Contacts of the helix formed by residues 321 - 336 (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 GLY 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLN* 1.3 75.1 - - - +
322B ILE* 1.3 63.0 + - - +
323B ASN* 2.7 13.6 + - - -
324B ASP* 3.1 19.9 + - - +
325B LEU* 3.6 10.3 + - - +
423B ASN* 3.6 16.5 - - - +
424B ASN* 3.3 26.5 + - - +
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.7 21.5 - - + +
309B TRP* 3.6 33.2 - - + -
317B GLY 4.0 2.7 - - - +
318B TYR* 4.8 3.8 - - + -
319B VAL* 3.1 31.2 + - + +
321B GLY* 1.3 74.8 - - - +
323B ASN* 1.3 64.5 + - - +
325B LEU* 3.1 22.8 + - + +
326B VAL* 3.8 3.1 + - - +
367B MET* 4.3 4.4 - - + +
371B LEU* 3.9 26.0 - - + -
378B TYR* 3.9 39.3 - - + -
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Residues in contact with ASN 323 (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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283B ASP* 4.5 10.5 + - - +
284B ILE* 3.8 12.3 - - + -
287B MET* 3.7 38.5 - - - +
302B PHE* 4.7 0.2 - - - -
306B LEU* 3.5 27.4 - - + +
318B TYR* 3.4 20.8 + - - +
320B GLN* 3.8 5.5 - - - +
321B GLY* 2.7 33.2 + - - +
322B ILE* 1.3 77.9 - - - +
324B ASP* 1.3 68.4 + - - +
326B VAL* 3.1 22.2 + - - +
424B ASN* 5.2 0.6 + - - +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B MET* 3.8 19.9 - - - +
288B SER 4.3 0.9 - - - +
321B GLY 3.1 12.6 + - - +
323B ASN* 1.3 86.2 + - - +
325B LEU* 1.3 62.1 + - + +
326B VAL 3.3 1.0 + - - -
327B THR* 3.3 9.9 + - - -
328B PRO* 3.4 0.2 - - - +
424B ASN* 2.9 25.2 + - + +
427B MET* 3.0 41.7 - - + +
428B ARG* 2.8 46.0 + - - +
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Residues in contact with LEU 325 (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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321B GLY 3.7 14.1 - - - +
322B ILE* 3.1 14.4 + - + +
324B ASP* 1.3 77.2 - - + +
326B VAL* 1.3 61.8 + - - +
327B THR 3.5 0.2 + - - -
328B PRO* 3.5 5.5 - - - +
329B PHE* 3.4 23.4 - - - -
367B MET* 4.1 11.8 - - + +
370B LEU* 4.2 15.7 - - + -
371B LEU* 3.7 30.7 - - + -
374B ILE* 4.6 0.2 - - + -
378B TYR* 3.9 16.4 - - + +
424B ASN 4.3 14.1 - - - +
425B LEU* 3.7 29.2 - - + -
427B MET* 4.3 0.7 - - - -
439B TRP* 3.9 18.8 - - + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.9 30.7 - - + -
305B ILE* 4.0 18.8 - - + -
306B LEU* 3.7 26.7 - - + -
322B ILE 4.0 0.4 - - - +
323B ASN 3.1 16.1 + - - +
325B LEU* 1.3 77.5 - - - +
327B THR* 1.3 63.3 + - - +
329B PHE* 3.2 8.8 + - - +
330B PHE* 3.2 18.1 + - + -
363B THR* 3.9 19.7 - - + -
367B MET* 3.5 25.8 - - - -
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B MET* 3.4 28.2 - - - +
288B SER 4.5 2.0 + - - +
289B PRO* 4.1 17.9 - - + -
292B LEU* 4.2 7.0 - - + -
293B ILE* 5.8 0.2 - - + -
302B PHE* 3.5 16.6 - - + -
324B ASP* 3.3 7.1 + - - -
326B VAL* 1.3 77.1 - - - +
328B PRO* 1.3 65.7 - - - +
330B PHE* 4.0 0.4 - - - -
331B VAL* 2.9 42.1 + - + +
427B MET* 4.4 6.2 - - + +
432B LEU* 3.8 25.4 - - + -
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Residues in contact with PRO 328 (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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232B TRP* 4.1 4.9 - - + -
324B ASP 3.4 13.5 - - - +
325B LEU 3.5 11.4 - - - +
327B THR* 1.3 91.4 - - - +
329B PHE* 1.3 60.4 + - - +
331B VAL* 4.0 1.5 - - + -
332B VAL* 3.0 30.5 + - - +
427B MET* 4.0 7.0 - - + -
432B LEU* 4.0 9.4 - - + -
435B THR* 3.7 19.1 - - + -
436B ILE* 4.1 19.1 - - + -
439B TRP* 3.6 32.8 - - + -
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.7 28.3 - + + -
236B SER* 5.8 0.2 - - - -
325B LEU 3.4 20.0 - - - -
326B VAL 3.2 5.7 + - - +
328B PRO* 1.3 77.2 - - - +
330B PHE* 1.3 57.7 + - - +
332B VAL* 3.8 0.6 - - - -
333B PHE* 2.8 45.4 + + + -
363B THR* 3.8 16.6 - - + -
366B CYS* 3.5 40.4 - - + -
367B MET* 3.6 25.6 - - + -
370B LEU* 3.7 18.6 - - + -
439B TRP* 3.7 21.5 - + - -
443B GLN* 3.8 20.0 - - - -
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.2 13.9 - - + -
298B VAL* 4.0 22.9 - - + -
301B ILE* 3.8 39.5 - - + -
302B PHE* 3.7 27.1 - + + -
326B VAL 3.2 12.2 + - - +
327B THR 4.0 2.9 - - - +
329B PHE* 1.3 78.8 - - - +
331B VAL* 1.3 67.2 + - + +
333B PHE* 3.9 1.4 - - - +
334B ILE* 2.8 54.9 + - + +
348B VAL* 4.3 13.0 - - + -
356B LEU* 4.5 1.8 - - + -
359B ILE* 4.0 23.7 - - + +
360B GLU 5.6 0.4 - - - -
363B THR* 3.7 19.9 + - + +
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Residues in contact with VAL 331 (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 33.4 - - + -
327B THR* 2.9 23.2 + - + +
328B PRO* 4.2 3.4 - - + +
330B PHE* 1.3 76.9 - - + +
332B VAL* 1.3 63.4 + - - +
334B ILE* 3.3 8.8 - - + +
335B CYS* 3.1 42.6 + - - -
346B VAL* 5.2 9.2 - - + -
432B LEU* 3.7 19.7 - - + -
436B ILE* 4.2 17.9 - - + -
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Residues in contact with VAL 332 (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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228B ARG* 3.9 29.4 - - + +
229B PRO* 3.5 25.4 - - + +
232B TRP* 3.9 13.9 - - + -
328B PRO 3.0 21.9 + - - +
329B PHE 3.8 2.0 - - - +
331B VAL* 1.3 78.3 - - - +
333B PHE* 1.3 76.4 + - + +
335B CYS* 3.5 13.6 + - - +
336B GLU 3.9 0.5 + - - -
436B ILE* 3.8 38.8 - - + -
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Residues in contact with PHE 333 (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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229B PRO* 3.7 33.2 - - + -
232B TRP* 4.5 9.2 - + + -
233B LYS* 3.8 20.2 - - + +
329B PHE* 2.8 33.3 + + + +
332B VAL* 1.3 86.3 - - + +
334B ILE* 1.3 62.0 - - - +
335B CYS 3.5 0.5 + - - -
336B GLU* 3.6 19.0 - - - +
337B TYR* 3.6 12.0 - - - -
359B ILE* 3.9 20.9 - - + -
362B ASP* 3.7 36.8 - - + +
363B THR* 3.7 17.7 - - - -
366B CYS* 3.8 22.4 - - + -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 5.8 1.3 - - + -
330B PHE* 2.8 42.3 + - + +
331B VAL* 3.3 20.2 - - + +
333B PHE* 1.3 70.9 - - - +
335B CYS* 1.3 65.8 + - - +
337B TYR* 3.0 22.1 + - + +
338B ILE* 3.6 30.8 + - + +
346B VAL* 5.0 5.6 - - + -
348B VAL* 4.7 12.8 - - + -
351B VAL* 4.2 13.5 - - + -
356B LEU* 3.4 33.0 - - + -
359B ILE* 3.8 16.9 - - + +
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Residues in contact with CYS 335 (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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225B LYS* 5.3 23.6 - - + -
331B VAL* 3.1 38.1 + - - +
332B VAL* 3.9 7.6 - - - +
333B PHE 3.3 0.8 - - - -
334B ILE* 1.3 80.7 - - - +
336B GLU* 1.3 61.1 + - - +
337B TYR 3.0 1.7 + - - -
338B ILE* 3.3 33.4 - - - +
346B VAL* 4.8 7.4 - - - -
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Residues in contact with GLU 336 (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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226B PRO 4.4 9.7 - - - +
229B PRO* 3.4 37.4 - - + +
230B MET* 5.1 4.5 + - - +
233B LYS* 5.3 5.2 + - - -
332B VAL 3.9 2.4 + - - -
333B PHE* 3.6 14.8 + - - +
334B ILE 3.1 0.4 + - - -
335B CYS* 1.3 75.8 - - - +
337B TYR* 1.3 80.7 + - + +
338B ILE 3.7 0.7 - - - -
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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
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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