Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 3V6A
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 THR 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A VAL* 1.3 81.4 - - - +
188A GLY* 1.3 59.0 + - - +
189A GLU* 3.2 19.2 + - - +
190A GLU* 3.0 37.8 + - - +
191A PHE* 3.0 21.5 + - - +
220A GLN* 5.1 0.7 - - - -
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Residues in contact with GLY 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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187A THR* 1.3 74.7 - - - +
189A GLU* 1.3 66.2 + - - +
191A PHE* 3.1 11.6 + - - +
192A VAL* 3.1 26.0 + - - +
220A GLN* 5.3 3.3 - - - +
240A GLN* 3.4 25.3 - - - +
241A CYS* 6.4 2.0 - - - -
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Residues in contact with GLU 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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187A THR* 3.2 20.1 + - - +
188A GLY* 1.3 79.1 + - - +
190A GLU* 1.3 62.2 + - + +
192A VAL* 3.4 9.1 + - - +
193A LEU* 3.3 28.5 + - + +
240A GLN* 4.2 17.8 + - - +
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Residues in contact with GLU 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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148A ARG* 2.7 46.5 + - - +
149A GLU* 5.7 2.3 - - - +
152A ILE* 4.0 18.6 - - + +
186A VAL* 3.3 11.4 - - + -
187A THR* 3.0 45.3 + - - +
189A GLU* 1.3 74.7 - - + +
191A PHE* 1.3 62.6 + - - +
193A LEU* 3.0 13.2 + - + +
194A PHE* 2.8 37.8 + - + -
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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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183A LEU* 3.8 29.6 - - + -
186A VAL* 4.0 8.9 - - + +
187A THR 3.0 13.1 + - - +
188A GLY* 3.3 14.6 - - - +
190A GLU* 1.3 76.9 - - - +
192A VAL* 1.3 57.9 + - + +
194A PHE* 3.3 1.0 + - - -
195A MET* 2.9 70.7 + - + +
216A LEU 4.3 4.9 - - - -
217A VAL* 3.8 20.4 - - + -
220A GLN* 3.6 45.3 - - + +
240A GLN* 5.2 1.8 - - + -
241A CYS* 4.6 12.6 - - - -
244A GLN* 4.0 20.6 - - + -
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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 GLY 3.1 15.1 + - - +
189A GLU* 3.7 9.0 - - - +
190A GLU 3.1 0.4 - - - -
191A PHE* 1.3 73.4 - - + +
193A LEU* 1.3 71.1 + - + +
195A MET* 3.3 3.9 + - - +
196A LYS* 3.1 23.5 + - + +
240A GLN* 4.0 25.4 - - + +
244A GLN* 3.6 39.0 - - + +
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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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149A GLU 5.9 0.7 - - - +
152A ILE* 3.8 28.5 - - + -
153A LYS* 3.8 28.3 - - + +
156A SER* 3.4 26.0 - - - +
189A GLU* 3.3 16.5 + - + +
190A GLU* 3.0 12.7 + - + +
192A VAL* 1.3 81.1 - - + +
194A PHE* 1.3 58.5 + - - +
196A LYS* 3.1 10.2 + - + +
197A ILE* 2.9 33.2 + - - +
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Residues in contact with PHE 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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137A PHE* 4.1 17.5 - + - -
140A ILE* 4.4 3.4 - - + -
152A ILE* 3.8 37.9 - - + -
155A LEU* 4.7 1.8 - - + -
179A SER* 3.6 32.1 - - - -
182A VAL* 3.4 34.8 - - + -
183A LEU* 3.9 29.4 - - + -
186A VAL* 4.4 4.0 - - + -
190A GLU* 2.8 31.3 + - + +
191A PHE 4.0 1.1 - - - +
193A LEU* 1.3 72.7 - - - +
195A MET* 1.3 58.7 + - - +
197A ILE* 3.7 20.3 - - + +
198A LEU* 3.0 35.9 + - + +
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Residues in contact with MET 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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183A LEU* 5.5 1.3 - - - -
191A PHE* 2.9 59.7 + - + +
192A VAL 3.7 4.7 - - - +
193A LEU 3.2 0.2 - - - -
194A PHE* 1.3 77.9 - - - +
196A LYS* 1.3 53.1 + - - +
198A LEU* 3.9 5.9 - - - +
199A SER* 2.4 41.7 + - - +
213A LEU* 4.2 25.8 - - + +
216A LEU* 5.0 6.5 - - - -
217A VAL* 3.6 22.7 - - + -
244A GLN* 4.0 23.8 - - + +
248A LEU* 3.9 19.1 - - + -
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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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156A SER* 3.2 40.0 + - - +
157A THR* 5.0 4.8 - - - +
160A LYS* 4.4 16.8 - - - +
192A VAL* 3.1 13.1 + - + +
193A LEU* 3.1 12.6 + - + +
195A MET* 1.3 74.2 - - - +
197A ILE* 1.3 65.5 + - - +
199A SER* 3.4 5.6 + - - -
200A GLY* 3.1 21.0 + - - -
244A GLN* 5.5 0.2 + - - -
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Residues in contact with ILE 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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152A ILE* 4.1 10.1 - - + +
155A LEU* 3.6 41.3 - - + +
156A SER* 3.9 12.6 - - - +
159A LEU* 4.1 22.6 - - + +
175A ILE* 4.1 20.6 - - + -
179A SER* 5.0 3.6 - - - +
193A LEU 2.9 23.2 + - - +
194A PHE* 3.7 28.3 - - + +
196A LYS* 1.3 78.7 - - - +
198A LEU* 1.3 66.2 + - + +
200A GLY* 3.4 7.4 + - - -
201A LEU* 3.6 14.0 + - - +
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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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175A ILE* 4.2 4.5 - - + +
176A LEU* 3.8 31.6 - - + -
179A SER* 3.8 32.1 - - - +
180A LYS* 5.9 0.2 - - + -
183A LEU* 4.4 10.8 - - + -
194A PHE* 3.0 23.8 + - + +
195A MET* 4.2 4.5 - - - +
197A ILE* 1.3 73.8 - - + +
199A SER* 1.3 65.3 + - - +
200A GLY 3.1 2.0 - - - -
201A LEU* 3.1 35.1 + - + +
204A LEU* 3.6 13.3 - - + +
213A LEU* 3.7 17.5 - - + -
216A LEU* 4.1 26.2 - - + -
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Residues in contact with SER 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 MET* 2.4 31.2 + - - +
196A LYS* 3.4 8.5 + - - -
198A LEU* 1.3 76.4 - - - +
200A GLY* 1.3 58.0 + - - +
201A LEU 3.8 0.6 - - - +
204A LEU 4.6 1.1 - - - +
205A GLN* 3.0 28.6 + - - +
213A LEU* 3.7 22.8 - - - +
248A LEU* 4.4 13.0 - - - -
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Residues in contact with GLY 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 3.1 12.6 + - - -
197A ILE 3.9 5.8 - - - -
198A LEU 3.1 1.0 - - - -
199A SER* 1.3 77.0 - - - +
201A LEU* 1.3 65.5 + - - +
202A LYS* 3.4 6.4 + - - +
205A GLN* 3.4 13.9 + - - -
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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