Contacts of the helix formed by residues 183 - 201 (chain F) in PDB entry 6V3O
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 ARG 183 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331E SER* 4.0 20.0 + - - -
369E GLU* 2.9 28.9 + - - -
372E ARG* 3.6 17.1 - - - +
181F SER 4.1 1.0 + - - -
182F ALA* 1.3 75.6 - - - +
184F ARG* 1.3 67.5 + - - +
185F SER* 4.1 13.1 + - - +
186F LEU* 3.0 16.7 + - - +
187F LEU* 3.2 12.0 + - - +
227F THR* 4.3 3.0 - - - +
229F GLU* 2.4 43.6 + - - +
232F ARG* 3.9 25.0 - - - +
243F TYR* 3.6 45.7 + - + -
246F SER* 4.4 2.0 - - - -
1003F SO4 4.8 10.5 + - - +
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Residues in contact with ARG 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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328E PHE* 4.6 10.8 - - + -
360E GLU* 5.5 3.7 + - - -
362E TRP* 6.1 0.6 - - - +
182F ALA 4.1 0.8 + - - -
183F ARG* 1.3 73.7 - - - +
185F SER* 1.3 62.9 + - - +
187F LEU* 3.3 7.9 + - - +
188F GLN* 3.0 36.6 + - - +
242F ARG* 3.9 33.5 + - - +
243F TYR* 5.6 1.3 - - - +
245F MET* 4.5 0.6 - - - +
246F SER* 3.8 24.2 - - - +
249F HIS* 3.5 45.4 + - - -
250F GLU* 3.9 23.8 - - + +
314F MET* 5.1 5.1 - - - +
1003F SO4 2.5 37.9 + - - +
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Residues in contact with SER 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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328E PHE* 3.9 20.5 - - - -
331E SER* 4.8 1.1 - - - -
372E ARG* 2.8 33.0 + - - -
183F ARG* 4.3 8.4 + - - +
184F ARG* 1.3 76.7 - - - +
186F LEU* 1.3 56.9 + - - +
188F GLN* 3.5 5.7 + - - +
189F LYS* 3.2 37.1 + - - +
192F ARG* 4.7 0.5 + - - -
229F GLU* 4.6 12.1 - - - -
1003F SO4 3.5 14.1 + - - -
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Residues in contact with LEU 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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180F GLN* 5.3 6.3 - - + +
181F SER 5.3 2.2 - - - +
182F ALA* 4.8 20.9 - - + -
183F ARG 3.0 8.9 + - - +
185F SER* 1.3 76.7 - - - +
187F LEU* 1.3 61.3 + - + +
188F GLN 3.1 1.6 - - - -
189F LYS* 3.1 17.0 + - + +
190F ASN* 2.8 45.7 + - - +
224F ALA* 5.4 12.8 - - + +
229F GLU* 3.8 42.8 + - + +
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Residues in contact with LEU 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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182F ALA* 4.3 10.3 - - + -
183F ARG 3.2 12.6 + - - +
184F ARG* 3.3 6.3 + - - +
186F LEU* 1.3 78.5 - - + +
188F GLN* 1.3 56.5 + - - +
190F ASN* 3.4 14.8 + - - +
191F ALA* 3.1 24.6 + - - +
194F ARG* 4.6 3.3 + - - -
246F SER* 3.9 34.3 - - - +
247F TYR* 3.6 46.9 - - + +
250F GLU* 3.9 21.8 - - + -
678F GLU* 3.8 9.9 - - - +
682F GLY* 6.1 1.3 - - - -
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Residues in contact with GLN 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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328E PHE* 4.2 34.5 - - - +
184F ARG* 3.0 28.2 + - - +
185F SER* 3.8 4.7 - - - +
186F LEU 3.1 0.2 - - - -
187F LEU* 1.3 75.4 - - - +
189F LYS* 1.3 65.2 + - - +
191F ALA* 3.3 7.4 + - - +
192F ARG* 3.1 47.7 + - - +
250F GLU* 3.1 35.6 + - - +
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Residues in contact with LYS 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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328E PHE 3.8 10.5 + - - -
329E GLU* 3.2 30.6 + - - +
331E SER* 3.2 11.3 + - - -
332E MET* 5.7 0.2 - - - -
185F SER* 3.2 18.9 + - - +
186F LEU* 3.1 16.9 + - + +
188F GLN* 1.3 76.1 - - - +
190F ASN* 1.3 63.5 + - - +
192F ARG* 3.4 20.7 + - - +
193F ILE* 3.2 30.7 + - + +
220F GLU* 4.3 7.2 - - - +
223F ALA* 4.0 19.1 - - + -
224F ALA* 4.0 31.9 - - + +
227F THR* 3.8 18.8 - - + +
229F GLU* 5.9 0.2 + - - -
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Residues in contact with ASN 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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107F ASN* 6.1 0.5 - - - +
111F LEU* 3.7 31.8 - - + +
186F LEU* 2.8 34.6 + - - +
187F LEU* 3.4 26.6 - - - +
189F LYS* 1.3 75.1 - - - +
191F ALA* 1.3 66.1 + - - +
193F ILE* 3.2 6.6 + - - +
194F ARG* 3.0 42.3 + - - +
678F GLU* 4.2 11.9 + - - -
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Residues in contact with ALA 191 (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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187F LEU 3.1 14.2 + - - +
188F GLN* 3.3 11.2 + - - +
190F ASN* 1.3 75.0 - - - +
192F ARG* 1.3 53.2 - - + +
194F ARG* 3.1 22.3 + - - +
195F ASN* 2.7 50.7 + - - +
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Residues in contact with ARG 192 (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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328E PHE 5.8 0.2 - - - -
329E GLU* 3.6 38.2 + - - +
185F SER 4.7 0.4 + - - -
188F GLN* 3.1 40.3 + - - +
189F LYS* 3.4 36.1 - - - +
190F ASN 3.3 0.2 - - - -
191F ALA* 1.3 76.5 - - + +
193F ILE* 1.3 59.8 + - - +
195F ASN* 3.9 9.4 - - - +
196F CYS* 3.0 36.5 + - - -
220F GLU* 3.0 41.3 + - + +
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Residues in contact with ILE 193 (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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41F LEU* 4.0 19.7 - - + -
108F LEU* 4.4 15.0 - - + -
111F LEU* 4.1 27.6 - - + -
189F LYS* 3.2 20.0 + - + +
190F ASN* 3.2 7.8 + - - +
192F ARG* 1.3 77.3 - - - +
194F ARG* 1.3 62.7 + - - +
196F CYS 3.4 0.2 + - - -
197F LEU* 3.1 21.2 + - + +
217F LEU* 3.7 22.2 - - + +
220F GLU* 3.7 29.2 - - + +
221F ILE* 4.4 12.6 - - + -
224F ALA* 4.6 11.4 - - + -
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Residues in contact with ARG 194 (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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111F LEU* 3.5 32.1 - - + +
114F GLU* 2.9 29.6 + - - -
115F VAL* 3.6 28.2 - - + +
187F LEU 4.6 2.8 + - - -
190F ASN* 3.0 20.9 + - - +
191F ALA* 3.5 32.0 - - - +
193F ILE* 1.3 75.0 - - - +
195F ASN* 1.3 67.2 + - - +
197F LEU* 3.1 5.9 + - - +
198F THR* 3.0 29.3 + - + +
678F GLU* 3.8 9.9 + - - -
682F GLY 2.8 26.5 + - - -
683F GLU* 3.7 24.2 - - + +
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Residues in contact with ASN 195 (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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191F ALA* 2.7 35.3 + - - +
192F ARG* 3.9 9.7 - - - +
194F ARG* 1.3 77.0 + - - +
196F CYS* 1.3 62.5 + - - +
198F THR* 3.2 10.0 + - - +
199F GLN* 3.0 40.9 + - - +
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Residues in contact with CYS 196 (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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192F ARG* 3.0 28.3 + - - +
195F ASN* 1.3 76.8 - - - +
197F LEU* 1.3 57.9 + - - +
199F GLN* 4.2 6.9 - - - +
200F LEU* 3.0 36.0 + - - +
213F LEU* 4.4 13.7 - - + +
216F ALA* 4.0 16.6 - - - -
217F LEU* 3.6 44.9 - - + -
220F GLU* 4.8 5.2 - - - -
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Residues in contact with LEU 197 (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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37F TYR* 3.9 41.1 - - + -
40F LEU* 3.9 29.8 - - + -
41F LEU* 4.0 38.8 - - + -
111F LEU 5.3 0.7 - - - +
112F ALA* 4.4 9.2 - - - -
115F VAL* 4.4 11.2 - - + -
193F ILE* 3.1 13.6 + - + +
194F ARG* 3.1 11.2 + - - +
196F CYS* 1.3 78.1 - - - +
198F THR* 1.3 62.6 + - + +
200F LEU* 3.6 4.5 + - + +
201F ASN* 3.1 27.4 + - - +
217F LEU* 4.5 6.7 - - + +
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Residues in contact with THR 198 (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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37F TYR* 5.4 3.1 - - - -
115F VAL* 3.6 28.3 - - + -
119F HIS* 3.9 24.8 - - + +
194F ARG* 3.0 18.0 + - + +
195F ASN* 3.2 12.7 + - - +
197F LEU* 1.3 75.7 - - - +
199F GLN* 1.3 71.7 + - - +
201F ASN* 3.1 15.3 + - - +
202F ALA* 3.5 9.2 + - - +
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Residues in contact with GLN 199 (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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195F ASN* 3.0 29.5 + - - +
196F CYS* 4.5 1.4 - - - -
198F THR* 1.3 87.1 + - - +
200F LEU* 1.3 62.5 + - - +
201F ASN 3.1 0.9 + - - -
202F ALA* 3.1 21.4 + - - +
205F ILE* 4.2 10.4 - - - +
213F LEU* 3.3 36.5 - - + +
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Residues in contact with LEU 200 (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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40F LEU* 4.7 15.7 - - + -
44F ARG* 5.3 2.2 - - - +
196F CYS 3.0 21.0 + - - +
197F LEU* 3.7 7.2 - - - +
198F THR 3.3 0.2 - - - -
199F GLN* 1.3 75.8 - - - +
201F ASN* 1.3 64.7 + - - +
202F ALA 3.4 2.8 + - - +
205F ILE* 4.3 10.3 - - - +
210F LYS* 3.8 46.9 - - + +
213F LEU* 4.0 20.3 - - + +
214F ASP* 4.2 20.4 - - + +
217F LEU* 3.9 25.8 - - + -
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Residues in contact with ASN 201 (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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33F LYS* 5.1 10.9 - - + +
37F TYR* 3.0 41.5 - - - +
40F LEU* 4.6 11.3 - - - +
197F LEU* 3.1 15.0 + - - +
198F THR* 3.1 10.5 + - - +
199F GLN 3.1 1.0 - - - -
200F LEU* 1.3 82.2 + - - +
202F ALA* 1.3 66.1 + - - +
203F LYS* 3.7 8.5 + - - +
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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