Contacts of the helix formed by residues 295 - 313 (chain B) in PDB entry 2QFZ
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 GLN 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ALA* 3.2 21.8 + - - +
292B LEU* 3.1 17.6 + - - +
293B ILE 3.5 1.9 - - - +
294B LEU* 1.3 75.7 - - + +
296B PRO* 1.3 67.4 - - + +
297B LYS* 3.3 2.0 - - + +
298B VAL* 2.8 35.5 + - + +
299B THR* 3.4 5.2 + - - -
346B VAL 3.2 23.6 + - - -
347B ASP* 3.8 12.3 + - - +
348B VAL* 2.9 38.3 + - + +
349B SER* 4.4 1.0 + - - -
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Residues in contact with PRO 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU 3.6 6.5 - - - +
295B GLN* 1.3 86.2 - - + +
297B LYS* 1.3 66.9 + - + +
299B THR* 3.8 7.2 + - - +
300B GLU* 3.6 19.9 + - - +
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLN* 3.3 1.1 - - + -
296B PRO* 1.3 83.3 - - + +
298B VAL* 1.3 60.0 + - + +
300B GLU* 3.4 7.5 + - - +
301B ILE* 3.0 36.1 + - + +
348B VAL* 4.6 15.9 - - + -
356B LEU* 5.1 11.9 - - + -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.5 29.8 - - + +
293B ILE* 4.1 13.9 - - + +
295B GLN* 2.8 18.9 + - + +
297B LYS* 1.3 74.3 - - - +
299B THR* 1.3 63.8 + - - +
301B ILE* 3.2 7.2 + - - +
302B PHE* 3.0 54.1 + - + -
330B PHE* 4.0 11.2 - - + -
348B VAL* 3.4 37.0 - - + -
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B HIS* 6.1 0.4 - - + -
284B ILE* 3.6 21.1 - - + -
285B PRO* 4.2 17.1 - - + +
293B ILE* 2.7 29.6 + - - +
294B LEU* 4.9 0.9 - - - -
295B GLN 3.4 4.7 + - - -
296B PRO* 4.2 8.8 - - - +
297B LYS 3.4 0.2 - - - -
298B VAL* 1.3 78.3 - - - +
300B GLU* 1.3 57.4 + - - +
302B PHE* 3.3 2.1 + - - +
303B GLU* 3.0 55.9 + - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 5.1 1.0 + - - -
296B PRO 3.6 11.5 + - - +
297B LYS* 3.4 11.2 + - - +
298B VAL 3.3 0.2 - - - -
299B THR* 1.3 80.1 - - - +
301B ILE* 1.3 63.6 + - + +
303B GLU* 3.5 10.3 + - - +
304B ARG* 3.1 48.7 + - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LYS* 3.0 26.9 + - + +
298B VAL* 3.2 4.9 + - - +
300B GLU* 1.3 75.0 - - + +
302B PHE* 1.3 67.2 + - + +
304B ARG* 3.2 14.8 + - - +
305B ILE* 3.0 43.3 + - + +
330B PHE* 3.8 36.8 - - + -
348B VAL* 5.7 0.7 - - + -
356B LEU* 3.9 33.9 - - + +
360B GLU* 3.8 23.7 - - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 3.8 15.9 - - + -
287B MET* 4.0 12.6 - - + -
292B LEU* 4.9 2.0 - - + -
293B ILE* 3.5 28.3 - - + -
298B VAL* 3.0 36.2 + - + +
299B THR 3.7 3.6 - - - +
301B ILE* 1.3 82.4 - - + +
303B GLU* 1.3 61.6 + - - +
305B ILE* 3.9 4.7 - - - +
306B LEU* 3.1 32.8 + - + +
323B ASN 4.7 0.7 - - - -
326B VAL* 3.9 31.0 - - + -
327B THR* 3.5 37.5 - - + -
330B PHE* 3.7 29.6 - + - -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 4.4 5.7 + - - +
277B TYR* 3.4 27.7 + - + -
280B ILE* 3.8 19.3 - - + +
281B HIS* 3.0 35.6 + - - +
284B ILE* 3.7 19.6 - - + +
285B PRO* 4.4 0.5 - - - +
299B THR* 3.0 40.7 + - - +
300B GLU* 4.1 8.8 - - - +
302B PHE* 1.3 76.5 - - - +
304B ARG* 1.3 57.6 + - - +
306B LEU* 4.2 0.3 - - - +
307B PHE* 2.9 32.1 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 4.0 0.7 - - - -
261B ILE* 3.9 32.1 - - - +
265B TYR* 4.0 36.0 + - + -
300B GLU* 3.1 41.8 + - - +
301B ILE* 3.7 17.4 - - - +
303B GLU* 1.3 74.5 - - - +
305B ILE* 1.3 65.8 + - - +
307B PHE* 3.3 0.7 + - - +
308B ILE* 2.9 42.9 + - + +
357B CYS* 5.9 3.6 - - - -
360B GLU* 2.9 39.2 + - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.7 9.4 - - + +
301B ILE* 3.0 38.0 + - + +
302B PHE* 3.9 3.8 - - - +
304B ARG* 1.3 74.3 - - - +
306B LEU* 1.3 60.1 + - - +
308B ILE* 3.9 0.2 - - - -
309B TRP* 2.9 27.7 + - - +
326B VAL* 4.0 15.5 - - + -
330B PHE* 5.4 0.7 - - + -
360B GLU* 3.7 29.2 - - + +
363B THR* 3.8 26.9 - - + -
364B TYR* 3.8 22.6 - - + -
367B MET* 3.9 28.7 - - + -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 4.0 16.1 - - + +
284B ILE* 3.7 15.9 - - + -
302B PHE* 3.1 21.1 + - + +
303B GLU 4.2 2.0 - - - +
305B ILE* 1.3 77.0 - - - +
307B PHE* 1.3 66.7 + - - +
309B TRP* 3.4 4.9 + - + +
310B ALA* 2.9 26.2 + - - +
318B TYR* 4.4 11.7 - - + -
322B ILE* 3.7 32.8 - - + +
323B ASN* 3.5 32.1 - - + +
326B VAL* 3.7 25.1 - - + -
367B MET* 4.3 6.5 - - + -
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 4.7 9.6 - - + -
265B TYR* 3.5 35.9 - + + +
273B HIS* 3.6 39.7 - + + -
276B THR* 4.1 17.0 - - + -
277B TYR* 4.2 17.5 - + + -
280B ILE* 3.6 12.3 - - + +
303B GLU 2.9 21.3 + - - +
304B ARG 3.8 2.9 - - - +
306B LEU* 1.3 78.7 - - - +
308B ILE* 1.3 61.5 + - - +
310B ALA* 3.3 2.1 + - - +
311B ILE* 3.2 61.2 + - + +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.6 30.1 - - + +
260B PHE* 3.8 35.4 - - + +
261B ILE* 3.9 29.6 - - + +
264B TYR* 5.0 2.0 - - + -
265B TYR* 4.4 14.4 - - + -
304B ARG* 2.9 23.1 + - + +
305B ILE 4.0 2.7 - - - +
307B PHE* 1.3 72.3 - - - +
309B TRP* 1.3 67.0 + - - +
311B ILE* 3.3 17.0 - - + +
312B ARG* 3.2 26.1 + - + +
364B TYR* 3.8 13.5 - - + +
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Residues in contact with TRP 309 (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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305B ILE 2.9 17.8 + - - +
306B LEU* 3.7 7.4 - - + +
307B PHE 3.3 0.2 - - - -
308B ILE* 1.3 77.8 - - - +
310B ALA* 1.3 66.3 + - - +
313B HIS* 2.9 68.9 + + + -
316B SER* 3.9 23.6 - - - -
317B GLY 3.3 24.7 - - - -
318B TYR* 5.6 0.7 - - - -
322B ILE* 3.6 25.1 - - + -
364B TYR* 3.7 13.3 - + + -
367B MET* 3.9 19.7 - - + -
368B SER* 3.6 25.6 + - - +
371B LEU* 3.6 35.1 - - + +
378B TYR* 5.2 3.6 - + + -
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Residues in contact with ALA 310 (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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276B THR* 3.8 21.5 - - + +
306B LEU 2.9 17.3 + - - +
307B PHE 3.6 4.5 - - - +
309B TRP* 1.3 85.9 - - + +
311B ILE* 1.3 62.1 + - + +
313B HIS 3.3 20.6 + - - +
314B PRO* 3.9 2.6 - - - +
317B GLY* 3.7 10.9 - - - -
318B TYR* 3.6 28.0 - - + +
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Residues in contact with ILE 311 (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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264B TYR* 3.1 57.1 - - + -
273B HIS* 3.7 31.3 + - + +
276B THR* 5.4 1.1 - - + -
307B PHE* 3.3 42.4 - - + +
308B ILE* 3.3 21.5 - - + +
310B ALA* 1.3 78.7 - - + +
312B ARG* 1.3 65.9 + - + +
313B HIS 3.4 0.9 + - - -
314B PRO* 3.8 14.2 - - - +
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Residues in contact with ARG 312 (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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260B PHE* 3.3 53.5 - - - -
263B HIS* 6.1 0.2 - - - -
264B TYR* 2.9 51.1 + - + +
308B ILE* 3.2 15.2 + - - +
309B TRP 4.0 1.8 - - - +
311B ILE* 1.3 75.6 - - + +
313B HIS* 1.3 74.2 + - + +
314B PRO* 3.5 8.2 - - - +
364B TYR* 3.8 10.7 + - - +
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Residues in contact with HIS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 2.9 80.3 + + + +
310B ALA 3.3 3.5 - - - +
311B ILE 3.3 0.2 - - - -
312B ARG* 1.3 88.1 + - + +
314B PRO* 1.4 59.4 - - - +
315B ALA* 3.3 3.4 - - - -
316B SER* 3.0 8.9 + - - +
317B GLY 3.0 24.1 + - - -
364B TYR* 4.0 13.7 - - - -
368B SER* 4.8 5.8 - - - -
372B ASP* 4.8 13.3 + - - -
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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