Contacts of the helix formed by residues 187 - 206 (chain A) in PDB entry 2V40
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 ASP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ASP 4.1 3.3 - - - +
186A SER* 1.3 78.8 + - - +
188A PHE* 1.3 57.9 + - - +
189A ASP* 2.9 40.4 + - - +
190A GLY* 3.0 13.7 + - - +
191A PHE* 2.9 26.0 + - - +
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Residues in contact with PHE 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 LEU* 3.9 31.4 - - + +
186A SER 3.1 8.7 + - - +
187A ASP* 1.3 70.2 + - - +
189A ASP* 1.3 58.2 + - - +
191A PHE* 3.7 20.2 - + + -
192A SER* 2.7 52.8 + - - -
217A LEU* 3.8 28.9 - - + -
220A LEU* 4.5 1.6 - - + -
221A LYS* 3.6 52.7 - - + -
224A MET* 4.8 14.6 - - + -
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 2.9 13.5 + - - +
188A PHE* 1.3 76.8 - - - +
190A GLY* 1.3 64.9 + - - +
192A SER* 3.3 6.4 + - - -
193A GLU* 3.0 24.1 + - - +
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Residues in contact with GLY 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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187A ASP* 3.0 18.1 + - - -
189A ASP* 1.3 71.4 - - - +
191A PHE* 1.3 66.0 + - - +
193A GLU* 3.3 13.7 + - - +
194A ARG* 3.1 27.1 + - - +
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Residues in contact with PHE 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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135A ILE* 4.0 17.5 - - + -
137A PHE* 3.8 24.9 - + - -
179A LEU* 4.0 20.9 - - + -
183A ASP* 3.6 24.9 + - + +
184A LEU* 3.6 44.0 - - + -
187A ASP 2.9 9.0 + - - +
188A PHE* 3.6 29.8 - + + +
189A ASP 3.3 0.2 - - - -
190A GLY* 1.3 76.0 - - - +
192A SER* 1.3 53.6 + - - +
194A ARG* 3.3 5.7 + - - +
195A PHE* 2.8 38.2 + + + +
217A LEU* 3.8 21.3 - - + -
220A LEU* 3.9 7.9 - - + -
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 2.7 49.8 + - - -
189A ASP* 3.5 7.0 - - - -
190A GLY 3.3 0.2 - - - -
191A PHE* 1.3 74.1 - - - +
193A GLU* 1.3 64.4 + - - +
195A PHE* 3.4 1.4 + - - +
196A LYS* 3.0 38.2 + - - +
217A LEU* 3.9 21.7 - - - +
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Residues in contact with GLU 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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189A ASP 3.0 13.5 + - - +
190A GLY* 3.3 14.3 + - - +
192A SER* 1.3 76.8 - - - +
194A ARG* 1.3 65.4 + - + +
196A LYS* 3.3 8.7 + - - +
197A VAL* 3.2 28.9 + - + +
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Residues in contact with ARG 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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176A ARG 3.3 22.8 + - - -
177A SER* 3.6 11.1 + - - +
178A GLY 2.8 24.4 + - - -
179A LEU* 3.5 24.0 - - + +
180A ARG* 5.9 0.4 - - - +
183A ASP* 3.6 26.8 + - - -
190A GLY 3.1 12.6 + - - +
191A PHE 3.7 3.4 - - - +
193A GLU* 1.3 80.1 - - + +
195A PHE* 1.3 66.0 + - - +
197A VAL* 3.3 9.3 + - - +
198A LEU* 3.1 23.9 + - - +
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Residues in contact with PHE 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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137A PHE* 3.4 44.6 - + - -
139A PHE* 3.6 18.8 - + - -
179A LEU* 3.5 11.8 - - + +
191A PHE* 2.8 21.6 + + + +
192A SER 3.6 3.4 - - - +
194A ARG* 1.3 75.1 - - - +
196A LYS* 1.3 60.2 + - - +
198A LEU* 3.3 2.4 + - - +
199A ALA* 2.8 35.2 + - + +
211A ILE* 6.3 0.2 - - + -
213A ILE* 3.6 35.9 - - + -
216A GLU* 3.6 32.8 - - + -
217A LEU* 3.7 29.2 - - + -
220A LEU* 4.1 6.3 - - + -
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Residues in contact with LYS 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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192A SER* 3.0 27.1 + - - +
193A GLU* 3.7 7.6 - - - +
195A PHE* 1.3 78.1 - - + +
197A VAL* 1.3 59.1 + - - +
199A ALA* 3.8 3.5 - - - +
200A ASN* 2.8 46.7 + - - +
213A ILE* 3.8 20.0 - - + -
214A GLU* 3.4 26.2 + - - -
217A LEU* 3.8 18.3 - - - +
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Residues in contact with VAL 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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193A GLU* 3.2 20.9 + - + +
194A ARG* 3.3 10.5 + - - +
196A LYS* 1.3 75.0 - - - +
198A LEU* 1.3 57.7 + - + +
200A ASN* 3.4 5.7 + - - +
201A GLN* 2.9 48.5 + - + +
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Residues in contact with LEU 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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137A PHE* 4.1 14.1 - - + -
139A PHE* 3.7 24.5 - - + -
140A HIS* 4.1 15.3 - - + +
172A SER* 4.0 3.8 - - - +
177A SER* 3.7 38.4 - - - +
178A GLY* 4.2 7.9 - - - -
179A LEU* 4.7 2.5 - - + -
194A ARG 3.1 15.5 + - - +
195A PHE* 3.8 4.3 - - - +
197A VAL* 1.3 74.4 - - - +
199A ALA* 1.3 66.1 + - - +
201A GLN* 3.3 28.6 + - - +
202A TYR* 3.1 41.7 + - + -
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Residues in contact with ALA 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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139A PHE* 3.7 19.4 - - + -
195A PHE* 2.8 27.2 + - + +
196A LYS* 3.8 2.7 - - - +
198A LEU* 1.3 72.2 - - - +
200A ASN* 1.3 58.6 + - - +
202A TYR* 3.3 2.3 + - - +
203A LYS* 2.9 24.9 + - - +
211A ILE* 3.3 31.7 - - + +
213A ILE* 3.8 20.6 - - + -
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Residues in contact with ASN 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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196A LYS* 2.8 34.7 + - - +
197A VAL* 3.8 5.3 - - - +
199A ALA* 1.3 74.9 - - - +
201A GLN* 1.3 59.3 + - - +
203A LYS* 3.5 26.8 + - - +
204A SER* 2.9 32.7 + - - -
213A ILE* 3.5 12.7 - - - +
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Residues in contact with GLN 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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177A SER* 4.4 13.7 + - - -
197A VAL* 2.9 35.8 + - + +
198A LEU* 3.4 29.9 - - - +
200A ASN* 1.3 75.2 - - - +
202A TYR* 1.3 66.8 + - + +
204A SER* 3.1 11.0 + - - -
205A ILE* 3.1 34.7 + - + +
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Residues in contact with TYR 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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139A PHE* 3.7 22.0 - + + -
140A HIS* 3.5 15.9 - + - -
143A ALA* 3.6 31.6 - - + -
147A GLN* 4.8 3.8 + - - -
168A PRO* 3.3 21.2 + - + +
171A SER* 4.9 3.5 - - - -
172A SER* 3.2 26.8 + - - -
198A LEU* 3.1 28.9 + - + +
199A ALA 3.7 7.0 - - - +
201A GLN* 1.3 82.4 - - + +
203A LYS* 1.3 53.3 + - - +
205A ILE* 3.2 6.3 + - + -
206A TYR* 2.8 56.6 + + - +
209A LEU* 4.3 11.9 - - + -
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Residues in contact with LYS 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 ALA 2.9 15.9 + - - +
200A ASN* 3.5 25.0 + - - +
201A GLN 3.3 0.2 - - - -
202A TYR* 1.3 75.8 - - - +
204A SER* 1.3 61.8 + - - +
206A TYR 3.3 22.3 - - - +
207A PRO* 3.5 8.8 - - + +
209A LEU* 4.3 10.4 - - - +
211A ILE* 3.4 30.3 + - + +
213A ILE* 3.5 23.3 - - - +
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Residues in contact with SER 204 (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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200A ASN 2.9 14.2 + - - -
201A GLN* 3.1 15.4 + - - -
203A LYS* 1.3 78.9 - - - +
205A ILE* 1.3 63.0 + - - +
207A PRO* 4.5 8.8 - - - +
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Residues in contact with ILE 205 (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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201A GLN* 3.1 26.4 + - + +
202A TYR* 3.8 6.7 - - + +
204A SER* 1.3 83.0 - - - +
206A TYR* 1.3 89.6 + - + +
207A PRO* 3.4 9.3 - - - +
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Residues in contact with TYR 206 (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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143A ALA* 4.0 13.7 - - + -
146A ILE* 3.6 34.3 - - + -
147A GLN* 2.8 34.1 + - + +
150A GLN* 3.9 20.7 + - - -
202A TYR* 2.8 48.4 + + - +
203A LYS* 3.3 9.2 - - - +
205A ILE* 1.3 102.0 - - + +
207A PRO* 1.4 59.8 - - - +
208A THR* 3.2 3.6 - - - +
209A LEU* 2.8 38.5 + - + +
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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