Contacts of the helix formed by residues 313 - 325 (chain A) in PDB entry 1ZXC
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 ASP 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A TYR 3.3 6.1 + - - -
305A PRO* 4.0 22.1 - - + +
312A TRP* 1.3 72.8 - - - +
314A VAL* 1.3 67.6 + - - +
315A LYS* 3.3 12.4 + - - +
316A MET* 3.1 40.5 + - + +
317A LEU 3.0 18.7 + - - -
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Residues in contact with VAL 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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312A TRP 3.5 3.8 + - - -
313A ASP* 1.3 73.7 + - - +
315A LYS* 1.3 69.5 + - + +
317A LEU* 3.3 4.5 + - - +
318A LEU* 3.1 18.9 + - - +
343A PHE* 4.1 41.2 - - + +
347A THR* 4.1 24.7 - - + -
349A GLY 4.7 1.1 - - - -
350A LEU* 3.6 38.1 - - + +
384A LEU* 4.1 9.1 - - + +
478A IH6 5.8 2.7 - - + -
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Residues in contact with LYS 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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313A ASP* 3.3 9.9 + - - +
314A VAL* 1.3 82.8 - - + +
316A MET* 1.3 58.3 + - + +
318A LEU* 3.4 2.6 + - + +
319A GLU* 3.0 54.5 + - + +
350A LEU* 3.5 19.1 - - + -
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Residues in contact with MET 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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296A LYS* 5.9 1.3 - - - -
304A TYR* 3.1 37.0 - - + +
305A PRO* 3.9 25.6 - - + -
312A TRP* 3.7 14.2 - - + -
313A ASP* 3.1 25.3 + - + +
315A LYS* 1.3 74.9 - - + +
317A LEU* 1.3 53.5 + - - +
319A GLU* 3.3 17.6 + - - +
320A GLN* 2.7 36.9 + - - +
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Residues in contact with LEU 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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232A ASP* 6.1 0.2 - - - +
298A TYR* 3.9 31.9 - - + +
312A TRP* 3.3 29.7 - - + -
313A ASP 3.0 11.5 + - - +
314A VAL* 3.3 8.9 + - - +
316A MET* 1.3 72.4 - - - +
318A LEU* 1.3 59.0 + - - +
321A PHE* 2.8 33.4 + - - +
337A LEU* 4.1 15.9 - - + -
339A THR* 4.4 3.6 - - + -
341A GLN* 3.4 26.0 - - - +
343A PHE* 3.7 24.5 - - + -
384A LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 318 (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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314A VAL 3.1 13.5 + - - +
315A LYS* 3.8 7.9 - - + +
316A MET 3.3 0.2 - - - -
317A LEU* 1.3 74.9 - - - +
319A GLU* 1.3 57.8 + - - +
321A PHE* 3.8 5.5 - - + +
322A SER* 2.9 34.6 + - - -
350A LEU* 3.8 23.1 - - + +
351A ALA* 3.8 23.8 - - - -
352A TYR* 3.7 29.8 - - + +
382A SER* 4.0 8.5 - - - +
383A GLY* 3.6 39.7 - - - +
384A LEU* 3.7 15.2 - - + +
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Residues in contact with GLU 319 (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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315A LYS* 3.0 49.4 + - + +
316A MET* 3.4 21.0 - - - +
318A LEU* 1.3 73.2 - - + +
320A GLN* 1.3 64.3 + - - +
322A SER* 3.2 5.7 + - - -
323A PHE* 3.1 22.2 + - - +
352A TYR* 3.6 21.5 + - - +
378A ILE* 4.6 2.6 - - - +
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Residues in contact with GLN 320 (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 LYS* 2.6 60.3 + - - +
297A HIS* 3.7 0.7 - - - -
298A TYR* 3.4 24.2 - - + +
312A TRP* 3.5 21.3 - - + -
316A MET 2.7 20.1 + - - +
317A LEU 3.7 2.7 - - - +
319A GLU* 1.3 73.1 - - - +
321A PHE* 1.3 62.8 + - - +
323A PHE* 3.1 17.2 + - - +
324A ASP* 2.9 52.8 + - - +
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Residues in contact with PHE 321 (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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230A VAL* 3.8 21.8 - - + -
298A TYR* 3.6 42.7 - + + +
317A LEU 2.8 21.2 + - - +
318A LEU* 3.8 9.6 - - + +
320A GLN* 1.3 72.6 - - - +
322A SER* 1.3 58.8 + - - +
324A ASP* 3.3 0.7 + - - +
325A ILE* 2.9 45.6 + - + +
335A ALA* 4.3 20.6 - - + -
336A HIS 3.8 11.4 - - - -
337A LEU* 3.6 55.9 - - + -
382A SER* 4.3 10.5 - - - -
383A GLY 4.0 9.2 - - - -
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Residues in contact with SER 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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318A LEU 2.9 21.2 + - - -
319A GLU* 3.5 6.7 - - - -
320A GLN 3.2 0.2 - - - -
321A PHE* 1.3 78.5 - - - +
323A PHE* 1.3 61.7 + - - +
325A ILE* 3.8 9.5 - - - +
326A ALA* 3.3 22.5 + - - +
329A ALA* 5.2 0.2 - - - +
352A TYR* 3.8 7.8 - - - -
378A ILE* 3.6 14.7 - - - +
379A TYR 3.9 16.8 - - - +
380A LEU* 4.2 6.3 - - - -
382A SER* 2.8 27.2 + - - -
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Residues in contact with PHE 323 (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 LYS* 6.1 1.3 - - - -
319A GLU 3.1 12.7 + - - +
320A GLN* 3.1 17.7 + - - +
322A SER* 1.3 76.7 - - - +
324A ASP* 1.3 81.4 + - - +
326A ALA* 3.3 6.9 + - - +
371A SER* 5.4 3.4 - - - -
374A GLY* 3.6 36.1 - - - -
376A LYS* 2.8 57.9 + - + +
378A ILE* 3.4 19.4 - - + +
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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
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296A LYS 4.8 1.0 - - - +
297A HIS* 3.2 25.6 - - - +
298A TYR* 3.0 50.7 + - + -
320A GLN* 2.9 31.5 + - - +
323A PHE* 1.3 94.3 - - - +
325A ILE* 1.3 60.9 + - - +
326A ALA 3.2 3.2 + - - -
327A GLU 4.9 1.6 + - - -
328A GLU* 6.0 0.2 - - - +
376A LYS* 4.6 4.8 + - - +
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Residues in contact with ILE 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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228A LEU* 3.7 22.9 - - + -
230A VAL* 4.4 6.7 - - + -
283A ARG* 5.1 7.4 - - - -
298A TYR* 4.1 19.1 - - + +
321A PHE* 2.9 47.9 + - + +
322A SER* 3.8 11.2 - - - +
324A ASP* 1.3 78.7 - - - +
326A ALA* 1.3 54.2 + - - +
327A GLU 3.3 2.5 - - - -
328A GLU* 3.1 28.8 + - + +
329A ALA* 2.7 47.4 + - + -
335A ALA* 4.4 5.6 - - + -
382A SER* 5.6 1.8 - - - -
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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