Contacts of the helix formed by residues 201 - 216 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ALA 3.4 0.2 + - - -
200A ASP* 1.3 82.6 + - - +
202A TRP* 1.3 63.7 + - - +
203A GLN* 3.2 11.3 + - - -
204A LYS* 3.1 23.8 + - - +
205A ALA* 3.1 11.1 + - - +
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Residues in contact with TRP 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 3.3 23.6 - - + +
199A ALA* 3.2 25.9 + - + +
200A ASP* 3.5 1.1 + - - -
201A GLY* 1.3 78.3 - - - +
203A GLN* 1.3 91.4 + - + +
205A ALA* 3.2 10.5 + - - +
206A ALA* 2.7 35.2 + - + +
334A ASP 5.7 0.2 - - - -
335A VAL* 3.8 11.6 - - + +
336A VAL 3.7 16.4 - - - +
337A THR* 3.5 26.4 + - + -
341A ALA* 3.6 30.1 - - + -
342A PHE* 3.8 20.6 - - - -
345A HIS* 3.8 24.7 - + + -
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Residues in contact with GLN 203 (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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201A GLY* 4.1 6.4 + - - -
202A TRP* 1.3 124.1 + - + +
204A LYS* 1.3 56.4 + - - +
206A ALA* 3.3 1.7 + - - -
207A ASP* 2.8 35.3 + - - +
345A HIS* 3.4 33.8 + - + +
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Residues in contact with LYS 204 (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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201A GLY* 3.1 15.7 + - - +
203A GLN* 1.3 76.5 - - - +
205A ALA* 1.3 58.4 + - - +
207A ASP* 3.2 12.4 + - + +
208A GLN* 2.9 45.0 + - + +
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Residues in contact with ALA 205 (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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201A GLY 3.1 11.2 + - - +
202A TRP* 3.4 12.6 - - - +
204A LYS* 1.3 76.7 - - - +
206A ALA* 1.3 56.6 + - - +
208A GLN* 3.2 15.2 + - - +
209A ALA 3.0 23.4 + - - -
333A VAL* 3.2 18.1 - - + +
334A ASP 3.6 24.9 - - - +
335A VAL* 4.0 7.4 - - + -
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Residues in contact with ALA 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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202A TRP* 2.7 19.4 + - + +
203A GLN* 3.5 9.4 - - - +
205A ALA* 1.3 72.5 - - - +
207A ASP* 1.3 58.5 + - - +
209A ALA* 3.3 6.6 + - - +
210A ALA* 3.0 26.7 + - - +
335A VAL* 3.9 10.4 - - + +
342A PHE* 3.9 26.5 - - + -
345A HIS* 3.6 22.0 - - + -
346A PHE* 3.8 6.3 - - + -
349A ALA* 5.1 0.2 - - - +
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Residues in contact with ASP 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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203A GLN* 2.8 18.7 + - - +
204A LYS* 3.2 14.0 + - + +
206A ALA* 1.3 73.9 - - - +
208A GLN* 1.3 62.8 + - + +
210A ALA* 3.2 8.7 + - - +
211A ALA* 3.1 21.7 + - - +
345A HIS* 3.0 23.7 + - - -
349A ALA* 3.9 13.9 - - - +
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Residues in contact with GLN 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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204A LYS* 2.9 34.4 + - + +
205A ALA* 3.5 18.1 - - - +
207A ASP* 1.3 77.9 - - + +
209A ALA* 1.3 60.7 + - - +
211A ALA* 3.3 9.8 + - - +
212A LEU* 3.1 25.3 + - - +
333A VAL* 4.1 20.4 - - + +
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Residues in contact with ALA 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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205A ALA 3.0 12.2 + - - +
206A ALA* 3.4 13.2 - - - +
207A ASP 3.3 0.2 - - - -
208A GLN* 1.3 72.7 - - - +
210A ALA* 1.3 60.0 + - - +
212A LEU* 3.3 5.4 + - - +
213A LEU* 3.0 26.7 + - - +
290A LEU* 4.8 1.9 - - - +
292A LEU* 4.7 2.3 - - + +
316A VAL* 3.7 42.6 - - + +
333A VAL* 4.2 3.4 - - + +
335A VAL* 4.9 0.2 - - + -
342A PHE* 4.8 2.9 - - + -
346A PHE* 3.9 14.0 - - + -
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Residues in contact with ALA 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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206A ALA 3.0 13.8 + - - +
207A ASP* 3.2 9.8 + - - +
209A ALA* 1.3 75.5 - - - +
211A ALA* 1.3 57.2 + - - +
213A LEU* 3.1 2.9 + - - -
214A ALA 2.9 25.3 + - - -
346A PHE* 3.5 12.5 - - + -
349A ALA* 3.9 17.7 - - + +
350A THR* 3.9 21.3 - - + -
353A PHE* 3.2 18.2 - - + -
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Residues in contact with ALA 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 ASP 3.1 11.3 + - - +
208A GLN* 3.4 13.0 - - - +
210A ALA* 1.3 77.4 - - - +
212A LEU* 1.3 61.4 + - + +
214A ALA* 3.5 10.4 - - - +
215A GLU* 3.3 26.6 + - - +
353A PHE* 5.3 0.2 - - - -
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Residues in contact with LEU 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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208A GLN 3.1 15.1 + - - +
209A ALA 3.5 6.7 - - - +
211A ALA* 1.3 75.4 - - + +
213A LEU* 1.3 60.6 + - - +
215A GLU* 3.3 7.8 + - + +
216A ALA* 2.9 29.1 + - - +
290A LEU* 3.8 20.9 - - + +
314A LYS* 4.0 40.6 - - + +
315A THR 4.8 0.2 - - - +
316A VAL* 4.1 15.3 - - + -
332A ASP* 4.7 6.1 - - + -
333A VAL* 3.8 27.1 - - + -
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Residues in contact with LEU 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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209A ALA 3.0 13.1 + - - +
210A ALA* 3.1 9.2 + - - +
212A LEU* 1.3 74.1 - - - +
214A ALA* 1.3 56.0 + - - +
216A ALA* 3.2 5.5 + - - +
219A PRO* 3.6 37.2 - - + -
243A LEU* 3.7 25.8 - - + -
245A ILE* 3.9 14.1 - - + -
290A LEU* 3.6 11.8 - - + +
292A LEU* 4.9 4.9 - - + -
346A PHE* 3.7 29.6 - - + -
350A THR* 4.2 7.4 - - + -
353A PHE* 4.3 7.0 - - + -
356A LYS* 2.7 39.6 + - + -
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Residues in contact with ALA 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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210A ALA 2.9 12.0 + - - +
211A ALA* 3.5 13.9 - - - +
212A LEU 3.4 0.2 - - - -
213A LEU* 1.3 74.4 - - - +
215A GLU* 1.3 66.7 + - + +
353A PHE* 3.5 26.1 - - + -
356A LYS* 3.2 15.9 + - - +
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Residues in contact with GLU 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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211A ALA 3.3 13.7 + - - +
212A LEU* 3.8 10.8 - - + +
213A LEU 3.1 0.6 - - - -
214A ALA* 1.3 84.3 - - + +
216A ALA* 1.3 62.2 + - - +
217A LYS* 3.6 6.8 + - - +
289A ASP* 4.5 1.6 - - - +
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Residues in contact with ALA 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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212A LEU 2.9 16.8 + - - +
213A LEU 3.2 6.8 + - - +
214A ALA 4.2 0.2 - - - +
215A GLU* 1.3 78.1 - - - +
217A LYS* 1.3 59.3 + - - +
219A PRO* 4.2 10.1 - - + -
289A ASP* 3.5 19.5 - - - +
290A LEU* 3.7 25.8 - - + -
356A LYS* 2.6 31.6 + - - -
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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