Contacts of the helix formed by residues 273 - 286 (chain B) in PDB entry 3QLC
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 LEU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 4.1 32.8 - - + +
194B VAL* 3.8 26.0 - - + -
222B TRP* 3.8 32.3 - - + -
248B LEU* 4.0 17.7 - - + -
266B TYR* 4.1 22.0 - - + +
270B PRO* 3.0 14.2 + - + +
271B GLU 3.0 0.2 + - - -
272B PRO* 1.3 81.9 - - - +
274B LEU* 1.3 65.0 + - - +
275B ASP 3.2 3.1 - - - -
276B LEU* 2.9 12.1 + - + +
277B VAL* 2.8 27.2 + - + +
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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
----------------------------------------------------------
166A MET* 4.0 28.9 - - + -
270B PRO 3.7 2.7 + - - -
271B GLU* 3.1 19.6 + - + +
272B PRO 3.4 0.6 - - - -
273B LEU* 1.3 77.3 - - - +
275B ASP* 1.3 61.2 + - - +
277B VAL* 3.3 15.3 + - + +
278B THR* 3.0 39.7 + - - +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PRO 5.0 2.8 + - - +
273B LEU 3.2 0.6 - - - -
274B LEU* 1.3 77.7 - - - +
276B LEU* 1.3 63.0 + - + +
278B THR* 3.3 9.0 + - - +
279B ALA* 2.8 29.6 + - - +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 4.3 20.2 - - + -
194B VAL* 3.9 17.6 - - + +
195B LEU 5.0 0.5 + - - -
222B TRP* 4.3 13.0 - - + -
247B ASN* 3.8 39.9 - - + +
248B LEU* 4.3 12.8 - - + -
272B PRO 5.1 0.6 + - - +
273B LEU* 2.9 13.7 + - + +
275B ASP* 1.3 80.0 - - + +
277B VAL* 1.3 61.1 + - - +
279B ALA* 3.3 9.4 + - + +
280B CYS* 3.0 23.6 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG* 3.5 15.4 + - - +
192B LEU 3.5 18.2 - - - +
193B GLN* 3.5 28.9 - - + +
194B VAL* 4.0 3.6 - - + -
273B LEU* 2.8 19.3 + - + +
274B LEU* 3.6 20.0 - - + +
276B LEU* 1.3 75.1 - - - +
278B THR* 1.3 57.9 + - - +
280B CYS* 3.2 2.3 + - - +
281B ASN* 2.9 36.0 + - - +
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Residues in contact with THR 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 LEU* 3.0 22.8 + - - +
275B ASP* 3.5 14.3 + - - +
277B VAL* 1.3 76.8 - - - +
279B ALA* 1.3 62.2 + - - +
281B ASN* 3.1 16.5 + - + +
282B SER* 2.9 25.6 + - - -
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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 ASP 2.8 20.9 + - - +
276B LEU* 3.3 13.9 + - + +
278B THR* 1.3 74.5 - - - +
280B CYS* 1.3 62.1 + - - +
282B SER* 3.5 8.6 - - - -
283B VAL* 3.2 27.4 + - - +
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Residues in contact with CYS 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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187B TYR 4.6 0.4 - - - -
188B ARG* 3.7 27.6 - - - +
193B GLN 4.1 3.4 - - - +
194B VAL 4.0 2.0 - - - -
195B LEU* 3.6 46.4 - - + +
276B LEU 3.0 13.2 + - - +
277B VAL 3.5 7.9 - - - +
279B ALA* 1.3 75.1 - - - +
281B ASN* 1.3 68.4 + - - +
283B VAL* 3.3 7.1 + - - +
284B TYR* 3.2 33.5 + - - -
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Residues in contact with ASN 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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188B ARG* 2.4 39.2 + - - +
277B VAL* 2.9 24.1 + - - +
278B THR* 3.3 18.3 + - + +
280B CYS* 1.3 71.9 - - - +
282B SER* 1.3 67.5 + - - +
284B TYR* 2.9 8.5 + - - +
285B GLU* 2.9 22.1 + - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B THR* 2.9 11.2 + - - -
279B ALA* 3.5 13.2 - - - -
281B ASN* 1.3 78.9 - - - +
283B VAL* 1.3 64.9 + - - +
285B GLU* 3.1 23.3 + - - +
286B ASN* 3.2 18.7 + - - -
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Residues in contact with VAL 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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169B VAL* 4.3 21.5 - - + -
180B HIS* 4.4 12.6 - - + +
186B ILE* 3.4 30.5 - - + -
195B LEU* 3.8 26.0 - - + -
279B ALA* 3.2 14.4 + - + +
280B CYS 3.6 7.9 - - - +
281B ASN 3.2 0.2 - - - -
282B SER* 1.3 79.8 - - - +
284B TYR* 1.3 65.9 + - - +
286B ASN* 2.9 23.8 + - - +
287B LEU* 3.8 5.7 - - - +
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Residues in contact with TYR 284 (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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183B LYS* 5.7 8.7 - - + -
186B ILE* 3.4 43.1 + - + -
187B TYR* 3.6 14.2 - - - -
188B ARG* 3.5 36.8 + - + +
280B CYS* 3.2 31.6 + - - -
281B ASN* 2.9 9.7 + - - +
283B VAL* 1.3 79.4 - - - +
285B GLU* 1.3 64.9 + - - +
286B ASN 3.0 1.2 + - - -
287B LEU* 3.3 31.4 + - + +
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Residues in contact with GLU 285 (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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281B ASN 2.9 11.9 + - - +
282B SER* 3.1 17.9 + - - +
284B TYR* 1.3 76.4 - - - +
286B ASN* 1.3 62.3 + - - +
287B LEU 3.2 11.3 + - - +
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Residues in contact with ASN 286 (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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180B HIS* 4.3 5.4 - - + +
181B PHE* 5.6 4.7 - - - -
282B SER* 3.6 19.3 + - - +
283B VAL* 2.9 12.9 + - - +
285B GLU* 1.3 86.3 - - - +
287B LEU* 1.3 73.0 + - + +
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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