Contacts of the helix formed by residues 185 - 203 (chain A) in PDB entry 1V0D
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 ALA 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A VAL* 4.2 4.9 - - + +
182A ASP* 3.0 10.1 + - + +
184A ALA* 1.3 74.7 - - + +
186A GLN* 1.3 64.3 + - - +
187A GLU 3.2 3.7 + - - -
188A GLU* 3.3 9.4 + - - +
189A TYR* 3.1 21.8 + - - +
279A ILE* 3.9 15.2 - - + +
280A GLN* 3.7 37.5 - - + +
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 3.2 33.5 + - + +
179A SER* 4.1 9.0 - - - +
181A VAL* 2.8 32.0 - - - +
182A ASP 2.8 6.3 + - - +
183A GLU* 3.3 26.1 + - - +
185A ALA* 1.3 77.9 - - - +
187A GLU* 1.3 61.5 + - - +
189A TYR* 3.6 3.8 - - - +
190A LEU* 3.3 30.2 + - + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU 4.4 2.5 + - - +
184A ALA 4.6 6.0 + - - +
185A ALA 3.2 0.8 - - - -
186A GLN* 1.3 76.3 - - - +
188A GLU* 1.3 67.2 + - - +
190A LEU* 3.0 13.5 + - - +
191A ARG* 3.0 19.6 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA 5.5 0.2 + - - -
185A ALA* 3.3 11.0 + - - +
187A GLU* 1.3 79.6 - - - +
189A TYR* 1.3 52.6 + - - +
191A ARG* 2.9 36.4 + - - -
192A VAL* 2.7 50.1 + - - +
279A ILE* 3.9 15.7 - - + +
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 2.9 35.1 + - + +
177A TYR* 3.5 20.3 - + - +
178A THR* 3.2 36.6 - - + -
181A VAL* 3.9 22.9 - - + -
185A ALA 3.1 13.4 + - - +
186A GLN* 3.6 13.7 - - - +
187A GLU 3.2 0.2 - - - -
188A GLU* 1.3 77.1 - - - +
190A LEU* 1.3 50.9 - - + +
192A VAL* 3.2 2.4 + - - +
193A LEU* 2.7 48.7 + - + +
196A MET* 6.4 0.2 - - + -
272A VAL* 3.9 5.4 - - - +
275A LEU* 3.2 24.3 - - + +
276A ALA* 4.2 13.5 - - + -
279A ILE* 3.6 24.8 - - + +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 5.9 1.3 - - - +
178A THR* 3.4 34.8 - - + +
186A GLN* 3.3 20.0 - - + +
187A GLU* 3.0 10.2 + - - +
189A TYR* 1.3 73.8 - - + +
191A ARG* 1.3 60.2 + - - +
193A LEU* 3.7 12.6 - - + +
194A GLY* 2.9 25.3 + - - -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU 3.0 11.5 + - - +
188A GLU* 2.9 40.3 + - - +
190A LEU* 1.3 78.2 - - - +
192A VAL* 1.3 84.8 + - - +
194A GLY* 3.2 8.9 + - - -
195A SER* 3.0 39.7 + - - +
287A TRP* 4.0 19.0 - - - +
324A ARG* 5.6 0.4 - - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 2.7 36.9 + - - +
189A TYR 3.5 3.6 - - - +
191A ARG* 1.3 82.5 - - - +
193A LEU* 1.3 62.8 + - - +
194A GLY 2.9 4.3 - - - -
195A SER* 3.0 14.3 + - - -
196A MET* 3.1 27.2 + - + +
275A LEU* 4.8 7.6 - - + -
279A ILE* 3.7 25.1 - - + -
285A VAL* 5.5 6.1 - - + +
287A TRP* 3.6 32.1 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.9 19.7 - - + +
174A VAL* 3.8 8.1 - - + +
175A SER* 3.2 50.3 - - - +
178A THR* 4.3 2.5 - - - +
189A TYR* 2.7 40.6 + - + +
190A LEU* 3.8 12.1 - - + +
192A VAL* 1.3 74.4 - - - +
194A GLY* 1.3 61.6 + - - +
196A MET* 3.4 17.4 + - + +
197A CYS* 3.4 18.3 + - + +
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU 2.9 15.5 + - - -
191A ARG 3.2 4.7 + - - -
192A VAL 2.9 0.8 - - - -
193A LEU* 1.3 78.8 - - - +
195A SER* 1.3 65.4 + - - +
197A CYS* 3.0 17.1 + - - +
198A GLN* 3.0 13.8 + - - +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ARG* 3.0 34.3 + - - -
192A VAL 3.0 6.3 + - - -
194A GLY* 1.3 75.5 - - - +
196A MET* 1.3 62.6 + - - +
198A GLN* 3.1 9.8 + - - +
199A LYS* 3.1 22.7 + - - +
287A TRP* 3.8 32.4 - - - -
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 5.4 2.5 - - + -
174A VAL* 4.7 12.3 - - + -
189A TYR* 6.4 0.2 - - + -
192A VAL* 3.1 22.5 + - + +
193A LEU* 3.4 37.7 - - + +
195A SER* 1.3 77.7 - - - +
197A CYS* 1.3 57.6 + - - +
199A LYS* 3.5 3.2 + - - +
200A LEU* 2.9 32.4 + - - +
275A LEU* 5.0 9.0 - - + -
287A TRP* 3.8 28.7 - - + +
290A PHE* 5.0 3.8 - - - -
291A TYR* 3.8 17.1 - - + -
294A LEU* 4.0 24.7 - - + -
295A PHE* 4.0 20.9 - - + -
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Residues in contact with CYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.9 24.2 - - + +
193A LEU* 3.4 12.0 + - + +
194A GLY* 3.0 11.0 + - - +
196A MET* 1.3 78.4 - - - +
198A GLN* 1.3 65.2 + - - +
200A LEU* 3.2 2.7 + - - +
201A LYS* 2.9 53.4 + - - +
205A TYR* 4.5 4.3 - - - -
601A PB 3.0 28.7 - - - -
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY 3.0 11.1 + - - +
195A SER* 3.5 10.8 - - - +
197A CYS* 1.3 75.7 - - - +
199A LYS* 1.3 53.3 + - - +
201A LYS* 3.0 15.0 + - - +
202A SER* 2.7 36.3 + - - -
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A SER 3.1 8.5 + - - +
196A MET* 3.7 9.4 - - - +
198A GLN* 1.3 80.5 - - - +
200A LEU* 1.3 60.2 + - - +
202A SER* 2.5 28.6 + - - +
203A VAL* 3.1 11.1 + - + +
287A TRP* 4.1 19.0 - - + -
288A GLU* 4.4 17.8 - - - +
291A TYR* 3.5 40.7 - - + +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 4.1 17.3 - - + -
171A LEU* 3.9 33.4 - - + -
196A MET 2.9 18.7 + - - +
197A CYS* 3.5 6.3 - - - +
198A GLN 3.2 0.2 - - - -
199A LYS* 1.3 73.2 - - - +
201A LYS* 1.3 61.4 + - - +
203A VAL* 3.1 5.4 + - + +
204A GLN 2.9 9.0 + - - -
205A TYR* 2.8 49.5 + - + -
206A ASN* 4.5 3.8 - - - +
291A TYR* 3.4 25.6 - - + +
295A PHE* 4.0 33.7 - - + -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 5.8 0.7 - - - +
197A CYS* 2.9 43.4 + - - +
198A GLN* 3.4 9.7 - - - +
200A LEU* 1.3 75.1 - - - +
202A SER* 1.3 58.5 + - - +
204A GLN* 2.9 23.2 + - - +
205A TYR* 3.1 33.4 - - + +
601A PB 3.9 6.4 - - - -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN 2.7 17.4 + - - -
199A LYS* 2.5 31.1 + - - +
201A LYS* 1.3 72.7 - - - +
203A VAL* 1.3 57.2 + - - +
204A GLN* 3.5 6.4 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LYS* 3.1 14.1 + - + +
200A LEU* 3.1 13.2 + - + +
201A LYS 3.0 0.4 - - - -
202A SER* 1.3 80.1 + - - +
204A GLN* 1.3 78.1 + - - +
205A TYR 3.9 0.4 - - - +
206A ASN* 3.4 41.6 + - - +
207A GLY 4.9 0.2 + - - -
208A SER* 5.7 2.8 - - - -
291A TYR* 3.7 14.8 - - - +
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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