Contacts of the helix formed by residues 266 - 286 (chain B) in PDB entry 1Q8Z
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 PRO 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TYR* 3.3 41.7 - - + +
264B GLY 4.0 0.9 - - - +
265B ILE* 1.3 93.6 - - + +
267B LEU* 1.3 66.7 + - - +
268B ILE* 4.3 10.3 - - + -
269B TYR* 2.9 31.8 + - + +
270B VAL 3.2 6.6 + - - -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE 3.2 10.0 + - - +
266B PRO* 1.3 68.0 - - - +
268B ILE* 1.3 66.3 + - + +
270B VAL* 4.2 6.5 - - + -
271B LYS* 2.9 40.8 + - - +
598B ILE* 4.2 27.4 - - + +
671B PHE* 4.7 10.5 - - + -
675B GLU* 3.8 22.0 - - - +
679B ILE* 5.1 1.1 - - + -
705B TRP* 4.0 34.1 - - + +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PRO* 4.3 9.0 - - + -
267B LEU* 1.3 78.1 - - + +
269B TYR* 1.3 92.9 + - + +
271B LYS* 4.6 5.5 - - - +
272B GLN* 3.0 28.0 + - - +
542B ASN* 4.3 21.5 - - + +
710B LEU* 3.8 27.6 + - + +
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Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 4.9 8.3 - - + -
260B TYR* 3.8 21.9 + + - -
265B ILE* 3.9 11.7 - - + -
266B PRO* 2.9 33.6 + - + +
268B ILE* 1.3 89.5 - - + +
270B VAL* 1.3 65.4 + - - +
271B LYS 3.3 0.2 - - - -
272B GLN* 3.3 4.9 + - - +
273B ILE* 3.0 28.3 + - - +
304B ILE* 6.1 3.1 - - + +
542B ASN* 3.1 47.2 + - + -
544B ILE* 3.7 32.9 - - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 3.5 40.8 - - + +
266B PRO 3.2 3.3 + - - +
267B LEU* 3.1 14.0 + - + +
269B TYR* 1.3 76.6 - - - +
271B LYS* 1.3 52.4 + - - +
273B ILE* 3.1 10.2 + - + +
274B SER* 2.7 50.5 + - - +
594B ILE* 4.3 3.1 - - + -
597B LEU* 3.9 27.4 - - + +
598B ILE* 3.9 22.0 - - + +
705B TRP* 4.1 9.9 - - + -
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 2.9 29.7 + - - +
268B ILE* 4.6 5.4 - - - +
270B VAL* 1.3 76.8 - - - +
272B GLN* 1.3 57.1 + - - +
274B SER* 3.3 2.3 + - - -
275B LYS* 2.8 32.2 + - - +
705B TRP* 2.9 68.1 + - + +
706B LEU* 3.9 8.4 - - + +
708B ASP* 2.7 35.9 + - - +
709B THR* 3.5 23.7 + - + +
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ILE 3.0 20.8 + - - +
269B TYR* 3.3 8.8 + - - +
270B VAL 3.2 0.8 - - - -
271B LYS* 1.3 78.0 - - - +
273B ILE* 1.3 65.0 + - - +
275B LYS* 3.3 0.7 + - - +
276B GLN* 3.0 41.6 + - - +
542B ASN 2.9 18.9 - - - +
543B LEU* 3.2 17.7 - - - +
544B ILE* 2.8 48.1 + - + +
709B THR* 3.5 11.9 - - + -
710B LEU* 3.6 28.8 + - - +
712B MET* 4.7 0.2 - - - -
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.9 26.5 - - + -
256B LEU* 3.6 31.0 - - + -
265B ILE* 5.2 1.3 - - + -
269B TYR* 3.0 22.4 + - + +
270B VAL* 3.4 8.3 - - - +
272B GLN* 1.3 75.0 - - - +
274B SER* 1.3 60.1 + - - +
276B GLN 4.0 0.2 - - - -
277B LEU* 3.0 33.0 + - + +
300B VAL* 4.9 3.6 - - + -
302B MET* 4.9 0.7 - - - -
544B ILE* 4.0 10.5 - - + +
546B ILE* 4.0 29.1 - - + +
593B LEU* 6.0 0.9 - - + -
597B LEU* 3.6 31.2 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 2.7 32.3 + - - +
271B LYS* 3.6 4.3 - - - -
273B ILE* 1.3 73.4 - - - +
275B LYS* 1.3 61.1 + - - +
277B LEU* 3.1 6.0 + - - +
278B LEU* 2.9 36.6 + - - +
594B ILE* 3.4 37.6 - - - +
597B LEU* 5.0 1.0 - - - +
682B PHE* 4.6 5.2 - - - -
705B TRP* 4.5 1.4 - - - -
706B LEU* 4.2 13.9 - - - -
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS 2.8 19.7 + - - +
272B GLN 4.0 2.9 - - - +
274B SER* 1.3 73.8 - - - +
276B GLN* 1.3 57.6 + - - +
278B LEU* 3.9 3.4 - - - +
279B LEU* 3.0 33.4 + - + +
701B VAL* 3.6 30.6 + - + +
706B LEU* 3.0 44.1 + - + +
707B LYS* 4.6 0.8 - - - +
709B THR* 3.7 13.0 - - + +
712B MET* 2.8 44.5 + - + +
713B GLU 3.5 7.1 + - - -
715B ILE* 3.0 29.8 + - - -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B HIS* 3.1 41.1 + - + +
272B GLN* 3.0 31.8 + - - +
275B LYS* 1.3 73.7 - - - +
277B LEU* 1.3 56.7 + - - +
279B LEU* 3.1 7.0 + - - +
280B GLY* 2.7 32.9 + - - -
544B ILE* 3.1 21.3 + - - -
545B GLN* 3.2 8.5 + - - +
546B ILE* 2.9 43.1 + - + +
712B MET* 3.6 26.5 - - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.0 24.5 + - + +
274B SER* 3.4 5.2 - - - +
276B GLN* 1.3 76.3 - - - +
278B LEU* 1.3 57.9 + - - +
280B GLY* 3.0 2.4 + - - -
281B LEU* 2.8 38.9 + - + +
295B ILE* 4.5 9.2 - - + -
300B VAL* 4.8 12.6 - - + -
546B ILE* 3.7 9.1 - - + +
548B ILE* 3.6 29.2 - - + -
590B THR* 3.5 34.5 - - + +
593B LEU* 4.1 23.6 - - + -
594B ILE* 5.4 3.8 - - + -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER* 2.9 17.9 + - - +
275B LYS 3.9 1.1 - - - +
277B LEU* 1.3 76.3 - - - +
279B LEU* 1.3 63.6 + - - +
281B LEU* 3.2 2.9 + - + -
282B ASP* 2.9 23.9 + - - +
587B ILE* 5.5 2.0 - - + -
590B THR* 4.0 25.6 - - + -
594B ILE* 5.5 0.2 - - + -
682B PHE* 3.9 14.4 - - + -
686B MET* 4.3 12.6 - - + -
697B ALA* 3.4 30.6 - - + +
700B LEU* 3.8 23.3 - - + +
701B VAL* 3.6 14.8 - - + +
706B LEU* 3.7 31.0 - - + -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B MET* 3.8 36.8 - - + +
221B GLY* 3.5 12.7 - - - -
224B HIS* 4.5 3.6 - - + +
275B LYS* 3.0 21.6 + - + +
276B GLN* 3.4 7.4 - - - +
278B LEU* 1.3 78.2 - - - +
280B GLY* 1.3 64.0 + - - +
282B ASP* 3.5 5.5 + - + +
283B TYR 3.3 13.0 + - - -
701B VAL* 4.2 11.9 - - + -
712B MET* 3.3 33.2 - - + -
715B ILE* 4.1 16.4 - - + -
716B ARG 5.0 2.5 - - - +
717B VAL* 4.2 24.2 - - + -
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Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLY 3.7 18.1 + - - -
224B HIS* 4.2 6.5 - - - +
225B ILE* 4.0 3.1 - - - +
276B GLN 2.7 18.5 + - - -
277B LEU 3.0 3.1 + - - -
279B LEU* 1.3 73.6 - - - +
281B LEU* 1.3 62.4 + - - +
283B TYR* 3.2 7.1 + - - +
284B MET* 3.1 22.0 + - - +
548B ILE* 3.9 15.5 - - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 2.8 36.6 + - + +
278B LEU* 4.8 0.9 - - + -
280B GLY* 1.3 70.7 - - - +
282B ASP* 1.3 60.7 + - - +
284B MET* 2.9 13.1 + - - +
285B HIS* 2.8 42.2 + - + +
292B HIS* 5.0 0.2 - - + -
295B ILE* 4.3 13.2 - - + -
548B ILE* 4.1 11.7 - - + -
586B ASP* 4.1 28.9 - - + +
587B ILE* 4.6 10.8 - - + -
590B THR* 3.1 31.0 - - + +
697B ALA* 3.7 15.5 - - + -
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 4.9 3.3 - - - +
278B LEU 2.9 17.2 + - - +
279B LEU* 3.8 6.9 - - + +
281B LEU* 1.3 77.0 - - - +
283B TYR* 1.3 64.0 + - - +
285B HIS* 4.9 3.6 - - - -
286B ARG* 2.8 73.4 + - - +
287B ARG* 5.2 1.7 - - - -
696B ASP* 4.3 1.0 - - - +
697B ALA* 3.8 5.5 - - - +
698B GLY* 3.2 32.1 + - - +
717B VAL* 4.3 7.3 - - + +
729B ILE* 5.4 0.3 - - - +
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Residues in contact with TYR 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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209B VAL* 2.5 30.1 + - + -
212B ALA* 3.0 18.9 - - + +
213B ASP* 3.0 19.8 + - - -
218B ASP* 3.5 28.3 - - + -
221B GLY* 3.8 8.5 - - - -
222B ALA* 3.8 22.0 - - + -
225B ILE* 3.5 24.7 - - + -
279B LEU 3.3 9.4 + - - +
280B GLY 3.2 8.7 + - - +
281B LEU 3.1 0.8 - - - -
282B ASP* 1.3 83.0 + - - +
284B MET* 1.3 62.6 + - - +
287B ARG* 3.2 28.0 + - + +
288B CYS* 3.0 40.9 + - - +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 4.9 6.1 - - + -
225B ILE* 3.5 30.7 - - + -
280B GLY 3.1 4.7 + - - +
281B LEU* 2.9 15.5 + - - +
283B TYR* 1.3 80.6 - - - +
285B HIS* 1.3 59.0 + - - +
288B CYS* 3.2 8.7 - - - +
289B GLY 2.8 25.1 + - - -
290B ILE* 2.8 48.3 + - + +
292B HIS* 3.5 33.0 - - + +
548B ILE* 4.4 21.1 - - - -
551B LEU* 3.9 18.6 - - + -
586B ASP* 5.0 1.1 - - - +
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Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 2.8 33.4 + - + +
282B ASP* 4.3 2.7 - - - +
284B MET* 1.3 73.1 - - + +
286B ARG* 1.3 63.9 + - + +
289B GLY* 3.2 18.2 + - - -
290B ILE 3.2 16.2 + - - +
291B ILE* 4.4 0.7 - - - -
292B HIS 4.8 0.2 - - - -
583B CYS* 3.3 42.1 + - + +
586B ASP* 2.8 38.2 + - + +
587B ILE* 4.2 11.1 - - + +
696B ASP* 6.0 0.2 - - + -
697B ALA* 5.3 2.5 - - + -
729B ILE* 4.2 15.6 - - + +
730B PRO* 5.2 1.6 - - - +
732B TRP* 3.6 31.0 - + + -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 3.2 11.1 + - - -
282B ASP* 2.8 56.4 + - - +
285B HIS* 1.3 80.3 - - + +
287B ARG* 1.3 100.3 + - - +
288B CYS 3.5 0.3 + - - -
289B GLY* 4.1 2.4 + - - -
717B VAL* 3.4 5.7 - - - +
719B ASP* 2.9 35.2 + - - -
720B ARG* 3.2 37.4 - - - +
729B ILE* 3.7 33.7 - - + -
730B PRO* 6.0 1.7 - - - +
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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
------------------------------------------------------------
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