Contacts of the helix formed by residues 177 - 190 (chain F) in PDB entry 2VHW
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 GLY 177 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175F GLY 3.4 4.8 + - - -
176F ALA* 1.3 78.3 - - - +
178F THR* 1.3 60.6 + - - -
179F ALA 3.5 2.0 - - - -
180F GLY 4.1 1.2 - - - +
181F TYR* 2.8 30.1 + - - +
203F LYS* 4.3 8.1 - - - -
1374F NAI 3.3 34.2 + - - -
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Residues in contact with THR 178 (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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205C ARG* 5.6 3.4 - - - +
131F ALA* 3.6 24.8 - - + +
134F SER* 3.6 5.4 - - - -
135F GLU* 3.5 32.3 - - + +
177F GLY* 1.3 69.8 - - - +
179F ALA* 1.3 63.2 + - - +
181F TYR* 3.9 3.7 - - - +
182F ASN* 2.9 34.4 + - - +
1374F NAI 3.0 28.0 + - - -
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Residues in contact with ALA 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F SER* 3.5 27.1 - - - +
138F GLY* 3.3 8.7 - - - -
178F THR* 1.3 74.9 - - - +
180F GLY* 1.3 56.8 - - - +
182F ASN 3.3 1.0 + - - -
183F ALA* 2.9 26.9 + - - +
238F ALA* 4.1 13.7 - - + -
267F ILE* 4.2 23.6 - - + -
1374F NAI 2.7 26.5 + - - +
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Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F VAL* 3.5 16.7 - - - +
175F GLY 3.2 25.6 - - - -
176F ALA* 4.8 0.9 - - - -
177F GLY 3.5 4.4 + - - +
178F THR 3.4 0.2 - - - -
179F ALA* 1.3 76.2 - - - +
181F TYR* 1.3 59.3 + - - +
183F ALA* 3.5 1.1 + - - -
184F ALA* 2.9 31.9 + - - +
196F VAL* 4.9 1.3 - - - +
238F ALA* 3.6 10.6 - - - +
1374F NAI 4.2 0.8 + - - -
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Residues in contact with TYR 181 (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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209C ALA* 3.5 10.6 - - + +
139F ARG* 5.4 0.2 - - - -
175F GLY 4.3 0.6 + - - -
176F ALA* 4.3 9.7 - - - +
177F GLY 2.8 25.4 + - - +
178F THR* 4.2 2.5 - - - -
180F GLY* 1.3 71.5 - - - +
182F ASN* 1.3 82.1 + - - +
184F ALA* 3.7 4.8 - - - +
185F ARG* 2.8 61.3 + - - +
207F LEU* 3.6 25.1 - - + -
210F GLU* 2.6 43.4 + - - -
211F PHE* 3.8 11.9 - + - -
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Residues in contact with ASN 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU* 3.7 44.3 + - - +
138F GLY* 3.9 3.8 - - - -
139F ARG* 2.7 42.9 + - + +
178F THR* 2.9 30.4 + - - +
179F ALA 3.9 2.7 - - - +
181F TYR* 1.3 94.8 - - - +
183F ALA* 1.3 63.1 + - - +
185F ARG* 3.4 5.6 + - - +
186F ILE* 3.1 30.7 + - - +
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Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F GLY* 3.1 22.7 + - - +
141F ALA* 4.5 0.2 - - + -
142F ALA* 3.7 5.3 - - - +
173F VAL* 4.5 4.5 - - + -
179F ALA 2.9 17.3 + - - +
180F GLY* 3.8 5.6 - - - +
182F ASN* 1.3 72.4 - - - +
184F ALA* 1.3 58.3 + - - +
186F ILE 3.4 0.5 + - - -
187F ALA* 2.9 32.9 + - - +
236F ILE* 4.0 36.5 - - + +
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Residues in contact with ALA 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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173F VAL* 4.1 3.7 - - + +
180F GLY 2.9 21.7 + - - +
181F TYR* 3.7 6.1 - - - +
183F ALA* 1.3 72.8 - - - +
185F ARG* 1.3 58.3 + - - +
187F ALA* 3.9 1.2 - - - +
188F ASN* 2.8 34.7 + - - +
194F VAL* 3.8 17.5 - - + +
196F VAL* 3.6 28.9 - - + -
207F LEU* 4.7 2.5 - - + -
215F ILE* 4.0 12.3 - - + -
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Residues in contact with ARG 185 (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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208C ASP* 3.0 56.5 + - - -
209C ALA* 3.7 3.6 - - - +
212C CYS* 3.4 25.6 + - - -
213C GLY* 3.4 13.5 - - - +
189E GLY 4.3 1.6 - - - +
191E GLY* 6.0 3.8 - - - -
139F ARG* 3.6 20.5 - - - +
181F TYR* 2.8 59.2 + - + +
182F ASN* 3.7 7.4 - - - +
183F ALA 3.3 0.2 - - - -
184F ALA* 1.3 77.3 - - - +
186F ILE* 1.3 68.5 + - + +
188F ASN* 3.8 3.3 + - - +
189F GLY* 3.0 23.6 + - - -
210F GLU* 4.3 0.6 + - - -
211F PHE* 3.9 25.8 - - + -
215F ILE* 4.2 2.2 - - - +
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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
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189E GLY 4.3 5.0 - - - +
190E MET* 3.7 46.4 - - + +
191E GLY* 5.2 1.3 - - - -
139F ARG* 3.6 46.2 - - + +
142F ALA* 3.6 21.5 - - + -
143F GLN* 4.8 0.4 - - - +
182F ASN 3.1 16.9 + - - +
185F ARG* 1.3 86.9 - - + +
187F ALA* 1.3 66.7 + - - +
189F GLY* 3.1 2.1 + - - -
190F MET* 3.0 33.8 + - - +
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Residues in contact with ALA 187 (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 ALA* 3.6 7.2 - - + +
160F MET* 3.8 25.4 - - + -
171F VAL* 4.2 15.3 - - + -
183F ALA 2.9 19.4 + - - +
184F ALA* 3.9 0.7 - - - +
186F ILE* 1.3 75.8 - - - +
188F ASN* 1.3 62.0 + - - +
190F MET* 3.2 9.9 + - - +
191F GLY 3.4 0.2 + - - -
192F ALA* 3.1 22.7 + - - +
194F VAL* 3.8 19.1 - - + -
236F ILE* 5.4 1.1 - - + -
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Residues in contact with ASN 188 (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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184F ALA 2.8 22.4 + - - +
185F ARG 3.8 3.3 + - - +
187F ALA* 1.3 72.5 - - - +
189F GLY* 1.3 61.4 + - - +
191F GLY* 2.9 20.3 + - - -
192F ALA 4.0 14.7 - - - +
194F VAL* 3.7 6.2 + - + +
211F PHE* 4.1 20.2 - - - -
214F ARG* 3.1 51.0 + - - +
215F ILE* 3.8 22.0 - - + +
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Residues in contact with GLY 189 (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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185E ARG* 4.3 2.8 - - - +
186E ILE* 4.2 10.2 - - - +
189E GLY* 3.3 43.5 - - - -
185F ARG 3.0 13.3 + - - -
186F ILE 3.1 2.2 + - - -
188F ASN* 1.3 77.6 - - - +
190F MET* 1.3 58.5 + - - +
191F GLY* 3.1 1.6 + - - -
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Residues in contact with MET 190 (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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143E GLN* 3.7 27.1 - - + +
186E ILE* 3.5 30.6 - - + +
190E MET* 3.7 41.1 - - + -
142F ALA 4.1 17.0 - - - +
143F GLN* 4.6 1.1 - - - -
146F ALA* 3.6 24.7 - - + -
160F MET* 4.0 19.4 - - + +
161F GLY* 3.3 19.8 + - - -
186F ILE* 3.0 23.9 + - - +
187F ALA 3.6 8.1 - - - +
188F ASN 3.2 0.6 - - - -
189F GLY* 1.3 77.7 - - - +
191F GLY* 1.3 57.3 + - - +
192F ALA 3.4 0.9 - - - -
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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