Contacts of the helix formed by residues 247 - 258 (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 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B THR* 3.7 7.2 - - - -
246B VAL* 1.3 74.9 - - - +
248B VAL* 1.3 66.8 + - - -
249B LYS 3.4 2.5 - - - -
250B THR 3.3 1.0 + - - -
251B ALA* 2.9 22.0 + - - +
901B NA 4.5 0.4 - - - -
4Q T 3.0 25.7 + - - -
5Q A 3.7 12.6 - - - -
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Residues in contact with VAL 248 (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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168B GLY 3.8 26.7 - - - +
169B PHE* 4.0 35.7 - - + +
171B ALA* 4.6 12.3 - - + +
173B GLU* 5.5 3.6 - - - +
237B MET* 3.7 2.0 - - + +
241B THR* 3.7 11.8 - - + +
247B GLY* 1.3 71.6 - - - -
249B LYS* 1.3 67.9 + - - +
251B ALA* 3.1 2.5 + - - +
252B ASN* 2.9 25.7 + - + +
4Q T 4.8 1.2 + - - -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLY 3.4 0.4 - - - -
248B VAL* 1.3 79.5 - - - +
250B THR* 1.3 62.5 + - - +
252B ASN* 3.5 10.6 + - - +
253B ARG* 3.2 22.2 + - - +
3Q G 3.3 44.5 + - + +
4Q T 3.9 17.4 + - - +
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 3.9 10.1 - - + -
247B GLY 3.6 4.4 + - - -
248B VAL 3.2 0.6 - - - -
249B LYS* 1.3 76.0 - - - +
251B ALA* 1.3 65.7 + - - +
253B ARG* 3.0 31.8 + - - +
254B TRP* 3.0 44.6 + - + -
276B GLN* 3.9 14.5 + - - +
3Q G 3.5 8.1 + - - -
4Q T 2.4 30.1 + - - -
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Residues in contact with ALA 251 (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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237B MET* 3.5 20.5 - - - +
240B PHE* 3.5 37.3 - - + -
241B THR* 3.6 13.7 - - + -
246B VAL* 3.9 3.3 - - + +
247B GLY 2.9 17.0 + - - +
248B VAL 3.1 3.3 + - - +
250B THR* 1.3 77.1 - - - +
252B ASN* 1.3 57.3 + - - +
254B TRP* 3.4 1.0 + - - -
255B TYR* 3.0 27.5 + - - +
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Residues in contact with ASN 252 (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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233B ARG* 3.0 27.7 + - - +
237B MET* 3.6 15.4 - - + +
248B VAL* 2.9 18.8 + - + +
249B LYS* 3.8 10.1 + - - +
251B ALA* 1.3 74.7 - - - +
253B ARG* 1.3 68.2 + - - +
255B TYR* 3.6 2.0 - - - +
256B GLN* 3.1 41.5 + - - +
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Residues in contact with ARG 253 (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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249B LYS* 3.2 13.2 + - - +
250B THR* 3.0 22.8 + - - +
252B ASN* 1.3 82.8 - - - +
254B TRP* 1.3 94.7 + - - +
256B GLN* 3.6 6.3 + - - +
257B GLU* 3.3 44.1 + - - +
271B ARG* 3.5 23.2 + - - +
276B GLN* 5.8 0.4 + - - -
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Residues in contact with TRP 254 (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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240B PHE* 3.6 27.6 - + + -
243B VAL* 5.9 0.4 - - + -
246B VAL* 3.7 37.9 - - + -
250B THR* 3.0 24.9 + - + -
251B ALA 3.8 2.9 - - - +
253B ARG* 1.3 114.9 - - - +
255B TYR* 1.3 65.0 + - - +
257B GLU* 3.4 6.4 + - - +
258B GLY 3.3 4.2 + - - -
259B LEU* 3.1 34.5 + - + +
265B LEU* 3.4 40.8 - - + -
271B ARG* 3.3 24.3 - - - +
272B LEU* 4.7 15.7 - - + -
276B GLN* 4.0 19.3 - - + -
280B LEU* 6.0 2.5 - - + -
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Residues in contact with TYR 255 (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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232B GLU* 3.2 14.8 + - + +
233B ARG* 3.2 65.9 + - + +
236B THR* 3.5 36.8 - - + -
237B MET* 4.6 2.7 - - - -
240B PHE* 4.3 1.5 - - - -
251B ALA 3.0 18.7 + - - +
252B ASN 3.6 5.6 - - - +
253B ARG 3.3 0.2 - - - -
254B TRP* 1.3 76.7 - - - +
256B GLN* 1.3 68.3 + - - +
258B GLY 2.9 16.5 + - - -
259B LEU 4.1 4.0 - - - -
260B ARG* 2.9 55.2 + - - -
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Residues in contact with GLN 256 (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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233B ARG* 4.8 1.1 + - - -
252B ASN* 3.1 36.7 + - - +
253B ARG* 3.8 6.7 - - - +
254B TRP 3.3 0.2 - - - -
255B TYR* 1.3 92.4 - - - +
257B GLU* 1.3 62.9 + - + +
258B GLY* 3.2 1.2 + - - -
260B ARG* 5.3 0.5 + - - -
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Residues in contact with GLU 257 (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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253B ARG* 3.3 43.5 + - - +
254B TRP* 3.4 9.6 + - - +
255B TYR 3.3 0.4 - - - -
256B GLN* 1.3 77.5 - - + +
258B GLY* 1.3 57.4 + - - +
259B LEU* 3.7 6.9 - - + +
271B ARG* 2.8 29.4 + - - -
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Residues in contact with GLY 258 (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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255B TYR 2.9 12.9 + - - -
256B GLN 3.0 1.5 - - - -
257B GLU* 1.3 79.8 - - - +
259B LEU* 1.3 69.5 + - - +
260B ARG* 3.2 22.4 + - - +
264B GLU* 3.7 6.6 - - - +
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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