Contacts of the helix formed by residues 222 - 231 (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 CYS 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B VAL* 3.4 36.1 - - + -
215B GLU* 3.2 15.3 - - - -
216B LEU* 3.5 18.6 - - + +
221B THR* 1.3 77.2 - - - +
223B GLU* 1.3 69.2 + - - +
224B GLU* 4.0 8.7 - - - -
225B VAL* 2.7 42.9 + - + +
226B LYS* 2.8 13.0 + - - +
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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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215B GLU* 2.5 20.6 + - - +
221B THR* 4.1 1.4 + - - -
222B CYS* 1.3 69.3 - - - +
224B GLU* 1.3 58.8 + - - +
226B LYS* 3.0 14.5 + - - +
227B GLN* 2.4 61.9 + - + +
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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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163B LEU* 4.0 25.6 - - + +
208B HIS* 2.8 38.3 + - - -
211B ARG* 4.5 4.3 + - - -
212B VAL* 4.1 5.4 - - - +
215B GLU* 5.0 1.4 + - - +
222B CYS* 3.2 9.4 - - - -
223B GLU* 1.3 78.4 - - - +
225B VAL* 1.3 62.9 + - - +
227B GLN* 3.2 11.0 + - + +
228B VAL* 3.1 25.6 + - + +
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Residues in contact with VAL 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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159B ALA* 3.9 29.6 - - + +
162B THR* 4.2 7.4 - - + -
163B LEU* 4.1 19.3 - - + -
212B VAL* 4.5 0.4 - - + -
222B CYS* 2.7 35.4 + - + +
224B GLU* 1.3 75.7 - - - +
226B LYS* 1.3 61.8 + - - +
228B VAL* 3.3 8.3 + - - +
229B ARG* 3.2 61.5 + - - +
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Residues in contact with LYS 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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221B THR* 6.4 1.1 - - - -
222B CYS 2.8 12.4 + - - +
223B GLU* 3.0 23.1 + - - +
225B VAL* 1.3 76.4 - - - +
227B GLN* 1.3 64.7 + - - +
228B VAL 3.4 0.2 + - - -
229B ARG* 3.4 7.6 + - - +
230B CYS* 3.2 31.9 + - - -
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Residues in contact with GLN 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* 2.4 59.0 + - + +
224B GLU* 3.2 11.9 + - - +
226B LYS* 1.3 76.0 - - - +
228B VAL* 1.3 59.1 + - + +
230B CYS* 3.1 7.2 + - - +
231B SER* 2.9 31.4 + - - -
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Residues in contact with VAL 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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162B THR* 3.8 20.2 - - + -
163B LEU* 4.1 18.6 - - + -
166B ALA* 3.9 14.4 - - + -
224B GLU* 3.1 16.3 + - + +
225B VAL* 3.4 9.9 - - - +
227B GLN* 1.3 81.4 - - + +
229B ARG* 1.3 61.2 + - - +
230B CYS 3.1 1.2 + - - -
231B SER* 3.1 10.2 + - - +
234B TYR* 3.0 53.0 - - + +
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Residues in contact with ARG 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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158B GLU* 3.9 23.8 + - - +
159B ALA* 4.4 1.6 - - - +
162B THR* 2.9 33.8 + - + -
225B VAL* 3.2 33.9 + - - +
226B LYS* 3.4 7.7 + - - +
227B GLN 3.4 0.2 - - - -
228B VAL* 1.3 75.1 - - - +
230B CYS* 1.3 63.0 + - - +
234B TYR* 3.8 23.4 + - + +
235B GLN* 3.8 16.2 + - - +
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Residues in contact with CYS 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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226B LYS* 3.2 23.3 - - - +
227B GLN* 3.1 5.9 + - - +
228B VAL 3.0 0.4 - - - -
229B ARG* 1.3 82.5 - - - +
231B SER* 1.3 60.4 + - - +
232B GLU 3.6 1.0 + - - -
235B GLN* 2.7 22.6 + - - +
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Residues in contact with SER 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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227B GLN* 2.9 14.0 + - - -
228B VAL* 3.1 16.6 + - - -
230B CYS* 1.3 78.9 - - - +
232B GLU* 1.3 66.4 + - - +
233B ARG* 4.2 9.0 - - - +
234B TYR* 3.4 13.2 + - - +
235B GLN* 3.1 23.0 + - - +
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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