Contacts of the helix formed by residues 273 - 283 (chain B) in PDB entry 2C10
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 SER 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ILE* 5.9 3.6 - - - -
264B VAL* 3.8 12.7 - - - +
271B TYR* 3.3 6.2 - - - +
272B ASP* 1.3 82.7 - - - +
274B LEU* 1.3 63.0 + - - +
275B ALA* 3.4 10.3 + - - +
276B GLN* 3.0 26.0 + - - +
277B LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 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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187B GLU* 3.4 56.4 + - + +
188B LEU* 4.3 11.7 - - + +
190B GLN* 4.6 7.6 - - + +
191B ALA* 3.9 25.1 - - + +
245B LEU* 4.5 7.2 - - + -
247B LEU* 4.1 26.0 - - + -
261B ILE* 5.0 4.2 - - + +
264B VAL* 4.0 10.8 - - + +
273B SER* 1.3 71.9 - - - +
275B ALA* 1.3 55.8 + - - +
277B LEU* 3.2 21.2 + - + +
278B GLU* 2.7 36.5 + - - +
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Residues in contact with ALA 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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190B GLN* 3.9 25.0 + - + +
273B SER* 3.4 9.2 + - - +
274B LEU* 1.3 78.7 - - - +
276B GLN* 1.3 51.0 + - - +
278B GLU* 3.2 8.2 + - - +
279B ALA* 2.8 36.0 + - - +
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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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270B TYR 5.2 1.0 + - - -
271B TYR* 3.7 14.9 - - - +
272B ASP* 2.7 46.7 + - + +
273B SER* 3.0 20.5 + - - +
275B ALA* 1.3 72.8 - - - +
277B LEU* 1.3 59.3 + - - +
279B ALA* 3.3 5.2 + - - +
280B GLN* 2.8 62.2 + - - +
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Residues in contact with LEU 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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191B ALA* 5.3 1.1 - - + -
194B LEU* 3.6 32.3 - - + -
245B LEU* 4.0 15.7 - - + -
264B VAL* 4.0 11.0 - - + -
266B TYR* 3.9 24.9 - - + -
271B TYR* 3.6 44.5 - - + +
273B SER 3.1 14.3 + - - +
274B LEU* 3.4 17.5 - - + +
276B GLN* 1.3 77.0 - - - +
278B GLU* 1.3 56.1 + - - +
280B GLN* 3.3 2.3 + - - +
281B PHE* 2.9 29.2 + - + +
286B VAL* 4.5 8.5 - - + -
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Residues in contact with GLU 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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190B GLN 3.2 23.8 - - - +
191B ALA* 3.2 13.7 - - - +
193B GLY* 3.2 25.4 + - - -
194B LEU* 3.0 27.8 + - - +
274B LEU 2.7 17.3 + - - +
275B ALA* 3.4 6.1 - - - +
277B LEU* 1.3 72.6 - - - +
279B ALA* 1.3 58.7 + - - +
281B PHE* 3.2 4.8 + - - +
282B GLU* 2.6 59.1 + - - +
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Residues in contact with ALA 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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275B ALA 2.8 20.8 + - - +
276B GLN* 3.9 6.1 - - - +
278B GLU* 1.3 75.1 - - - +
280B GLN* 1.3 57.6 + - - +
282B GLU* 3.4 6.9 + - - +
283B ALA* 3.0 30.0 + - - +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ARG* 6.1 1.0 - - - +
271B TYR* 3.3 26.0 + - + -
276B GLN* 2.8 45.3 + - + +
277B LEU 3.8 3.8 - - - +
279B ALA* 1.3 77.5 - - - +
281B PHE* 1.3 60.9 + - - +
283B ALA* 3.4 5.7 + - + -
284B GLY 3.4 4.2 + - - -
285B LEU* 3.0 56.8 + - + +
286B VAL* 3.8 10.4 - - + +
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Residues in contact with PHE 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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193B GLY* 3.7 7.9 - - - -
194B LEU* 3.7 51.8 - - + -
197B HIS* 3.8 31.6 - + + -
277B LEU* 2.9 16.7 + - + +
278B GLU* 3.6 11.0 - - - +
280B GLN* 1.3 74.8 - - - +
282B GLU* 1.3 73.5 + - + +
284B GLY* 3.2 14.2 + - - -
285B LEU 4.3 0.3 + - - -
286B VAL* 3.7 22.4 + - + +
288B VAL* 3.9 22.4 - - + -
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Residues in contact with GLU 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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193B GLY* 5.8 0.7 - - - -
278B GLU* 2.6 49.9 + - - +
279B ALA* 3.9 6.5 - - - +
281B PHE* 1.3 87.4 - - + +
283B ALA* 1.3 61.4 + - - +
284B GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 283 (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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279B ALA 3.0 19.0 + - - +
280B GLN* 3.9 7.9 - - + +
281B PHE 3.2 0.4 - - - -
282B GLU* 1.3 76.0 - - - +
284B GLY* 1.3 59.2 + - - +
285B LEU* 3.6 4.5 - - + +
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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