Contacts of the helix formed by residues 183 - 200 (chain A) in PDB entry 1O7F
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A SER* 1.3 84.9 + - - +
184A LYS* 1.3 95.0 + - - +
186A LEU* 3.6 7.9 + - - +
187A ARG* 3.3 19.2 + - - +
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Residues in contact with LYS 184 (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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182A SER* 3.4 5.3 + - - +
183A GLU* 1.3 101.6 + - - +
185A ILE* 1.3 61.6 + - + +
186A LEU 3.1 0.2 - - - -
187A ARG* 3.0 33.7 + - - +
188A ALA* 3.1 13.2 + - - +
293A GLU* 5.9 0.6 + - - -
300A LEU* 4.0 27.6 - - + +
304A MET* 6.3 1.6 - - - -
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Residues in contact with ILE 185 (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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182A SER* 3.9 8.3 + - - +
183A GLU 3.5 0.2 - - - -
184A LYS* 1.3 80.6 - - + +
186A LEU* 1.3 62.1 + - - +
188A ALA* 3.5 7.5 + - - +
189A GLY 3.3 16.6 + - - -
246A VAL* 3.8 23.1 - - + +
247A LEU* 3.9 18.7 - - + +
249A GLU* 5.7 3.6 - - - +
250A ASP* 3.0 43.7 - - + +
252A VAL* 3.6 12.6 - - + +
300A LEU* 6.2 1.8 - - + -
301A LEU* 6.2 2.0 - - + -
304A MET* 3.6 36.1 - - + -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO* 3.9 13.5 - - + +
182A SER 3.2 24.9 + - - +
183A GLU* 3.6 8.6 + - - +
184A LYS 3.1 0.6 - - - -
185A ILE* 1.3 81.1 - - - +
187A ARG* 1.3 58.7 + - - +
189A GLY* 3.8 1.8 + - - -
190A LYS* 3.0 41.6 + - - +
250A ASP* 4.7 0.2 + - - -
252A VAL* 3.5 22.8 - - + +
272A LEU* 3.6 25.8 - - + -
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Residues in contact with ARG 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* 3.3 10.8 + - - +
184A LYS* 3.0 26.7 + - - +
186A LEU* 1.3 78.0 - - - +
188A ALA* 1.3 59.5 + - - +
189A GLY 3.2 1.8 - - - -
190A LYS* 3.1 16.4 + - - +
191A ILE* 2.9 42.3 + - + +
289A GLU* 2.7 45.7 + - - +
293A GLU* 2.8 30.8 + - - +
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Residues in contact with ALA 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 LYS 3.1 11.8 + - - +
185A ILE* 3.9 9.9 - - - +
186A LEU 3.5 0.2 - - - -
187A ARG* 1.3 72.7 - - - +
189A GLY* 1.3 66.3 + - - +
191A ILE* 3.3 2.4 + - - -
192A LEU* 3.0 30.5 + - - +
247A LEU* 4.2 10.1 - - + -
297A THR* 3.5 28.9 - - + -
300A LEU* 5.4 3.6 - - + -
301A LEU* 4.0 20.0 - - + -
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Residues in contact with GLY 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 ILE 3.3 12.2 + - - -
186A LEU 3.8 2.9 + - - -
187A ARG 3.2 0.6 - - - -
188A ALA* 1.3 79.9 - - - +
190A LYS* 1.3 59.9 + - - +
193A ARG* 3.1 25.0 + - - +
247A LEU* 4.4 17.4 - - - +
252A VAL* 4.4 12.6 - - - -
271A PHE* 3.7 13.9 - - - -
273A ASP* 5.5 0.4 - - - -
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Residues in contact with LYS 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 LEU* 3.0 36.7 + - - +
187A ARG* 3.1 21.1 + - - +
189A GLY* 1.3 75.9 - - - +
191A ILE* 1.3 63.1 + - + +
192A LEU 3.3 0.2 + - - -
193A ARG* 3.3 5.1 + - - +
194A ILE* 3.2 30.7 + - + +
272A LEU* 5.2 8.1 - - - +
273A ASP* 2.6 50.3 + - - +
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Residues in contact with ILE 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 ARG* 2.9 37.5 + - + +
188A ALA* 3.8 5.8 - - - +
190A LYS* 1.3 78.4 - - + +
192A LEU* 1.3 60.5 + - + +
194A ILE* 3.0 29.0 - - + +
195A ALA* 3.4 2.9 + - - +
289A GLU* 5.8 0.9 - - + +
290A CYS* 3.3 16.1 - - - +
293A GLU* 3.0 61.5 - - + +
294A LEU* 3.8 21.5 - - + -
297A THR* 3.9 11.9 - - + +
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Residues in contact with LEU 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 ALA 3.0 17.5 + - - +
189A GLY 4.0 2.2 - - - +
191A ILE* 1.3 73.4 - - - +
193A ARG* 1.3 62.0 + - - +
194A ILE 3.1 2.2 - - - -
195A ALA* 3.0 5.3 + - - +
196A ILE* 2.8 39.4 + - + +
226A TRP* 4.3 14.1 - - + -
227A MET* 4.1 10.5 - - + -
244A TRP* 3.8 28.0 - - + -
247A LEU* 4.1 7.4 - - + -
271A PHE* 4.6 8.3 - - + -
294A LEU* 3.7 22.9 - - + -
297A THR* 4.0 17.7 - - + -
298A MET* 4.5 7.6 - - - -
301A LEU* 4.1 21.1 - - + -
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Residues in contact with ARG 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 GLY 3.1 18.6 + - - +
190A LYS* 3.6 5.2 - - - +
192A LEU* 1.3 77.7 - - - +
194A ILE* 1.3 68.9 + - - +
196A ILE* 3.5 5.0 + - - +
197A LEU* 2.9 54.1 + - + +
204A ILE* 4.3 8.4 - - + +
271A PHE* 3.6 33.8 - - + -
273A ASP* 3.5 34.3 + - - +
274A ASP* 2.7 41.6 + - - -
279A ALA* 4.3 14.6 - - - +
280A PRO 4.4 11.5 + - - -
281A LEU* 6.1 0.6 - - - +
282A PRO* 4.8 3.6 - - - +
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Residues in contact with ILE 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 LYS* 3.2 11.7 - - + +
191A ILE* 3.0 36.3 - - + +
193A ARG* 1.3 83.9 - - - +
195A ALA* 1.3 60.0 + - - +
196A ILE 3.2 0.2 - - - -
197A LEU* 3.6 4.4 - - - +
198A SER* 2.8 32.2 + - - -
282A PRO* 3.4 30.3 - - + -
286A GLU* 4.3 18.8 - - + +
287A LYS* 3.3 10.5 - - + +
289A GLU* 5.7 2.7 - - + +
290A CYS* 3.2 29.2 - - + -
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Residues in contact with ALA 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 ILE 3.6 4.9 - - - +
192A LEU 3.0 8.1 + - - +
194A ILE* 1.3 81.9 - - - +
196A ILE* 1.3 58.7 + - - +
198A SER* 4.1 1.3 - - - -
199A ARG* 2.8 45.9 + - - +
226A TRP* 3.9 21.7 - - + -
290A CYS* 3.5 22.9 - - - -
294A LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 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 LEU 2.8 19.8 + - - +
193A ARG* 3.8 4.0 - - - +
195A ALA* 1.3 73.4 - - - +
197A LEU* 1.3 60.7 + - - +
198A SER 3.0 1.3 - - - -
200A ALA 2.8 39.2 + - - +
201A PRO 5.9 0.2 - - - -
203A MET* 3.8 31.9 - - + -
204A ILE* 4.2 17.3 - - + -
218A CYS* 5.4 0.7 - - - -
223A LEU* 4.2 10.3 - - + -
226A TRP* 3.5 43.7 - - + -
244A TRP* 4.0 18.4 - - + -
271A PHE* 4.0 17.5 - - + -
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Residues in contact with LEU 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 ARG* 2.9 58.2 + - + +
194A ILE* 3.9 5.6 - - - +
196A ILE* 1.3 75.5 - - - +
198A SER* 1.3 57.7 + - - +
201A PRO* 3.1 36.0 - - + +
204A ILE* 3.8 30.7 - - + +
216A GLN* 5.9 1.3 - - - +
274A ASP* 5.6 0.2 - - - +
281A LEU* 5.7 5.2 - - + -
282A PRO* 4.5 20.4 - - + -
287A LYS* 4.7 3.8 + - - +
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Residues in contact with SER 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 ILE 2.8 18.4 + - - -
195A ALA* 3.5 5.4 - - - -
197A LEU* 1.3 80.8 - - - +
199A ARG* 1.3 76.6 + - - +
201A PRO* 3.6 8.1 - - - +
287A LYS* 3.4 29.0 + - - +
290A CYS* 6.0 0.2 - - - -
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Residues in contact with ARG 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 ALA* 2.8 38.9 + - - +
198A SER* 1.3 86.9 + - - +
200A ALA* 1.3 58.0 + - - +
201A PRO* 3.3 7.5 - - - +
202A HIS* 5.2 0.3 - - - -
226A TRP* 4.5 10.3 - - - +
230A GLN* 2.9 29.6 + - - +
290A CYS* 5.5 2.2 - - - -
291A ASP* 4.0 23.4 + - - +
294A LEU* 4.0 26.7 - - - +
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Residues in contact with ALA 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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195A ALA 4.1 0.2 + - - -
196A ILE* 2.8 19.6 + - - +
199A ARG* 1.3 76.2 - - + +
201A PRO* 1.3 63.8 - - - +
202A HIS* 3.2 27.6 - - + -
203A MET* 3.0 38.0 + - - +
226A TRP* 4.0 14.4 - - + +
229A GLN* 5.6 1.8 - - - +
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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
------------------------------------------------------------
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