Contacts of the helix formed by residues 256 - 265 (chain C) in PDB entry 1QPL
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 ILE 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C VAL* 1.3 73.8 - - - +
257C ARG* 1.3 66.6 + - - +
258C GLY 4.3 0.7 - - - +
259C TRP* 2.8 45.9 + - + +
260C GLU 3.3 3.8 + - - -
276C ILE* 4.2 6.3 - - + -
280C TYR 4.0 7.0 - - - +
281C ALA* 4.0 26.7 - - + +
282C TYR* 3.7 30.1 - - + -
297C LEU* 4.3 3.8 - - + -
299C PHE* 4.0 22.0 - - + -
308C 587 3.0 38.6 + - + +
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C VAL 3.5 2.9 + - - -
256C ILE* 1.3 69.5 - - - +
258C GLY* 1.3 64.4 + - - +
260C GLU* 3.0 30.5 + - - +
261C GLU* 3.0 51.3 + - - +
279C ASP 5.9 0.9 - - - +
280C TYR* 3.6 34.3 + - + +
281C ALA 5.3 0.6 + - - -
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Residues in contact with GLY 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 3.3 18.7 - - - +
256C ILE 2.9 3.2 + - - -
257C ARG* 1.3 72.6 - - - +
259C TRP* 1.3 52.5 + - - +
261C GLU 3.5 0.2 + - - -
262C GLY* 2.8 31.5 + - - -
274C LEU* 4.7 0.4 - - - +
276C ILE* 3.6 31.9 - - - -
280C TYR* 2.9 19.1 + - - +
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Residues in contact with TRP 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C VAL* 3.7 22.9 - - + -
226C TYR* 3.4 35.7 - + + -
246C PHE* 4.0 5.4 - + - -
248C PHE* 4.0 19.8 - + + -
250C LEU* 5.2 0.2 - - - +
255C VAL* 3.5 16.6 - - + -
256C ILE* 2.8 27.7 + - + +
258C GLY* 1.3 69.6 - - - -
260C GLU* 1.3 64.0 + - - +
263C VAL* 3.1 39.3 + - + +
274C LEU* 4.8 4.9 - - + -
276C ILE* 3.5 16.8 - - + -
299C PHE* 3.2 48.1 - + - +
301C VAL* 3.8 20.9 - - + -
308C 587 3.6 26.9 - - + +
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Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C MET 4.5 0.5 - - - +
250C LEU* 3.8 19.2 - - - +
251C GLY* 3.3 39.7 + - - +
252C LYS 3.4 16.3 - - - +
255C VAL* 3.5 32.9 - - + +
256C ILE 3.3 0.6 + - - +
257C ARG* 3.0 30.3 + - - +
259C TRP* 1.3 81.0 - - - +
261C GLU* 1.3 62.6 + - - +
264C ALA* 3.3 20.8 + - - +
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Residues in contact with GLU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLY* 5.9 0.2 - - - -
202C VAL* 3.5 22.8 + - + +
257C ARG* 3.0 44.6 + - - +
260C GLU* 1.3 78.1 - - - +
262C GLY* 1.3 69.2 + - - +
264C ALA* 3.5 11.0 + - - +
265C GLN* 3.1 24.4 + - - +
280C TYR* 3.2 29.7 + - - -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 3.9 5.1 - - - +
204C VAL* 4.4 3.7 - - - +
258C GLY 2.8 21.7 + - - -
261C GLU* 1.3 72.9 - - - +
263C VAL* 1.3 62.8 + - - +
265C GLN* 3.0 25.5 + - - +
266C MET* 3.7 7.9 + - - +
274C LEU* 3.7 26.9 - - - -
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Residues in contact with VAL 263 (chain C).
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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216C PRO* 3.7 15.3 - - + +
222C CYS* 4.4 8.7 - - + -
224C VAL* 5.0 2.0 - - + -
248C PHE* 4.2 27.8 - - + -
250C LEU* 5.5 3.1 - - + -
259C TRP* 3.1 32.7 + - + +
260C GLU 4.9 0.2 - - - +
262C GLY* 1.3 72.8 - - - +
264C ALA* 1.3 56.1 + - - +
266C MET* 2.8 47.6 + - + +
274C LEU* 4.4 5.3 - - + +
301C VAL* 4.5 9.4 - - + -
303C LEU* 4.7 17.0 - - + -
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 3.9 19.2 - - - +
216C PRO* 4.0 15.7 - - - +
250C LEU* 4.7 14.5 - - + +
260C GLU 3.3 20.5 + - - +
261C GLU* 3.5 7.4 + - - +
262C GLY 3.1 1.0 + - - -
263C VAL* 1.3 76.6 - - - +
265C GLN* 1.3 59.9 + - + +
266C MET 3.3 1.1 - - - -
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Residues in contact with GLN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.3 12.1 + - - +
204C VAL* 4.1 28.2 - - + +
215C PHE* 3.5 17.7 - - - -
261C GLU* 3.1 27.7 + - - +
262C GLY* 3.0 8.7 + - - +
264C ALA* 1.3 77.4 - - + +
266C MET* 1.3 61.9 + - - +
267C SER 4.1 0.2 + - - -
270C GLN* 4.3 4.9 + - - +
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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