Contacts of the helix formed by residues 267 - 288 (chain A) in PDB entry 1QF6
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 HIS 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ASP* 2.9 52.6 + - - +
253A LEU 3.0 7.5 + - - +
254A TYR* 3.7 5.6 - - - -
255A HIS* 2.8 49.9 + + - +
265A PHE* 3.6 8.4 + - + -
266A TRP* 1.3 76.2 - - - +
268A ASN* 1.3 67.4 + - - +
269A ASP 3.3 0.4 - - - +
270A GLY 2.9 3.3 + - - -
271A TRP* 2.9 19.5 + - - +
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TRP 4.0 0.2 + - - -
267A HIS* 1.3 73.0 - - - +
269A ASP* 1.3 76.1 + - - +
271A TRP* 3.2 6.8 + - - +
272A THR* 3.0 32.2 + - - -
275A ARG* 5.3 4.3 + - - +
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU 4.1 10.2 - - - +
252A ASP* 4.1 13.7 + - - +
253A LEU* 4.0 13.7 - - + -
267A HIS* 3.3 1.2 - - - +
268A ASN* 1.3 90.1 - - - +
270A GLY* 1.3 64.0 + - - +
272A THR* 3.3 14.6 + - - -
273A ILE* 3.4 16.8 + - - +
539A PRO* 3.6 28.7 - - + +
540A VAL* 4.6 14.0 - - - +
588A ARG* 4.7 10.0 + - - +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.2 36.7 + - - +
266A TRP* 3.7 18.2 - - - -
267A HIS 2.9 4.6 + - - -
269A ASP* 1.3 77.3 - - - +
271A TRP* 1.3 63.6 + - - +
273A ILE* 3.0 18.8 + - - +
274A PHE* 3.1 12.5 + - - +
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Residues in contact with TRP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TRP* 3.9 33.4 - + + +
267A HIS 2.9 17.7 + - - +
268A ASN* 3.6 7.2 - - - +
270A GLY* 1.3 73.9 - - - +
272A THR* 1.3 59.9 + - - +
274A PHE* 3.3 52.7 - + + -
275A ARG* 2.9 66.1 + - + +
278A GLU* 5.2 4.7 - - - -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 3.0 22.9 + - - -
269A ASP* 3.5 10.5 + - - -
270A GLY 3.1 0.4 - - - -
271A TRP* 1.3 78.0 - - - +
273A ILE* 1.3 64.8 + - - +
275A ARG* 3.5 23.7 + - - +
276A GLU* 3.1 26.8 + - - +
537A LEU 5.2 0.2 - - - +
538A ALA 5.1 0.2 - - - -
539A PRO* 4.0 12.4 + - + +
568A ARG* 3.6 45.9 - - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 4.4 12.1 - - + -
269A ASP 3.5 13.9 - - - +
270A GLY* 3.0 8.0 + - - +
272A THR* 1.3 77.9 - - - +
274A PHE* 1.3 61.6 - - - +
276A GLU* 3.2 6.6 + - - +
277A LEU* 3.1 25.8 + - + +
522A ILE* 4.1 25.1 - - + -
525A LEU* 5.4 2.2 - - + -
533A PHE* 3.6 44.2 - - + -
537A LEU* 3.5 36.1 - - + +
539A PRO* 4.0 12.1 - - + -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TRP* 4.1 13.9 - + + -
270A GLY 3.1 7.7 + - - +
271A TRP* 3.3 46.9 - + + +
273A ILE* 1.3 79.3 - - - +
275A ARG* 1.3 64.4 + - - +
276A GLU 3.0 0.3 + - - -
277A LEU* 3.1 7.3 + - - +
278A GLU* 2.9 41.8 + - + +
358A PHE* 6.2 0.4 - + - -
380A THR* 3.7 20.9 - - + -
518A MET* 3.5 36.6 - - + +
519A GLU* 4.0 17.9 - - - -
522A ILE* 3.8 26.0 - - + +
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 5.3 3.8 + - - +
271A TRP* 2.9 55.8 + - + +
272A THR* 3.8 30.3 + - - +
274A PHE* 1.3 76.9 - - - +
276A GLU* 1.3 60.3 + - - +
278A GLU* 3.2 20.2 - - - +
279A VAL* 3.1 31.2 + - + +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 3.1 19.7 + - - +
273A ILE* 3.2 11.7 - - - +
274A PHE 3.0 0.4 + - - -
275A ARG* 1.3 79.5 + - - +
277A LEU* 1.3 61.4 + - - +
278A GLU 3.0 1.3 - - - -
279A VAL* 3.4 21.5 + - - +
280A PHE* 3.0 25.3 + - - +
536A TRP* 3.2 37.5 - - + +
537A LEU* 3.7 10.1 - - + -
568A ARG* 3.3 26.9 + - - +
635A ARG* 5.1 2.3 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ILE* 3.1 14.1 + - + +
274A PHE 3.1 1.6 + - - +
276A GLU* 1.3 74.3 - - - +
278A GLU* 1.3 60.7 + - - +
280A PHE* 3.5 7.1 - - + +
281A VAL* 2.8 35.8 + - - +
411A PHE* 3.9 33.9 - - + -
515A LEU* 4.7 6.3 - - + -
518A MET* 3.2 26.7 - - + +
521A PHE* 4.3 13.9 - - + -
522A ILE* 3.5 36.6 - - + -
525A LEU* 4.2 12.1 - - + -
536A TRP* 4.4 7.4 - - + -
537A LEU* 4.3 5.6 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TRP* 5.2 4.5 - - - -
274A PHE* 2.9 36.3 + - + +
275A ARG* 3.2 26.1 - - - +
277A LEU* 1.3 79.7 - - - +
279A VAL* 1.3 60.4 + - + +
281A VAL 3.4 0.2 + - - -
282A ARG* 3.1 55.1 + - - +
358A PHE* 3.7 37.7 - - + +
380A THR* 5.8 0.2 - - - +
518A MET* 4.2 2.9 - - + +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ARG* 3.1 16.4 + - + +
276A GLU* 3.6 20.9 - - - +
278A GLU* 1.3 72.5 - - + +
280A PHE* 1.3 72.8 + - - +
282A ARG* 3.1 13.6 + - - +
283A SER* 2.9 24.3 + - - -
635A ARG* 3.7 20.0 - - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU 3.0 10.9 + - - +
277A LEU* 3.2 12.3 + - + +
279A VAL* 1.3 81.8 - - - +
281A VAL* 1.3 72.7 + - + +
283A SER* 2.9 22.8 + - - -
284A LYS* 3.2 20.1 + - + +
407A MET* 3.6 36.3 - - + -
410A THR* 3.5 29.6 - - + -
411A PHE* 3.8 28.9 - + - -
515A LEU* 5.3 2.0 - - + -
536A TRP* 4.0 9.6 - + + -
635A ARG* 3.5 43.5 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU 2.8 24.1 + - - +
278A GLU 3.7 3.1 - - - +
280A PHE* 1.3 79.6 - - + +
282A ARG* 1.3 55.8 + - - +
284A LYS* 2.7 28.2 + - - +
285A LEU* 2.8 29.5 + - + -
358A PHE* 3.6 29.8 - - + -
382A ASP* 4.8 12.3 - - + +
407A MET* 4.7 11.9 - - + -
512A ARG* 5.8 1.3 - - - +
515A LEU* 3.8 31.6 - - + -
518A MET* 4.9 0.7 - - - -
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU* 3.1 45.7 + - - +
279A VAL* 3.4 14.1 - - - +
281A VAL* 1.3 79.6 - - - +
283A SER* 1.3 65.8 + - - +
285A LEU* 2.9 21.4 + - + +
286A LYS* 3.0 12.6 + - - +
292A GLU* 2.6 40.4 + - - +
358A PHE* 3.5 21.6 - - + -
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A VAL 2.9 12.8 + - - -
280A PHE* 2.9 17.4 + - - -
282A ARG* 1.3 76.8 - - - +
284A LYS* 1.3 67.9 + - - +
286A LYS* 3.4 14.8 + - - +
287A GLU* 3.4 15.5 + - - +
635A ARG* 4.0 17.6 + - - -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 3.2 24.4 + - + +
281A VAL 2.7 18.0 + - - +
283A SER* 1.3 78.1 + - - +
285A LEU* 1.3 64.3 + - + -
286A LYS 3.1 2.2 + - - -
287A GLU* 3.2 33.6 + - - +
288A TYR* 3.1 35.9 + - + +
403A LEU* 4.3 4.5 - - + -
406A ASP* 2.7 40.6 + - - -
407A MET* 3.9 35.2 - - + -
410A THR* 5.6 1.1 - - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 2.8 36.4 + - + +
282A ARG* 2.9 15.2 + - + +
284A LYS* 1.3 74.6 - - + +
286A LYS* 1.3 57.2 + - - +
289A GLN 2.9 21.5 + - - -
290A TYR* 2.9 50.9 + - + +
291A GLN 5.9 0.2 - - - -
292A GLU* 4.4 18.8 - - + -
356A ALA* 3.9 24.9 - - + -
357A GLU 6.6 0.2 - - - -
358A PHE* 4.9 6.3 - - + -
403A LEU* 5.4 3.4 - - + -
407A MET* 6.2 1.6 - - + -
512A ARG* 4.1 20.0 - - - +
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ARG 3.0 9.9 + - - +
283A SER* 3.6 13.0 - - - +
284A LYS 3.1 0.2 - - - -
285A LEU* 1.3 76.6 - - - +
287A GLU* 1.3 68.4 + - - +
289A GLN* 3.2 17.7 + - - +
290A TYR 5.1 2.2 - - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER* 3.4 9.4 + - - +
284A LYS* 3.2 39.0 + - - +
286A LYS* 1.3 80.9 - - - +
288A TYR* 1.3 79.7 + - + +
289A GLN* 2.9 14.9 + - - +
406A ASP* 4.3 1.6 - - - +
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS* 3.1 20.4 + - + +
285A LEU 3.7 0.9 - - - -
287A GLU* 1.3 97.7 + - + +
289A GLN* 1.3 69.3 + - - +
290A TYR* 3.5 26.8 - + + -
354A ARG* 3.7 12.8 + - - -
399A GLY* 3.9 12.3 - - - -
402A ARG* 4.1 19.9 + - + +
403A LEU* 3.4 49.2 - - + -
406A ASP* 2.6 31.9 + - - +
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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
------------------------------------------------------------
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