Contacts of the helix formed by residues 262 - 283 (chain C) in PDB entry 1P5Q
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 ASN 262 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C MSE 1.3 75.9 - - - +
263C SER* 1.3 65.8 - - - +
264C GLU* 2.5 37.7 + - - +
265C GLU* 2.7 40.0 + - - +
266C LYS* 3.0 22.2 + - - +
303C GLU* 5.4 0.7 - - - -
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ASN* 1.3 75.8 - - - +
264C GLU* 1.3 63.7 + - - +
266C LYS* 3.1 4.5 + - - +
267C LEU* 3.1 26.9 + - - +
303C GLU* 3.6 26.3 + - - -
305C SER* 3.9 7.0 + - - -
306C PHE* 3.7 22.2 + - - -
310C GLU* 3.5 32.2 + - - -
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ASN* 2.5 17.4 + - - +
263C SER* 1.3 72.8 - - - +
265C GLU* 1.3 68.0 + - + +
267C LEU* 3.1 7.2 + - + +
268C GLU* 2.8 26.3 + - - +
310C GLU* 4.6 10.8 - - - +
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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
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256C LYS* 3.4 24.3 + - - +
260C GLU 3.6 7.0 - - - +
261C MSE 3.1 24.9 - - + +
262C ASN* 2.7 52.7 + - - +
264C GLU* 1.3 72.4 - - + +
266C LYS* 1.3 58.6 + - - +
268C GLU* 3.1 19.8 + - - +
269C GLN* 2.8 35.2 + - + +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C SER* 3.5 22.9 + - - -
259C TRP* 5.7 0.2 - - - +
261C MSE 3.0 43.3 + - + -
262C ASN 3.0 10.7 + - - +
263C SER* 3.4 10.5 - - - +
265C GLU* 1.3 77.4 - - - +
267C LEU* 1.3 54.8 + - - +
269C GLN* 4.0 1.0 - - - +
270C SER* 2.5 38.5 + - - +
299C TRP* 3.0 36.1 - - + +
300C LEU* 4.4 10.3 - - + -
303C GLU* 2.6 45.4 + - + +
306C PHE* 5.0 1.3 - - + -
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Residues in contact with LEU 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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263C SER 3.1 11.8 + - - +
264C GLU* 3.1 7.2 + - - +
266C LYS* 1.3 74.6 - - - +
268C GLU* 1.3 67.6 + - - +
270C SER* 4.0 3.7 - - - -
271C THR* 2.8 28.5 + - - +
300C LEU* 3.6 19.3 - - + -
306C PHE* 3.6 22.0 - - + -
310C GLU* 4.0 35.9 - - + +
313C LYS* 4.1 24.7 - - + +
314C ALA* 3.8 18.6 - - + +
317C LEU* 4.3 9.5 - - + +
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Residues in contact with GLU 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 GLU* 2.8 14.5 + - - +
265C GLU* 3.3 20.5 - - - +
267C LEU* 1.3 80.9 - - - +
269C GLN* 1.3 84.3 + - - +
271C THR* 3.0 13.5 + - - -
272C ILE* 3.1 25.0 + - + +
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Residues in contact with GLN 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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256C LYS* 5.4 9.7 - - + +
261C MSE 4.0 16.8 - - - -
265C GLU* 2.8 22.4 + - + +
266C LYS 4.1 1.6 - - - +
268C GLU* 1.3 96.0 + - - +
270C SER* 1.3 56.7 + - - +
272C ILE* 3.2 25.6 + - - +
273C VAL* 2.8 35.3 + - - +
276C ARG* 5.0 10.3 + - - +
299C TRP* 3.5 26.6 - - + -
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Residues in contact with SER 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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266C LYS 2.5 26.4 + - - -
269C GLN* 1.3 73.4 - - - +
271C THR* 1.3 59.7 + - - +
273C VAL* 4.2 0.2 - - - -
274C LYS* 2.9 28.8 + - - +
296C ILE* 3.4 24.6 - - - +
299C TRP* 3.5 17.1 - - - +
300C LEU* 3.7 19.3 - - - +
317C LEU* 4.0 22.3 - - - +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 2.8 17.0 + - - +
268C GLU* 3.0 10.2 + - - -
270C SER* 1.3 76.6 - - - +
272C ILE* 1.3 65.2 + - + +
274C LYS* 3.1 13.8 - - + +
275C GLU* 3.1 19.9 + - - +
317C LEU* 4.1 15.9 - - + +
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Residues in contact with ILE 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 GLU* 3.1 23.7 + - + +
269C GLN* 3.2 34.1 + - - +
271C THR* 1.3 77.4 - - + +
273C VAL* 1.3 60.2 + - + +
275C GLU* 2.7 29.3 + - - +
276C ARG* 3.2 38.0 + - + +
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLN* 2.8 22.2 + - - +
270C SER* 4.2 1.1 - - - -
272C ILE* 1.3 71.5 - - + +
274C LYS* 1.3 69.6 + - - +
276C ARG* 3.0 20.1 + - - +
277C GLY* 2.8 20.6 + - - -
292C GLN* 3.1 48.1 - - - +
295C LYS* 4.4 7.6 - - + -
296C ILE* 3.6 14.8 - - + -
299C TRP* 3.4 28.0 - - + -
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Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C SER 2.9 20.3 + - - +
271C THR* 3.1 12.8 - - + +
272C ILE 3.0 0.2 - - - -
273C VAL* 1.3 76.3 - - - +
275C GLU* 1.3 63.7 + - - +
277C GLY* 3.0 11.4 + - - -
278C THR* 3.2 14.3 + - - +
293C TYR* 3.7 15.1 + - + -
296C ILE* 3.7 17.0 - - + -
316C ALA 5.3 0.8 + - - -
317C LEU* 3.8 22.1 - - + +
320C ALA* 3.5 29.9 - - + +
321C SER* 6.0 0.2 - - - +
324C ASN* 4.9 7.4 - - - +
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C THR 3.1 7.3 + - - +
272C ILE* 2.7 16.7 + - + +
274C LYS* 1.3 79.1 - - - +
276C ARG* 1.3 59.6 + - + +
278C THR* 2.7 34.1 - - - +
279C VAL* 3.3 6.5 + - - +
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Residues in contact with ARG 276 (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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169C ILE* 5.0 10.7 - - - +
191C GLU* 4.2 15.7 + - - -
253C GLU* 6.0 0.2 + - - -
269C GLN* 5.0 8.9 + - - +
272C ILE* 3.5 36.3 - - + +
273C VAL* 3.5 13.5 - - - +
275C GLU* 1.3 71.6 - - + +
277C GLY* 1.3 71.5 + - - +
279C VAL* 3.0 16.0 + - - +
280C TYR* 3.1 28.2 + - + -
292C GLN* 3.5 26.7 + - - +
295C LYS* 4.5 12.9 - - - +
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Residues in contact with GLY 277 (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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273C VAL 2.8 13.4 + - - -
274C LYS 3.4 5.8 - - - -
275C GLU 3.0 0.4 - - - -
276C ARG* 1.3 79.1 - - - +
278C THR* 1.3 63.9 + - - +
280C TYR* 3.1 3.3 + - - +
281C PHE* 3.0 21.5 + - - +
289C ALA* 4.2 3.6 - - - +
292C GLN* 4.0 13.2 - - - +
293C TYR* 3.2 27.1 - - - -
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Residues in contact with THR 278 (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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274C LYS* 3.2 9.1 + - - +
275C GLU* 2.7 19.7 + - - +
277C GLY* 1.3 73.7 - - - +
279C VAL* 1.3 64.5 + - + +
281C PHE* 3.3 6.1 + - - +
282C LYS* 2.8 31.7 + - + +
293C TYR* 3.1 10.4 + - - -
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Residues in contact with VAL 279 (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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275C GLU 3.3 6.5 + - - +
276C ARG* 3.0 11.4 + - - +
278C THR* 1.3 82.3 - - + +
280C TYR* 1.3 73.5 + - + +
281C PHE 2.9 1.3 - - - -
282C LYS* 2.8 25.5 + - + +
283C GLU* 2.9 41.3 + - + +
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Residues in contact with TYR 280 (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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169C ILE* 5.9 1.2 - - - +
191C GLU* 4.7 7.4 + - - +
194C GLU* 3.8 18.7 + - - -
276C ARG* 3.1 33.6 + - + -
277C GLY 3.8 3.6 - - - +
279C VAL* 1.3 81.6 - - + +
281C PHE* 1.3 59.8 + - - +
283C GLU* 3.6 5.0 + - - -
284C GLY 3.3 1.6 + - - -
285C LYS* 2.7 59.0 + - + +
288C GLN* 3.7 35.0 - - + -
289C ALA 3.7 9.2 - - - +
292C GLN* 3.8 33.9 - - + -
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Residues in contact with PHE 281 (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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277C GLY 3.0 13.1 + - - +
278C THR* 3.5 9.6 - - - +
279C VAL 2.9 0.6 - - - -
280C TYR* 1.3 76.7 - - - +
282C LYS* 1.3 73.6 + - - +
284C GLY* 2.8 14.7 + - - -
286C TYR* 3.4 38.8 + + - -
289C ALA* 4.1 9.1 - - + +
293C TYR* 5.2 2.7 - - - +
327C MET* 3.9 45.1 - - + -
328C CYS* 3.9 17.0 - - - -
331C LYS* 4.1 20.6 - - + -
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Residues in contact with LYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C THR* 2.8 23.1 + - + +
279C VAL* 2.8 18.4 + - + +
281C PHE* 1.3 79.1 - - - +
283C GLU* 1.3 76.1 + - - +
284C GLY 3.3 2.8 + - - -
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Residues in contact with GLU 283 (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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279C VAL* 2.9 37.6 + - + +
280C TYR* 4.1 4.6 - - - +
282C LYS* 1.3 90.4 + - - +
284C GLY* 1.3 62.8 + - - +
285C LYS* 3.2 41.8 + - + +
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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
------------------------------------------------------------
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