Contacts of the helix formed by residues 186 - 202 (chain A) in PDB entry 3FEG
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 HIS 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A THR* 3.3 38.1 + - + +
184A GLU* 2.9 32.3 + - + +
185A PRO* 1.3 73.4 - - - +
187A TRP* 1.3 66.0 + - + +
188A LEU 3.3 0.4 - - - -
189A PHE* 4.5 1.1 - - - -
190A GLY* 2.8 35.4 + - - +
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Residues in contact with TRP 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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184A GLU 4.6 0.4 + - - -
185A PRO* 3.2 2.6 - - - +
186A HIS* 1.3 86.8 + - + +
188A LEU* 1.3 79.1 + - + +
191A THR* 2.6 51.1 + - + +
241A ASN* 3.7 17.9 - - + -
267A TYR* 3.5 34.4 + + + +
268A SER 5.2 0.4 + - - -
269A SER* 3.1 27.3 - - - +
270A TYR 3.8 11.9 - - - +
271A ASN* 3.4 31.9 - - + +
275A PHE* 4.0 11.9 - + - -
352A PHE* 3.4 41.1 - + - -
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Residues in contact with LEU 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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185A PRO 4.3 2.4 + - - +
186A HIS 3.3 0.8 - - - -
187A TRP* 1.3 88.1 - - + +
189A PHE* 1.3 83.3 + - + +
191A THR* 4.0 1.0 - - - -
192A MET* 3.0 46.5 + - + +
229A LEU* 4.3 6.3 - - + -
271A ASN* 3.6 16.7 + - - +
272A TYR* 4.1 24.2 - - + -
275A PHE* 3.8 32.3 - - + -
345A TYR* 4.8 3.4 - - + -
348A ALA* 4.0 17.7 - - + -
352A PHE* 4.1 12.2 - - + -
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Residues in contact with PHE 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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185A PRO 5.2 1.4 + - - -
186A HIS* 3.8 2.6 + - - +
188A LEU* 1.3 93.5 - - + +
190A GLY* 1.3 60.7 + - - +
192A MET* 3.6 23.1 - - + -
193A GLU* 2.8 38.8 + - - +
222A MET* 3.7 20.0 - - + -
225A LEU* 4.1 5.4 - - + -
226A ARG* 3.4 76.9 - - + +
229A LEU* 3.9 28.9 - - + -
272A TYR* 5.3 8.1 - + - -
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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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186A HIS* 2.8 23.0 + - - +
189A PHE* 1.3 79.4 - - - +
191A THR* 1.3 56.9 + - - +
193A GLU* 3.5 8.1 + - - +
194A ARG* 3.0 33.8 + - - +
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Residues in contact with THR 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 TRP* 2.6 45.6 + - + +
190A GLY* 1.3 76.2 - - - +
192A MET* 1.3 56.7 + - - +
194A ARG* 3.2 26.8 + - - +
195A TYR* 2.8 65.5 + - + +
352A PHE* 3.6 18.2 - - + -
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Residues in contact with MET 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 LEU* 3.0 33.3 + - + +
189A PHE* 3.6 39.7 - - + +
191A THR* 1.3 75.4 - - - +
193A GLU* 1.3 57.3 + - - +
195A TYR* 3.3 6.6 + - + +
196A LEU* 2.9 29.1 + - - +
222A MET* 3.7 16.3 - - + +
225A LEU* 4.5 10.3 - - + -
348A ALA* 4.4 1.8 - - + +
351A PHE* 3.9 15.0 - - - -
352A PHE* 3.6 49.4 - - + -
355A LEU* 3.7 13.5 - - + +
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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 PHE* 2.8 30.9 + - - +
190A GLY* 3.8 6.7 - - - +
192A MET* 1.3 73.5 - - - +
194A ARG* 1.3 56.9 - - - +
196A LEU* 3.3 8.7 + - + +
197A LYS* 3.0 28.9 + - - +
222A MET* 3.9 15.9 - - - -
226A ARG* 2.4 42.6 + - - +
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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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190A GLY 3.0 22.0 + - - +
191A THR* 3.2 31.8 + - - +
193A GLU* 1.3 74.9 - - - +
195A TYR* 1.3 68.1 + - - +
197A LYS* 3.2 7.2 + - + +
198A GLN* 2.9 53.2 + - + +
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Residues in contact with TYR 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 THR* 2.8 45.0 + - + +
192A MET* 3.3 7.2 + - - +
194A ARG* 1.3 86.8 - - + +
196A LEU* 1.3 58.1 + - - +
198A GLN* 3.2 11.1 + - - +
199A ILE* 2.8 36.1 + - - +
267A TYR* 4.7 7.6 - - - -
352A PHE* 3.8 24.0 - + - -
355A LEU* 4.1 16.8 - - + -
356A TRP* 3.5 47.7 - + + -
359A LEU* 3.5 26.2 - - + +
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Residues in contact with LEU 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 MET 2.9 17.4 + - - +
193A GLU* 3.6 7.4 - - + +
194A ARG 3.2 0.2 - - - -
195A TYR* 1.3 77.3 - - - +
197A LYS* 1.3 57.2 + - - +
199A ILE* 3.3 8.9 + - - +
200A GLN* 2.9 53.4 + - - +
213A LEU* 3.4 34.9 - - + +
218A LEU* 4.6 8.7 - - + -
219A LYS* 3.9 31.9 - - + +
222A MET* 4.3 16.6 - - + -
355A LEU* 4.0 11.2 - - + +
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Residues in contact with LYS 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 3.0 16.7 + - - +
194A ARG* 3.7 7.2 - - - +
196A LEU* 1.3 77.8 - - - +
198A GLN* 1.3 65.1 + - + +
200A GLN* 3.2 20.9 + - + +
201A ASP* 3.0 48.8 + - - +
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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 ARG* 2.9 43.7 + - + +
195A TYR* 3.6 15.4 - - - +
197A LYS* 1.3 77.6 - - + +
199A ILE* 1.3 61.4 + - - +
201A ASP* 3.2 15.1 + - - +
202A LEU* 3.2 18.0 + - - +
359A LEU* 3.4 32.1 - - + +
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Residues in contact with ILE 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 TYR 2.8 23.7 + - - +
196A LEU* 3.6 4.7 - - - +
198A GLN* 1.3 75.0 - - - +
200A GLN* 1.3 64.9 + - - +
201A ASP 3.1 0.9 + - - -
202A LEU* 3.1 28.3 + - + +
211A ASN* 4.4 16.2 + - - +
213A LEU* 3.7 23.6 - - + -
355A LEU* 3.7 45.8 - - + +
358A ILE* 3.9 31.2 - - + -
359A LEU* 3.7 17.0 - - + -
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Residues in contact with GLN 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 LEU* 2.9 40.3 + - - +
197A LYS* 3.5 27.6 - - + +
199A ILE* 1.3 77.5 - - - +
201A ASP* 1.3 65.4 + - - +
202A LEU 3.7 3.5 + - - +
211A ASN* 6.3 0.4 - - - +
213A LEU* 4.0 14.2 - - + +
219A LYS* 3.9 17.0 - - - +
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Residues in contact with ASP 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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197A LYS* 3.0 38.8 + - - +
198A GLN* 3.7 7.6 - - - +
199A ILE 3.1 0.6 - - - -
200A GLN* 1.3 81.7 - - - +
202A LEU* 1.3 64.9 + - - +
203A PRO* 3.5 4.0 - - - +
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Residues in contact with LEU 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 3.2 14.5 + - - +
199A ILE* 3.1 32.0 + - + +
200A GLN 4.4 3.6 - - - +
201A ASP* 1.3 79.9 - - - +
203A PRO* 1.3 82.8 - - + +
204A PRO* 3.5 5.7 - - - +
358A ILE* 4.8 9.0 - - + +
359A LEU* 4.3 14.1 - - + -
362A SER* 3.7 37.5 - - - +
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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