Contacts of the helix formed by residues 273 - 282 (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 THR 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B LEU* 1.3 76.1 - - - +
274B GLN* 1.3 66.1 + - + +
275B GLN* 2.9 26.5 - - + +
276B GLN* 3.0 26.2 + - - -
277B LYS* 2.7 32.4 + - - +
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Residues in contact with GLN 274 (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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273B THR* 1.3 79.0 - - + +
275B GLN* 1.3 57.6 + - - +
277B LYS* 3.6 15.3 - - + +
278B ALA* 3.0 28.1 + - - +
362B TYR* 3.9 14.9 - - + +
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Residues in contact with GLN 275 (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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244B PHE* 3.2 44.0 - - + +
245B GLY* 3.9 19.0 - - - +
273B THR* 3.2 18.2 - - + +
274B GLN* 1.3 79.3 - - - +
276B GLN* 1.3 56.4 + - + +
278B ALA* 3.4 4.9 + - - +
279B GLY 3.0 19.9 + - - -
362B TYR* 3.7 27.6 + - - +
364B GLN* 5.8 4.0 - - - +
391B PHE* 6.3 1.2 - - - -
4Q T 3.5 24.9 + - - +
5Q A 4.8 7.5 + - - -
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Residues in contact with GLN 276 (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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243B VAL* 4.3 1.8 - - + +
244B PHE 3.5 9.2 - - - +
245B GLY* 2.9 32.2 + - - +
246B VAL* 4.0 9.9 - - + +
250B THR* 3.9 27.1 + - - +
253B ARG* 5.8 0.3 + - - -
254B TRP* 4.0 11.9 - - + -
271B ARG 4.5 0.3 - - - +
272B LEU* 3.1 22.0 - - + +
273B THR* 3.0 39.4 + - - +
275B GLN* 1.3 71.5 - - - +
277B LYS* 1.3 66.7 + - - +
279B GLY* 2.9 9.5 + - - -
280B LEU* 2.9 22.8 + - + +
4Q T 5.1 1.8 - - - -
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Residues in contact with LYS 277 (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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272B LEU* 4.1 17.7 - - + +
273B THR 2.7 22.2 + - - +
274B GLN* 3.6 14.4 - - + +
276B GLN* 1.3 74.9 - - - +
278B ALA* 1.3 61.9 + - - +
280B LEU* 3.2 5.6 + - - +
281B GLN* 3.1 43.6 + - + +
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Residues in contact with ALA 278 (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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274B GLN 3.0 18.5 + - - +
275B GLN* 3.6 5.4 - - - +
277B LYS* 1.3 78.0 - - - +
279B GLY* 1.3 62.4 + - - +
281B GLN* 4.6 4.7 - - - -
282B TYR* 3.2 39.4 + - + +
361B LEU 5.5 0.4 - - - +
362B TYR* 3.9 29.4 - - + -
393B ILE* 4.2 14.9 - - + +
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Residues in contact with GLY 279 (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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243B VAL* 3.9 8.4 - - - +
244B PHE* 3.7 32.4 + - - -
275B GLN 3.0 8.0 + - - -
276B GLN 2.9 8.9 + - - -
278B ALA* 1.3 78.9 - - - +
280B LEU* 1.3 55.8 + - - +
282B TYR 3.9 0.5 - - - -
283B TYR* 3.1 31.2 + - - +
286B LEU* 4.7 5.2 - - - +
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Residues in contact with LEU 280 (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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243B VAL* 3.8 30.7 - - + -
254B TRP* 6.0 2.7 - - + -
262B LEU* 4.3 16.4 - - + +
265B LEU* 4.4 15.5 - - + +
266B ARG* 3.1 59.1 + - + +
272B LEU* 3.8 29.4 - - + -
276B GLN* 2.9 19.3 + - + +
277B LYS* 3.2 5.4 + - - +
279B GLY* 1.3 72.4 - - - +
281B GLN* 1.3 66.2 + - - +
282B TYR 3.2 2.5 + - - -
283B TYR* 3.4 8.0 + - + -
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Residues in contact with GLN 281 (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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277B LYS* 3.1 37.1 + - + +
278B ALA* 3.5 6.1 + - - +
280B LEU* 1.3 78.5 - - - +
282B TYR* 1.3 96.6 + - + +
283B TYR 3.6 0.2 - - - -
414B TRP* 5.8 1.2 - - - -
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Residues in contact with TYR 282 (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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278B ALA* 3.2 32.3 + - + +
279B GLY 3.9 2.7 - - - -
280B LEU 3.2 0.2 - - - -
281B GLN* 1.3 112.9 + - + +
283B TYR* 1.3 66.2 + - - +
284B GLN* 3.2 2.9 - - - -
285B ASP* 3.1 9.6 + - + +
286B LEU* 2.9 29.0 + - + +
361B LEU* 3.3 56.3 + - + +
393B ILE* 4.6 10.5 - - + -
414B TRP* 3.7 25.0 - + - -
416B ALA* 3.4 28.0 - - + -
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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