Contacts of the helix formed by residues 201 - 216 (chain C) in PDB entry 2IHU
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 GLY 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C ALA 3.4 0.6 + - - -
200C ASP* 1.3 80.5 + - - +
202C TRP* 1.3 64.2 + - - +
203C GLN* 3.2 11.1 + - - -
204C LYS* 3.1 16.6 + - - +
205C ALA* 3.1 18.9 + - - +
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Residues in contact with TRP 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C VAL* 3.4 30.1 - - + +
199C ALA* 3.3 19.0 + - + +
200C ASP 3.3 0.4 + - - -
201C GLY* 1.3 77.4 - - - +
203C GLN* 1.3 95.7 + - + +
205C ALA* 3.2 10.6 + - - +
206C ALA* 2.8 28.5 + - + +
335C VAL* 3.7 12.3 - - + +
336C VAL 3.7 17.0 - - - +
337C THR* 3.5 26.7 - - + -
341C ALA* 3.5 30.5 - - + -
342C PHE* 3.8 19.7 - - - -
345C HIS* 3.8 22.7 - + + -
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Residues in contact with GLN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLY* 4.2 7.1 + - - -
202C TRP* 1.3 125.9 + - + +
204C LYS* 1.3 58.2 + - - +
206C ALA* 3.2 1.1 + - - -
207C ASP* 2.9 35.3 + - - +
345C HIS* 3.4 30.5 + - + +
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLY* 3.1 16.6 + - - +
203C GLN* 1.3 77.6 - - - +
205C ALA* 1.3 57.5 + - - +
207C ASP* 3.3 13.2 + - + +
208C GLN* 3.0 46.3 + - + +
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Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLY 3.1 11.7 + - - +
202C TRP* 3.3 13.5 - - - +
204C LYS* 1.3 74.3 - - - +
206C ALA* 1.3 59.4 + - - +
208C GLN* 3.2 14.3 + - - +
209C ALA* 3.0 22.7 + - - +
333C VAL* 3.1 18.0 - - + +
334C ASP 3.8 21.8 - - - +
335C VAL* 3.9 9.2 - - + -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TRP* 2.8 19.9 + - + +
203C GLN* 3.5 3.4 - - - +
205C ALA* 1.3 72.0 - - - +
207C ASP* 1.3 58.6 + - - +
209C ALA* 3.3 10.0 + - - +
210C ALA* 2.8 27.6 + - - +
335C VAL* 4.0 5.5 - - + +
342C PHE* 3.9 25.8 - - + -
345C HIS* 3.5 27.6 - - + -
346C PHE* 3.9 6.9 - - + -
349C ALA* 5.6 0.4 - - - -
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN* 2.9 17.2 + - - +
204C LYS* 3.4 15.6 - - + +
205C ALA 3.3 0.2 - - - -
206C ALA* 1.3 73.3 - - - +
208C GLN* 1.3 59.5 + - + +
210C ALA* 3.2 9.2 + - - +
211C ALA* 3.0 26.5 + - - +
345C HIS* 2.9 27.2 + - - -
349C ALA* 4.0 11.3 - - - +
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Residues in contact with GLN 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LYS* 3.0 37.0 + - + +
205C ALA* 3.2 19.2 + - - +
207C ASP* 1.3 74.0 - - - +
209C ALA* 1.3 61.6 + - - +
211C ALA* 3.3 9.8 + - - +
212C LEU* 3.1 25.8 + - - +
333C VAL* 4.3 19.6 - - + +
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ALA 3.0 13.1 + - - +
206C ALA* 3.3 13.7 - - - +
208C GLN* 1.3 73.7 - - - +
210C ALA* 1.3 63.2 + - - +
212C LEU* 3.3 5.7 + - - +
213C LEU* 3.0 22.3 + - - +
290C LEU* 4.7 2.3 - - - +
292C LEU* 4.9 1.2 - - + +
316C VAL* 3.7 40.5 - - + +
333C VAL* 4.2 3.7 - - + +
335C VAL* 4.9 0.2 - - + -
342C PHE* 4.8 2.5 - - + -
346C PHE* 3.8 14.8 - - + -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ALA 2.8 13.3 + - - +
207C ASP* 3.2 10.3 + - - +
209C ALA* 1.3 76.3 - - - +
211C ALA* 1.3 56.3 + - - +
213C LEU* 3.1 3.4 + - - +
214C ALA 2.9 24.8 + - - -
346C PHE* 3.5 15.8 - - + -
349C ALA* 3.9 26.9 - - + +
350C THR* 4.0 8.3 - - + -
353C PHE* 3.3 17.6 - - + -
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ASP 3.0 12.4 + - - +
208C GLN* 3.3 13.2 + - - +
210C ALA* 1.3 76.5 - - - +
212C LEU* 1.3 63.0 + - + +
214C ALA* 3.3 9.7 + - - +
215C GLU* 3.2 28.5 + - - +
353C PHE* 5.4 0.9 - - - -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLN 3.1 16.5 + - - +
209C ALA 3.5 6.7 - - - +
211C ALA* 1.3 76.9 - - + +
213C LEU* 1.3 58.3 + - - +
215C GLU* 3.2 18.0 + - - +
216C ALA* 3.0 27.2 + - - +
290C LEU* 3.8 28.3 - - + +
314C LYS* 4.1 35.2 - - + -
315C THR 4.7 0.2 - - - +
316C VAL* 4.2 7.4 - - + -
332C ASP* 4.6 6.3 - - + -
333C VAL* 3.7 26.9 - - + -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ALA 3.0 13.6 + - - +
210C ALA 3.1 8.7 + - - +
212C LEU* 1.3 73.0 - - - +
214C ALA* 1.3 55.8 + - - +
216C ALA* 3.1 6.6 + - - +
219C PRO* 3.6 36.1 - - + -
243C LEU* 3.9 19.1 - - + -
245C ILE* 4.2 12.3 - - + -
290C LEU* 3.5 12.6 - - + +
292C LEU* 4.9 4.0 - - + -
346C PHE* 3.6 31.9 - - + -
350C THR* 3.9 15.3 - - + -
353C PHE* 4.2 6.7 - - + -
356C LYS* 2.7 41.5 + - + -
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Residues in contact with ALA 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA 2.9 13.0 + - - +
211C ALA* 3.3 12.5 + - - +
213C LEU* 1.3 73.9 - - - +
215C GLU* 1.3 60.4 + - + +
353C PHE* 3.7 26.4 - - + -
356C LYS* 3.3 16.4 + - - +
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ALA* 3.2 13.7 + - - +
212C LEU* 3.2 18.7 + - - +
213C LEU 3.2 0.8 - - - -
214C ALA* 1.3 76.7 - - + +
216C ALA* 1.3 62.2 + - - +
217C LYS* 3.7 1.4 + - - +
289C ASP* 4.7 1.0 - - - +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU 3.0 14.6 + - - +
213C LEU* 3.1 8.1 + - - +
215C GLU* 1.3 78.4 - - - +
217C LYS* 1.3 59.1 + - - +
219C PRO* 4.3 9.9 - - + -
289C ASP* 3.6 18.2 - - - +
290C LEU* 3.8 24.5 - - + -
356C LYS* 2.8 32.6 + - - +
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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