Contacts of the helix formed by residues 321 - 335 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLN* 1.3 75.7 - - - +
322A ILE* 1.3 63.3 + - - +
323A ASN* 2.8 15.3 + - - -
324A ASP* 3.2 19.4 + - - +
325A LEU* 3.7 9.0 + - - +
423A ASN* 3.6 24.6 - - - +
424A ASN* 3.7 18.4 + - - -
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Residues in contact with ILE 322 (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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306A LEU* 3.9 19.7 - - + +
309A TRP* 3.6 36.8 - - + -
317A GLY 4.6 0.9 - - - +
318A TYR* 5.0 3.8 - - + -
319A VAL 3.2 25.5 + - - +
320A GLN 3.5 0.2 - - - -
321A GLY* 1.3 74.6 - - - +
323A ASN* 1.3 63.2 + - - +
325A LEU* 3.1 23.0 + - + +
326A VAL* 3.7 3.6 + - - +
367A MET* 4.4 5.8 - - + +
371A LEU* 3.9 25.4 - - + -
378A TYR* 3.9 41.4 - - + -
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Residues in contact with ASN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 4.6 5.9 - - - +
284A ILE* 3.5 13.1 - - + +
287A MET* 3.1 51.8 - - - +
302A PHE* 4.5 0.3 - - - -
306A LEU* 3.5 31.3 - - + +
318A TYR* 3.4 19.4 + - - +
320A GLN* 3.9 6.8 - - - +
321A GLY* 2.8 31.4 + - - -
322A ILE* 1.3 77.8 - - - +
324A ASP* 1.3 66.5 + - - +
326A VAL* 3.4 17.7 + - - +
327A THR* 4.1 0.2 + - - -
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 3.7 18.6 - - - +
288A SER 4.3 3.3 - - - +
321A GLY 3.2 12.1 + - - +
323A ASN* 1.3 81.6 + - - +
325A LEU* 1.3 64.3 + - + +
326A VAL 3.1 5.6 - - - -
327A THR* 3.1 11.8 + - - -
328A PRO* 3.3 0.5 - - - +
424A ASN* 2.8 23.6 + - - +
427A MET* 3.1 38.2 - - + +
428A ARG* 2.7 45.8 + - - +
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Residues in contact with LEU 325 (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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321A GLY 3.8 10.5 - - - +
322A ILE* 3.1 13.5 + - + +
324A ASP* 1.3 76.1 - - - +
326A VAL* 1.3 60.8 + - - +
327A THR 3.4 0.2 - - - -
328A PRO* 3.6 5.0 - - - +
329A PHE* 3.4 24.3 - - - -
367A MET* 4.0 12.4 - - + +
370A LEU* 4.1 16.8 - - + -
371A LEU* 4.0 23.6 - - + -
374A ILE* 4.6 1.1 - - + -
378A TYR* 3.8 20.4 - - - +
424A ASN* 4.0 22.7 - - - +
425A LEU* 3.9 25.1 - - + -
427A MET* 4.1 2.7 - - - -
439A TRP* 3.8 18.9 - - + -
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Residues in contact with VAL 326 (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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302A PHE* 3.9 33.9 - - + +
305A ILE* 4.1 14.6 - - + -
306A LEU* 3.7 27.8 - - + -
322A ILE 3.7 0.6 + - - +
323A ASN 3.4 14.6 - - - +
324A ASP 3.1 0.6 - - - -
325A LEU* 1.3 78.3 - - - +
327A THR* 1.3 62.9 + - - +
329A PHE* 3.4 4.0 + - - +
330A PHE* 3.2 16.3 + - + +
363A THR* 3.8 22.7 - - + +
367A MET* 3.4 26.9 - - - -
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Residues in contact with THR 327 (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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287A MET* 3.5 26.9 - - - +
288A SER 4.3 2.7 + - - -
289A PRO* 3.9 18.2 - - + -
292A LEU* 4.2 7.6 - - + -
293A ILE* 5.2 0.4 - - + +
302A PHE* 3.5 14.2 - - + -
324A ASP* 3.1 9.1 + - - -
326A VAL* 1.3 76.8 - - - +
328A PRO* 1.3 66.9 - - - +
330A PHE 3.3 0.2 + - - -
331A VAL* 3.0 30.7 + - + +
427A MET* 4.3 5.8 - - + +
432A LEU* 3.5 28.7 - - + -
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Residues in contact with PRO 328 (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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232A TRP* 4.0 11.2 - - + -
324A ASP 3.3 13.5 - - - +
325A LEU 3.6 11.9 - - - +
327A THR* 1.3 91.6 - - - +
329A PHE* 1.3 61.7 + - - +
332A VAL* 3.0 30.0 + - - +
427A MET* 3.9 2.9 - - + -
432A LEU* 3.9 13.7 - - + -
435A THR* 3.8 19.1 - - + -
436A ILE* 4.3 13.2 - - + -
439A TRP* 3.6 32.5 - - + -
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Residues in contact with PHE 329 (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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232A TRP* 3.7 22.7 - + + -
325A LEU 3.4 20.0 - - - -
326A VAL 3.4 5.7 + - - +
327A THR 3.4 0.4 - - - -
328A PRO* 1.3 76.2 - - - +
330A PHE* 1.3 64.6 + - - +
333A PHE* 2.9 43.7 + + + -
363A THR* 3.9 13.2 - - + -
366A CYS* 3.6 37.2 - - + -
367A MET* 3.7 22.7 - - + -
370A LEU* 3.6 24.5 - - + -
439A TRP* 3.5 21.8 - + - -
443A GLN* 3.8 25.1 - - - -
449A PHE* 5.2 0.7 - + - -
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Residues in contact with PHE 330 (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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292A LEU* 4.2 19.3 - - + -
298A VAL* 4.2 12.3 - - + -
301A ILE* 3.8 38.1 - - + -
302A PHE* 3.8 26.2 - + + -
305A ILE* 5.6 0.2 - - + -
326A VAL 3.2 15.3 + - - +
327A THR 3.9 2.2 - - - +
329A PHE* 1.3 77.9 - - - +
331A VAL* 1.3 67.8 + - + +
333A PHE* 4.1 0.8 - - - +
334A ILE* 2.8 67.2 + - + +
348A VAL* 4.2 8.1 - - + -
356A LEU* 5.1 1.1 - - + -
359A ILE* 4.0 22.4 - - + -
360A GLU 5.6 0.4 - - - -
363A THR* 3.6 18.2 - - + +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.5 35.0 - - + -
327A THR* 3.0 19.6 + - + +
328A PRO 4.3 1.6 - - - +
330A PHE* 1.3 77.5 - - + +
332A VAL* 1.3 65.9 + - - +
334A ILE* 3.5 5.7 - - - +
335A CYS* 3.1 42.5 + - - -
346A VAL* 4.6 12.6 - - + -
432A LEU* 4.0 17.7 - - + -
436A ILE* 4.0 19.1 - - + -
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Residues in contact with VAL 332 (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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228A ARG* 3.8 26.0 - - + +
229A PRO* 3.6 24.4 - - + +
232A TRP* 3.8 30.1 - - + -
328A PRO 3.0 21.5 + - - +
329A PHE 3.9 2.2 - - - +
331A VAL* 1.3 78.9 - - - +
333A PHE* 1.3 76.0 + - + +
335A CYS* 3.3 15.2 + - - +
336A GLU 3.8 0.7 + - - -
436A ILE* 3.8 27.8 - - + -
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Residues in contact with PHE 333 (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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229A PRO* 3.8 31.0 - - + -
232A TRP* 4.4 9.0 - + + -
233A LYS* 3.8 22.2 - - + +
329A PHE* 2.9 40.3 + + + +
332A VAL* 1.3 87.0 - - + +
334A ILE* 1.3 63.1 + - - +
335A CYS 3.3 0.3 + - - -
336A GLU* 3.3 19.3 + - - +
337A TYR* 3.7 11.1 - - - -
359A ILE* 4.0 19.3 - - + -
362A ASP* 3.8 36.6 - - + +
363A THR* 3.6 14.4 - - - -
366A CYS* 3.9 20.4 - - - -
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Residues in contact with ILE 334 (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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330A PHE* 2.8 55.2 + - + +
331A VAL* 3.5 13.0 - - - +
333A PHE* 1.3 71.9 - - - +
335A CYS* 1.3 60.0 + - - +
337A TYR* 3.1 22.7 + - - +
338A ILE* 3.7 13.0 + - + +
346A VAL* 4.0 22.2 - - + -
348A VAL* 3.7 20.0 - - + -
351A VAL* 4.2 12.8 - - + -
356A LEU* 3.5 25.6 - - + -
359A ILE* 3.7 18.5 - - + +
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Residues in contact with CYS 335 (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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225A LYS* 4.9 23.3 - - + +
229A PRO* 5.6 0.4 - - - -
331A VAL* 3.1 31.2 + - - +
332A VAL* 3.5 8.5 - - - +
333A PHE 3.2 0.8 - - - -
334A ILE* 1.3 73.4 - - - +
336A GLU* 1.3 57.5 + - - +
337A TYR 3.1 6.7 + - - -
338A ILE* 3.8 27.5 - - + +
346A VAL* 4.0 27.8 - - - -
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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
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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