Contacts of the helix formed by residues 205 - 218 (chain A) in PDB entry 1V0O
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 SER 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A HIS* 6.2 0.4 - - - -
164A LEU* 3.2 12.5 - - - +
203A GLY 3.5 0.4 - - - -
204A VAL* 1.3 85.3 + - - +
206A GLU* 1.3 59.6 + - - +
207A ALA* 3.6 8.6 + - - +
208A ASP* 3.2 22.6 + - - +
209A GLN* 2.8 30.5 + - - +
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Residues in contact with GLU 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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159A HIS* 3.2 44.4 - - + +
164A LEU* 3.4 10.3 - - + +
167A ARG* 6.1 1.1 - - - -
172A LEU* 4.0 28.9 - - + +
205A SER* 1.3 72.3 - - - +
207A ALA* 1.3 63.0 + - - +
209A GLN* 3.4 6.0 + - - +
210A LEU* 3.2 29.1 + - - +
233A LYS* 3.9 22.5 + - - +
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Residues in contact with ALA 207 (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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205A SER* 3.2 7.9 + - - +
206A GLU* 1.3 80.8 - - - +
208A ASP* 1.3 61.4 + - - +
210A LEU* 3.5 7.9 + - - +
211A MET* 3.2 27.1 + - - +
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Residues in contact with ASP 208 (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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203A GLY* 3.4 6.8 - - - -
204A VAL* 3.3 29.6 + - + +
205A SER* 3.2 22.3 + - - +
207A ALA* 1.3 77.0 - - - +
209A GLN* 1.3 59.9 + - - +
211A MET* 3.6 7.8 + - - +
212A ARG* 3.0 47.0 + - - +
215A ARG* 5.2 4.2 + - - -
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Residues in contact with GLN 209 (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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164A LEU* 3.2 37.5 + - + +
165A TRP* 3.4 11.6 + - - -
167A ARG 4.7 1.0 + - - -
172A LEU* 3.4 21.3 - - + -
201A PHE* 3.0 37.6 + - - +
203A GLY* 3.0 28.8 + - - -
205A SER 2.8 18.4 + - - +
206A GLU* 3.5 8.5 - - - +
207A ALA 3.3 0.2 - - - -
208A ASP* 1.3 77.8 - - - +
210A LEU* 1.3 60.9 + - - +
212A ARG* 3.4 4.3 + - - +
213A ILE* 3.1 34.6 + - - +
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Residues in contact with LEU 210 (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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169A PRO* 3.9 28.9 - - + +
172A LEU* 3.9 27.6 - - + +
173A MET* 3.5 24.2 - - + -
206A GLU 3.2 12.9 + - - +
207A ALA* 3.8 7.2 - - - +
209A GLN* 1.3 79.5 - - - +
211A MET* 1.3 65.8 + - + +
213A ILE* 3.1 5.5 + - + +
214A PHE* 2.9 59.2 + - + -
233A LYS* 5.2 2.9 - - + +
238A PHE* 4.2 17.0 - - + -
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Residues in contact with MET 211 (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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207A ALA 3.2 16.5 + - - +
208A ASP* 3.9 7.9 - - - +
209A GLN 3.4 0.2 - - - -
210A LEU* 1.3 82.4 - - + +
212A ARG* 1.3 57.2 + - - +
214A PHE* 3.7 17.9 - - + +
215A ARG* 2.8 53.4 + - - +
238A PHE* 3.6 34.5 - - + -
239A THR* 4.6 15.9 - - - +
241A TYR* 4.1 23.3 - - + +
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Residues in contact with ARG 212 (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 LEU 5.1 3.2 + - - -
201A PHE* 3.7 24.5 - - + -
202A PRO* 3.6 45.6 + - - +
203A GLY 4.7 6.3 - - - +
208A ASP* 3.0 39.6 + - - +
209A GLN* 3.6 6.7 - - - +
211A MET* 1.3 76.2 - - - +
213A ILE* 1.3 63.7 + - - +
215A ARG* 3.5 36.5 + - - +
216A ILE* 3.6 18.5 + - - +
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Residues in contact with ILE 213 (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 ARG 3.9 13.2 - - - +
169A PRO* 4.5 12.8 - - + -
172A LEU* 3.8 24.5 - - + -
185A TRP* 3.8 31.4 - - + +
201A PHE* 3.7 27.1 - - + -
209A GLN* 3.1 21.9 + - - +
210A LEU* 3.1 7.6 + - - +
212A ARG* 1.3 76.3 - - - +
214A PHE* 1.3 68.8 + - + +
216A ILE* 3.3 2.6 + - - +
217A LEU* 3.0 35.9 + - + +
267A LEU* 4.4 7.4 - - + -
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Residues in contact with PHE 214 (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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169A PRO* 4.6 11.4 - - + -
173A MET* 4.2 4.0 - - - -
210A LEU* 2.9 41.8 + - + +
211A MET* 3.8 27.4 - - + +
213A ILE* 1.3 83.6 - - + +
215A ARG* 1.3 58.7 + - - +
218A GLY* 2.8 36.0 + - - +
219A THR* 3.8 20.6 - - + +
220A PRO* 3.3 39.0 - - + -
238A PHE* 3.7 37.2 - + + -
241A TYR* 3.3 13.5 - - + +
267A LEU* 4.7 2.5 - - + -
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Residues in contact with ARG 215 (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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208A ASP* 5.2 4.0 + - - -
211A MET* 2.8 40.5 + - - +
212A ARG* 3.7 31.3 - - - +
213A ILE 3.2 0.4 - - - -
214A PHE* 1.3 77.3 - - - +
216A ILE* 1.3 64.3 + - + +
241A TYR* 3.9 45.7 + - + +
242A GLU 4.5 4.6 - - - +
244A LEU* 4.0 14.2 - - - +
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Residues in contact with ILE 216 (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 LEU* 3.7 22.2 - - + +
201A PHE* 3.7 26.9 - - + -
212A ARG* 3.6 16.6 + - - +
213A ILE 3.3 1.2 + - - -
214A PHE 3.1 0.2 - - - -
215A ARG* 1.3 85.7 - - + +
217A LEU* 1.3 67.2 + - + +
218A GLY 3.5 1.1 - - - -
242A GLU 4.9 0.4 - - - -
244A LEU* 3.0 43.6 + - + +
249A PHE* 3.7 44.6 - - + -
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Residues in contact with LEU 217 (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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185A TRP* 3.7 20.4 - - + -
201A PHE* 3.7 22.0 - - + -
213A ILE* 3.0 14.5 + - + +
216A ILE* 1.3 87.3 - - + +
218A GLY* 1.3 61.4 + - - +
243A PRO* 3.4 21.1 - - - +
244A LEU 5.8 0.9 - - - +
246A TRP* 3.3 40.4 - - + -
249A PHE* 4.1 4.0 - - + -
265A LEU* 3.9 14.1 - - + +
267A LEU* 3.7 34.7 - - + +
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Residues in contact with GLY 218 (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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214A PHE* 2.8 25.6 + - - -
216A ILE 3.5 1.8 + - - -
217A LEU* 1.3 78.5 - - - +
219A THR* 1.3 65.2 + - - -
220A PRO* 3.5 1.7 - - - +
241A TYR 3.3 13.0 - - - -
242A GLU 3.9 0.7 - - - -
243A PRO* 3.9 13.6 - - - +
267A LEU* 3.3 21.2 - - - +
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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