F TYR* 3.1 0.7 + - - -
185F GLU* 2.8 50.7 + - + +
229F ASN* 4.0 10.8 - - - +
233F TRP* 4.2 7.9 - - + -
503L ALA* 4.3 14.8 - - + +
504L ILE 3.8 26.0 - - - +
505L SEP 4.3 9.9 - - - +
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Residues in contact with PHE 182 (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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132F ARG* 3.9 16.1 - - + +
147F VAL* 3.7 20.6 - - + -
150F SER* 3.4 28.3 - - - -
151F GLU* 3.8 28.0 - - + -
154F TYR* 3.8 15.0 - + + -
178F ASN 3.0 13.8 + - - +
179F TYR* 3.2 24.7 + + - +
181F VAL* 1.3 76.5 - - - +
183F TYR* 1.3 63.5 + + - +
186F ILE* 3.0 57.7 + - + +
187F GLN* 3.1 39.8 + - + -
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Residues in contact with TYR 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F GLU* 4.3 9.9 + - - -
179F TYR* 2.9 55.6 + + - -
180F SER* 3.2 8.7 + - - +
182F PHE* 1.3 79.4 - + - +
184F TYR* 1.3 52.2 + - - +
187F GLN* 3.4 20.0 - - + +
188F ASN 3.2 9.0 + - - -
189F ALA* 2.8 33.7 + - + +
192F GLN* 3.7 57.7 + - + -
193F ALA* 3.7 12.8 - - + +
196F LEU* 3.7 26.5 - - + -
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Residues in contact with TYR 184 (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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180F SER 3.0 15.5 + - - +
181F VAL* 3.7 3.4 - - - +
183F TYR* 1.3 76.8 - - - +
185F GLU* 1.3 75.7 + - + +
188F ASN* 3.4 21.7 - - - +
189F ALA 4.5 2.5 - - - +
190F PRO* 3.8 33.2 - - + +
193F ALA* 3.7 8.7 - - + +
232F LEU* 5.1 2.6 + - + +
233F TRP* 3.3 67.3 + + + -
502L ARG* 6.2 3.1 - - + -
503L ALA* 4.8 2.7 - - + -
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Residues in contact with GLU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ARG* 6.2 0.4 - - - -
143F ARG* 4.5 3.5 + - - -
181F VAL* 2.8 32.6 + - + +
184F TYR* 1.3 89.3 - - + +
186F ILE* 1.3 73.1 + - + +
188F ASN* 4.4 3.2 + - - +
502L ARG 6.3 0.4 - - - +
503L ALA* 4.7 10.5 - - + +
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Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ARG* 3.8 41.5 - - + +
135F ALA* 4.3 8.3 - - + -
136F GLU* 4.4 17.5 - - + +
143F ARG* 3.1 35.6 + - - +
147F VAL* 3.6 33.4 - - + -
182F PHE* 3.0 32.9 + - + +
185F GLU* 1.3 87.8 - - + +
187F GLN* 1.3 65.0 + - - +
188F ASN* 3.2 4.0 + - - +
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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
------------------------------------------------------------
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