Contacts of the helix formed by residues 219 - 231 (chain B) in PDB entry 2H1H
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 ALA 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B TRP* 3.4 6.3 - - - -
218B GLY* 1.3 73.6 - - - -
220B PRO* 1.3 65.7 - - + +
221B HIS* 3.2 31.9 - - + +
222B GLU* 2.8 42.1 + - - +
223B GLU 3.2 4.3 + - - -
400B AFH 3.9 2.4 + - - +
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Residues in contact with PRO 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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217B TRP* 4.2 7.8 - - + -
218B GLY 4.6 2.0 - - - +
219B ALA* 1.3 87.9 - - + +
221B HIS* 1.3 60.6 + - - +
223B GLU* 3.1 14.3 + - + +
224B GLU* 3.1 32.3 + - - +
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Residues in contact with HIS 221 (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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187B THR 5.5 3.4 + - - -
193B HIS* 6.1 2.0 - + - -
219B ALA* 3.3 28.9 - - + +
220B PRO* 1.3 79.3 - - - +
222B GLU* 1.3 75.9 + - + +
223B GLU 3.3 0.2 - - - -
224B GLU* 3.7 9.8 + - - +
225B ARG* 3.3 34.7 + - - +
228B ARG* 4.7 2.8 + - - -
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Residues in contact with GLU 222 (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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185B HIS* 3.4 8.4 - - + -
186B ALA* 3.5 14.0 - - + +
187B THR 4.2 5.0 - - - +
217B TRP* 3.8 10.7 - - + +
218B GLY 2.6 32.7 + - - -
219B ALA* 2.8 20.5 + - - +
221B HIS* 1.3 97.2 + - + +
223B GLU* 1.3 60.5 + - - +
225B ARG* 3.5 25.2 + - - +
226B ALA* 2.9 26.3 + - - +
400B AFH 2.5 35.6 + - - -
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Residues in contact with GLU 223 (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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217B TRP* 3.1 61.4 + - + +
219B ALA 3.2 3.8 + - - -
220B PRO* 3.1 11.8 + - - +
222B GLU* 1.3 75.3 - - - +
224B GLU* 1.3 74.1 + - - +
226B ALA* 2.9 5.3 + - - +
227B LYS* 2.8 53.8 + - - +
238B VAL* 4.5 6.7 - - + +
239B LEU 5.4 0.2 - - - +
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Residues in contact with GLU 224 (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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220B PRO* 3.1 19.3 + - + +
221B HIS* 4.0 8.5 - - - +
223B GLU* 1.3 91.0 - - - +
225B ARG* 1.3 61.4 + - - +
227B LYS* 3.5 27.0 + - - +
228B ARG* 3.1 43.4 + - - +
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Residues in contact with ARG 225 (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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185B HIS* 3.2 37.2 + - - -
186B ALA* 3.6 15.2 - - - +
193B HIS* 3.7 23.7 + - - -
194B TRP 6.0 1.1 - - - -
196B GLU* 3.4 37.2 - - + -
199B TRP* 5.7 2.9 - - - -
221B HIS* 3.3 26.3 + - - +
222B GLU* 3.5 31.5 - - - +
223B GLU 3.1 0.6 - - - -
224B GLU* 1.3 75.8 - - - +
226B ALA* 1.3 60.8 + - - +
228B ARG* 3.1 20.4 + - - +
229B LEU* 2.8 40.8 + - + +
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Residues in contact with ALA 226 (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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185B HIS* 3.9 17.7 - - - +
215B LEU* 3.3 27.3 - - + +
217B TRP* 4.7 2.5 - - + -
222B GLU 2.9 16.8 + - - +
223B GLU* 3.3 10.1 - - - +
225B ARG* 1.3 76.7 - - - +
227B LYS* 1.3 57.7 + - - +
229B LEU* 3.1 3.0 + - - -
230B ALA* 2.8 25.6 + - - +
238B VAL* 3.8 21.8 - - + -
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Residues in contact with LYS 227 (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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223B GLU* 2.8 46.7 + - + +
224B GLU* 3.8 35.2 + - - +
226B ALA* 1.3 71.8 - - - +
228B ARG* 1.3 60.7 + - + +
230B ALA* 3.0 2.7 + - - +
231B GLU* 2.7 29.9 + - - +
238B VAL* 3.8 21.3 - - + -
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Residues in contact with ARG 228 (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 GLU* 2.6 47.5 + - - +
200B ARG* 3.1 22.9 + - - -
221B HIS 4.7 2.6 + - - -
224B GLU* 3.1 36.7 + - - +
225B ARG* 3.4 26.1 - - - +
227B LYS* 1.3 81.6 - - + +
229B LEU* 1.3 63.6 + - - +
230B ALA 3.3 0.3 + - - -
231B GLU* 3.4 18.3 + - - +
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Residues in contact with LEU 229 (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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185B HIS* 4.1 29.8 - - + -
196B GLU* 3.5 43.3 - - + +
199B TRP* 3.7 30.7 - - + -
200B ARG* 2.8 26.4 + - + +
203B ILE* 3.5 17.6 - - + +
215B LEU* 3.7 15.3 - - + -
225B ARG* 2.8 25.2 + - + +
226B ALA* 3.5 6.7 - - - +
228B ARG* 1.3 76.3 - - - +
230B ALA* 1.3 58.5 + - - +
233B PHE* 3.4 9.7 - - - -
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Residues in contact with ALA 230 (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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200B ARG* 4.1 0.2 - - - -
215B LEU* 4.3 0.2 - - + -
226B ALA 2.8 16.7 + - - +
227B LYS 3.0 4.2 + - - +
229B LEU* 1.3 79.1 - - - +
231B GLU* 1.3 66.0 + - - +
232B GLY 3.3 0.5 + - - -
233B PHE* 3.0 23.3 + - - +
236B VAL* 3.9 34.1 - - + +
238B VAL* 3.9 17.9 - - + +
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Residues in contact with GLU 231 (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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200B ARG* 2.5 39.5 + - - +
227B LYS 2.7 18.5 + - - +
228B ARG* 3.4 18.5 + - - +
230B ALA* 1.3 73.9 - - - +
232B GLY* 1.3 63.2 + - - +
233B PHE* 3.3 0.7 + - - -
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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