Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 4ZZH
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A PHE* 3.4 44.9 - - + +
303A ARG 4.5 3.4 - - - +
304A LYS 4.2 3.6 - - - +
305A ASP* 1.3 86.5 - - - +
307A ARG* 1.3 68.1 + - + +
308A PRO* 3.3 2.2 - - - -
309A PHE* 3.2 7.6 + - + +
310A PHE* 3.2 30.8 + - + -
392A VAL* 4.4 13.2 - - + -
406A ILE* 3.6 25.1 - - + -
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Residues in contact with ARG 307 (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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286A ASP 5.8 0.2 + - - -
287A PHE* 3.4 34.2 - - + -
305A ASP* 3.1 31.3 + - - +
306A PRO* 1.3 82.3 - - + +
308A PRO* 1.4 64.3 - - + +
310A PHE* 3.3 8.1 + - - +
311A LYS* 3.2 21.5 + - - +
390A GLN* 4.4 5.4 + - - +
392A VAL* 4.2 19.3 - - + -
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Residues in contact with PRO 308 (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 LEU* 4.1 11.3 - - + +
287A PHE* 4.2 29.4 - - + -
290A LEU* 4.2 19.7 - - + -
296A MET* 5.2 4.7 - - + -
301A TYR* 4.1 21.5 - - + +
305A ASP* 3.5 33.9 - - - +
306A PRO 3.4 2.5 - - - -
307A ARG* 1.4 90.3 - - + +
309A PHE* 1.3 62.5 + - + +
311A LYS* 3.2 5.6 + - - +
312A PHE* 3.2 19.4 + - - +
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Residues in contact with PHE 309 (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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296A MET* 3.4 36.6 - - + +
297A PHE* 4.5 6.1 - + - -
302A PHE* 3.8 26.0 - + + -
305A ASP 5.7 0.2 - - - +
306A PRO 3.2 8.2 + - - +
308A PRO* 1.3 81.8 - - + +
310A PHE* 1.3 61.0 + + - +
312A PHE* 3.1 28.9 + + - +
313A ALA* 2.7 41.4 + - + +
366A PHE* 4.4 17.0 - + - -
409A PRO* 4.1 26.5 - - + -
411A ILE* 4.4 11.2 - - + -
413A PHE* 3.4 28.0 - + - -
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Residues in contact with PHE 310 (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* 3.7 26.9 - + - -
306A PRO* 3.2 29.0 + - + -
307A ARG* 3.8 8.5 - - - +
308A PRO 3.2 1.0 - - - -
309A PHE* 1.3 83.0 - + - +
311A LYS* 1.3 60.6 + - - +
313A ALA* 3.7 4.0 - - + -
314A LYS* 3.1 24.1 + - - +
387A ILE* 3.6 41.7 - - + +
390A GLN* 3.8 10.9 - - - +
391A VAL 5.7 2.5 - - - +
392A VAL* 4.1 13.5 - - + -
393A PRO* 3.6 28.3 - - + -
406A ILE* 4.1 8.7 - - + -
407A MET 3.5 22.2 - - - -
409A PRO* 4.1 12.1 - - + -
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Residues in contact with LYS 311 (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 ILE* 5.3 0.2 - - - -
282A ARG* 4.4 8.1 + - - +
283A LEU* 4.1 19.8 - - + +
286A ASP* 3.8 20.4 + - - -
287A PHE* 4.1 20.4 - - + -
307A ARG 3.2 8.7 + - - +
308A PRO* 3.2 10.8 + - + +
310A PHE* 1.3 75.0 - - - +
312A PHE* 1.3 64.7 + - - +
314A LYS* 3.4 5.6 + - + +
315A GLU* 3.4 36.8 + - + +
390A GLN* 3.6 30.5 - - + +
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Residues in contact with PHE 312 (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 PRO 5.3 0.2 - - - -
273A PHE* 3.8 31.4 - + + -
279A ILE* 3.5 37.2 - - + -
283A LEU* 4.4 2.6 - - + +
296A MET* 4.1 14.6 - - - -
297A PHE* 3.8 28.7 - + - -
308A PRO 3.2 11.1 + - - +
309A PHE* 3.1 25.3 + + - +
311A LYS* 1.3 72.9 - - - +
313A ALA* 1.3 68.3 + - - +
314A LYS 3.0 4.5 - - - -
315A GLU* 2.9 18.9 + - - +
316A ILE* 3.3 41.9 - - + +
347A ILE* 4.9 6.7 - - + -
366A PHE* 4.0 22.0 - + - -
411A ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 313 (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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309A PHE* 2.7 28.3 + - + +
310A PHE* 3.8 15.5 - - + +
311A LYS 3.4 0.2 - - - -
312A PHE* 1.3 76.5 - - + +
314A LYS* 1.3 57.1 + - - +
316A ILE* 4.0 0.9 - - - -
317A TYR* 3.1 34.0 + - - -
366A PHE* 3.5 30.6 - - + -
387A ILE* 4.1 13.2 - - + -
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Residues in contact with LYS 314 (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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310A PHE 3.1 13.9 + - - +
311A LYS* 3.5 11.9 - - + +
312A PHE 3.0 0.8 - - - -
313A ALA* 1.3 73.7 - - - +
315A GLU* 1.3 60.0 + - + +
316A ILE 3.0 6.9 + - - -
317A TYR* 3.6 7.7 + - - +
320A GLN* 2.9 34.9 + - - +
387A ILE* 3.9 19.0 - - - +
388A PHE* 3.8 42.9 + - + +
390A GLN* 3.5 23.5 + - - +
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Residues in contact with GLU 315 (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 PRO* 3.9 11.1 - - + +
279A ILE* 3.8 16.0 - - + +
282A ARG* 2.6 43.2 + - - +
283A LEU* 5.6 0.7 - - - +
311A LYS* 3.4 28.6 + - + +
312A PHE 2.9 8.9 + - - +
314A LYS* 1.3 80.4 - - + +
316A ILE* 1.3 62.8 + - + +
320A GLN* 3.2 14.2 - - - +
321A PHE* 3.2 19.2 - - - -
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Residues in contact with ILE 316 (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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270A ILE* 3.6 32.1 - - + -
271A PRO* 3.8 17.5 - - + +
273A PHE* 5.1 2.0 - - + -
279A ILE* 5.6 0.4 - - + -
312A PHE* 3.3 50.5 + - + +
313A ALA* 4.3 4.0 - - - +
314A LYS 3.0 0.6 - - - -
315A GLU* 1.3 90.8 - - + +
317A TYR* 1.3 69.5 + - - +
318A PRO* 3.4 4.8 - - + +
320A GLN* 4.1 1.6 - - - -
321A PHE* 4.0 15.2 - - + -
347A ILE* 5.1 2.0 - - + +
348A ASP* 4.6 25.1 - - + +
366A PHE* 4.7 13.2 - - + -
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Residues in contact with TYR 317 (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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313A ALA 3.1 25.9 + - - +
314A LYS* 3.6 10.6 + - - +
316A ILE* 1.3 76.8 - - - +
318A PRO* 1.3 78.9 - - + +
320A GLN* 3.2 25.1 + - + +
321A PHE 4.7 0.2 + - - -
366A PHE* 3.6 32.9 + + - -
380A CYS* 2.9 48.6 + - - -
383A VAL* 3.2 18.5 - - + +
384A ARG* 4.1 35.4 - - + -
387A ILE* 3.8 25.6 - - + -
409A PRO* 5.3 1.4 - - + +
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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