Contacts of the helix formed by residues 259 - 274 (chain C) in PDB entry 3QN3
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 259 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C GLY 4.9 2.9 - - - -
250C LYS* 3.7 21.4 - - - +
251C TYR* 4.3 0.7 - - - -
257C ALA 3.8 1.0 + - - -
258C PHE* 1.3 78.9 - - - +
260C SER* 1.3 53.5 + - - +
261C GLU* 3.5 16.5 + - - +
262C ALA* 2.9 27.5 + - - +
263C LEU* 2.8 32.1 + - - +
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PHE* 5.0 1.0 - - - -
249C GLY 4.9 6.2 + - - -
251C TYR* 3.6 18.0 - - - -
258C PHE 3.9 0.4 + - - -
259C SER* 1.3 71.7 - - - +
261C GLU* 1.3 68.0 + - - +
263C LEU* 3.3 4.3 + - - +
264C ILE* 3.0 34.2 + - - +
283C LEU* 3.9 4.5 - - - +
287C ASP* 2.5 34.8 + - - -
290C GLY* 4.3 13.7 - - - -
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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
----------------------------------------------------------
259C SER* 3.8 16.8 + - - +
260C SER* 1.3 86.4 + - - +
262C ALA* 1.3 63.5 + - - +
264C ILE* 3.3 13.5 + - + +
265C GLU* 3.1 26.4 + - - +
290C GLY* 5.9 0.7 - - - -
293C LYS* 2.5 46.6 + - + +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PHE* 4.0 18.0 - - + -
259C SER* 2.9 29.5 + - - +
261C GLU* 1.3 73.4 - - - +
263C LEU* 1.3 65.7 + - - +
265C GLU* 3.2 10.1 + - - +
266C ARG* 3.1 20.8 + - - +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C SER* 4.8 0.2 - - - -
245C PHE* 4.5 7.6 - - + -
251C TYR* 3.4 41.1 - - + -
253C MET* 3.8 24.9 - - + -
258C PHE* 4.0 12.3 - - + -
259C SER 2.8 15.6 + - - +
260C SER 3.6 5.2 - - - +
262C ALA* 1.3 75.0 - - - +
264C ILE* 1.3 65.4 + - - +
266C ARG* 3.2 10.9 + - + -
267C TYR* 3.1 56.0 + - + +
282C GLY 3.6 8.7 - - - +
283C LEU* 4.0 4.7 - - + -
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Residues in contact with ILE 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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260C SER* 3.0 22.9 + - - +
261C GLU* 3.5 17.3 - - + +
262C ALA 3.3 0.2 - - - -
263C LEU* 1.3 77.0 - - - +
265C GLU* 1.3 61.6 + - - +
267C TYR* 3.1 14.8 + - - +
268C VAL* 2.9 25.8 + - + +
283C LEU* 4.0 9.4 - - + -
290C GLY* 3.7 11.7 - - - +
293C LYS* 3.8 13.0 - - + -
294C LEU* 3.6 44.6 - - + +
297C LYS* 3.9 34.8 - - + -
298C LEU* 4.4 0.4 - - + +
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Residues in contact with GLU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C GLU* 3.1 18.0 + - + +
262C ALA* 3.2 11.8 + - - +
264C ILE* 1.3 76.5 - - - +
266C ARG* 1.3 63.9 + - - +
268C VAL* 3.3 18.0 + - - +
269C GLU* 3.0 31.3 + - + +
297C LYS* 3.2 37.4 + - - +
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Residues in contact with ARG 266 (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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214C ASN* 5.5 0.4 - - - +
215C THR* 3.7 24.2 - - - +
253C MET* 4.5 12.6 - - + -
254C GLU* 2.9 40.6 + - - +
258C PHE* 4.4 12.8 - - + -
262C ALA 3.1 12.2 + - - +
263C LEU* 3.4 18.4 - - + +
265C GLU* 1.3 74.4 - - - +
267C TYR* 1.3 58.7 + - + +
269C GLU* 3.2 32.8 + - - +
270C LEU* 2.8 63.5 + - + +
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Residues in contact with TYR 267 (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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161C PHE* 4.2 12.6 - + - -
238C LEU* 5.9 1.8 - - + -
240C VAL* 3.3 31.7 - - + +
263C LEU* 3.1 43.7 + - + +
264C ILE* 3.1 12.3 + - - +
266C ARG* 1.3 73.8 - - + +
268C VAL* 1.3 64.3 + - - +
270C LEU* 4.3 12.8 - - + -
271C CYS* 2.9 31.7 + - - -
279C ILE* 3.9 24.0 - - + -
282C GLY* 2.6 47.5 + - - -
283C LEU* 4.9 2.0 - - + -
294C LEU* 4.1 14.8 - - + -
298C LEU* 3.8 14.8 - - + -
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Residues in contact with VAL 268 (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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264C ILE 2.9 20.3 + - - +
265C GLU* 3.3 25.3 + - - +
267C TYR* 1.3 75.8 - - - +
269C GLU* 1.3 64.4 + - + +
271C CYS* 3.8 2.1 - - - +
272C ALA* 3.0 24.8 + - + +
297C LYS* 3.7 31.4 - - + -
298C LEU* 4.1 20.0 - - + -
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Residues in contact with GLU 269 (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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265C GLU* 3.0 19.6 + - + +
266C ARG* 3.5 41.0 + - - +
268C VAL* 1.3 75.9 - - + +
270C LEU* 1.3 64.7 + - - +
272C ALA* 3.2 7.6 + - - +
273C LYS* 3.1 24.1 + - - +
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Residues in contact with LEU 270 (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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161C PHE* 4.5 22.4 - - + -
214C ASN* 6.3 0.2 - - + -
215C THR* 3.7 30.1 - - + -
218C ILE* 4.9 6.1 - - + -
238C LEU* 5.5 1.6 - - + -
254C GLU* 5.6 0.2 - - - +
266C ARG* 2.8 59.8 + - + +
267C TYR* 3.8 12.6 - - + +
269C GLU* 1.3 78.0 - - - +
271C CYS* 1.3 58.3 + - - +
273C LYS* 3.2 2.7 + - + -
274C TYR* 2.9 50.7 + - + +
276C ILE* 3.9 18.2 - - + -
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Residues in contact with CYS 271 (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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267C TYR* 2.9 24.7 + - - +
268C VAL* 3.8 5.2 - - - +
270C LEU* 1.3 78.3 - - - +
272C ALA* 1.3 60.6 + - - +
274C TYR 3.1 19.8 - - - +
276C ILE* 4.0 19.3 + - - +
279C ILE* 3.9 24.9 - - - -
298C LEU* 4.9 8.7 - - + -
302C ILE* 3.9 28.5 - - + -
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Residues in contact with ALA 272 (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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268C VAL* 3.0 20.0 + - + +
269C GLU* 3.2 9.2 + - - +
271C CYS* 1.3 78.1 - - - +
273C LYS* 1.3 60.2 + - - +
274C TYR 5.4 0.2 - - - -
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Residues in contact with LYS 273 (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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219C ASP* 4.2 4.8 + - - -
269C GLU 3.1 14.5 + - - +
270C LEU* 3.9 4.5 - - + +
272C ALA* 1.3 78.2 - - - +
274C TYR* 1.3 101.4 + - + +
275C PRO* 4.8 0.7 - - - +
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Residues in contact with TYR 274 (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 THR* 3.9 15.8 - - + -
218C ILE* 3.5 38.4 - - + -
219C ASP* 2.7 34.5 + - - -
222C MET* 4.4 15.5 - - + -
236C ILE* 5.4 0.2 - - + -
270C LEU* 2.9 39.3 + - + +
271C CYS 3.1 19.7 - - - +
272C ALA 5.4 0.2 - - - -
273C LYS* 1.3 115.0 + - + +
275C PRO* 1.3 67.8 - - + +
276C ILE* 2.8 23.5 + - + -
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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