Contacts of the helix formed by residues 206 - 220 (chain B) in PDB entry 2IHM
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 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B TYR 3.5 3.4 + - - -
205B PHE* 1.3 71.9 - - - +
207B GLU* 1.3 58.0 + - - -
210B THR* 2.5 34.3 + - - -
2E C 3.0 44.7 + - - -
3E C 4.5 3.6 - - - -
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLY* 1.3 71.0 - - - -
208B HIS* 1.3 69.6 + - - +
210B THR* 4.0 4.6 - - - -
211B ARG* 3.0 58.9 + - - +
1E G 4.9 3.1 + - - -
2E C 3.4 6.6 + - - +
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Residues in contact with HIS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.4 0.6 - - - +
179B PHE* 4.0 22.1 - + + -
207B GLU* 1.3 85.9 - - - +
209B SER* 1.3 65.1 + - - +
211B ARG* 3.0 29.3 + - - +
212B VAL* 3.1 30.5 + - + +
224B GLU* 2.8 34.5 + - - -
1E G 2.9 40.1 + - - +
2E C 3.1 17.5 + - - +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 4.3 12.6 - - - +
178B SER 5.4 0.2 - - - -
179B PHE* 3.8 21.1 - - - -
182B ALA* 3.9 15.2 - - - +
204B TYR 4.5 1.0 + - - -
205B PHE* 3.8 23.3 - - - -
206B GLY 4.4 2.7 - - - -
208B HIS* 1.3 77.1 - - - +
210B THR* 1.3 56.7 + - - +
212B VAL* 3.4 3.8 + - - +
213B ILE* 3.0 34.8 + - - +
1E G 4.0 1.4 + - - -
2E C 2.9 21.6 + - - -
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.9 30.7 - - + +
199B LEU* 4.2 15.6 - - + +
205B PHE* 3.3 17.4 + - - +
206B GLY 2.5 23.8 + - - -
207B GLU* 4.0 6.3 - - - -
208B HIS 3.3 0.2 - - - -
209B SER* 1.3 74.2 - - - +
211B ARG* 1.3 66.9 + - - +
213B ILE* 3.3 2.1 + - - +
214B GLN* 3.0 22.9 + - + +
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU* 3.0 59.3 + - - +
208B HIS* 3.0 50.9 + - - +
210B THR* 1.3 79.1 - - - +
212B VAL* 1.3 63.5 + - + +
214B GLN* 3.3 7.3 + - - +
215B GLU* 3.1 25.5 + - - +
224B GLU* 4.5 3.0 + - - -
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.4 6.3 - - + -
160B LEU* 4.4 17.5 - - + -
163B LEU* 4.0 14.8 - - + -
208B HIS* 3.1 34.2 + - + +
209B SER* 3.7 6.3 - - - +
211B ARG* 1.3 78.4 - - + +
213B ILE* 1.3 63.5 + - + +
215B GLU* 3.3 5.5 + - - +
216B LEU* 3.1 34.1 + - + +
222B CYS* 3.4 28.7 - - + -
224B GLU* 4.1 7.0 - - - +
225B VAL* 4.5 4.9 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 3.9 39.7 - - + +
160B LEU* 4.3 11.7 - - + -
186B LEU* 4.1 15.7 - - + -
193B VAL* 4.8 3.1 - - + -
196B LEU* 4.1 6.7 - - + -
199B LEU* 4.0 23.3 - - + -
205B PHE* 4.0 17.9 - - + -
209B SER 3.0 21.0 + - - +
210B THR 3.6 4.9 - - - +
212B VAL* 1.3 77.4 - - - +
214B GLN* 1.3 58.0 + - - +
216B LEU* 3.1 8.6 + - + +
217B LEU* 2.9 42.2 + - + +
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Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU* 4.0 33.1 - - + +
210B THR 3.0 17.1 + - - +
211B ARG* 3.7 6.8 + - - +
213B ILE* 1.3 75.8 - - - +
215B GLU* 1.3 67.4 + - - +
217B LEU* 3.3 7.0 + - + +
218B GLU* 2.9 33.6 + - + +
219B HIS* 6.1 0.2 + - - -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 3.1 18.4 + - + +
212B VAL* 3.6 10.3 - - - +
213B ILE 3.2 0.4 - - - -
214B GLN* 1.3 82.3 - - - +
216B LEU* 1.3 58.2 + - - +
218B GLU* 3.2 4.8 + - - +
219B HIS* 2.9 42.1 + - + -
221B THR* 3.3 12.1 + - - +
222B CYS* 3.2 12.5 - - - -
223B GLU* 2.5 43.5 + - - +
224B GLU* 5.0 1.2 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.7 6.1 - - + +
156B LEU* 3.6 29.2 - - + -
159B ALA* 3.4 32.5 - - + -
212B VAL* 3.1 24.1 + - + +
213B ILE* 3.1 7.8 + - + +
215B GLU* 1.3 76.8 - - - +
217B LEU* 1.3 58.2 + - - +
220B GLY* 2.6 35.8 + - - +
221B THR* 3.3 35.9 - - - +
222B CYS* 3.5 9.0 - - + +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.3 17.5 - - + -
193B VAL* 3.6 26.9 - - + +
194B ALA* 3.7 21.2 - - - +
195B SER* 3.7 4.7 - - - +
196B LEU* 3.7 32.1 - - + +
213B ILE* 2.9 34.2 + - + +
214B GLN* 3.8 6.3 - - + +
216B LEU* 1.3 76.6 - - - +
218B GLU* 1.3 62.3 + - - +
220B GLY 4.8 0.3 + - - -
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLN* 2.9 28.6 + - + +
215B GLU* 3.6 4.0 - - - +
216B LEU 3.1 0.2 - - - -
217B LEU* 1.3 80.7 - - - +
219B HIS* 1.3 91.2 + - + +
220B GLY 3.7 0.2 - - - -
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLU* 2.9 29.1 + - + +
218B GLU* 1.3 106.4 + - + +
220B GLY* 1.3 62.4 + - - +
221B THR* 3.1 21.5 + - - +
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Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 5.8 4.2 - - - +
216B LEU* 2.6 34.7 + - - +
217B LEU 4.6 0.4 + - - -
218B GLU 3.7 0.6 - - - -
219B HIS* 1.3 71.6 - - - +
221B THR* 1.3 66.0 + - - +
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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