Contacts of the helix formed by residues 312 - 329 (chain A) in PDB entry 1ZUM
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 GLU 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A VAL 3.4 1.2 + - - -
311A GLN* 1.3 73.2 - - + +
313A ASP* 1.3 77.4 + - - +
314A ILE 3.0 1.6 + - - -
315A TYR* 3.2 13.7 + - - +
316A ASP* 4.7 4.0 + - - +
409A LYS* 3.9 28.3 - - + +
410A PHE 2.8 17.0 + - - +
411A LYS* 3.0 53.1 + - + +
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Residues in contact with ASP 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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279A SER* 4.5 19.4 + - - -
311A GLN* 3.1 6.5 + - + +
312A GLU* 1.3 91.4 - - - +
314A ILE* 1.3 63.7 + - + +
411A LYS* 5.4 3.3 + - - -
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 4.0 13.5 - - + +
278A MET 3.5 26.2 - - - +
279A SER* 3.7 28.9 - - - +
281A ALA* 5.3 2.5 - - + +
283A MET* 3.7 27.6 - - + -
310A VAL* 3.7 16.2 - - + -
311A GLN 3.1 12.3 + - - +
313A ASP* 1.3 81.8 - - + +
315A TYR* 1.3 59.7 + - - +
316A ASP 3.5 2.2 - - - -
317A GLU* 3.4 11.9 + - - +
318A PHE* 2.9 30.4 + - + +
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Residues in contact with TYR 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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310A VAL* 3.9 19.5 - - + -
311A GLN 3.2 8.6 + - - +
312A GLU 3.2 14.1 + - - +
314A ILE* 1.3 75.6 - - - +
316A ASP* 1.3 73.0 + - - +
318A PHE* 3.2 1.7 + - - +
319A VAL* 2.8 54.3 + - + +
387A GLY* 3.7 6.1 - - - -
388A ASP* 2.7 48.8 + - - -
407A ILE* 3.8 19.7 + - + +
408A LEU 4.1 1.3 - - - -
409A LYS* 3.6 58.1 - - + -
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Residues in contact with ASP 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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312A GLU 4.7 4.0 + - - +
314A ILE 3.5 0.6 - - - -
315A TYR* 1.3 92.6 - - - +
317A GLU* 1.3 63.2 + - - +
319A VAL* 3.8 3.8 - - - +
320A GLU* 3.0 24.3 + - - +
409A LYS* 5.4 2.6 + - - -
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Residues in contact with GLU 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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283A MET* 3.9 19.3 - - + +
314A ILE* 3.4 14.5 + - - +
315A TYR 3.4 0.4 - - - -
316A ASP* 1.3 77.0 - - - +
318A PHE* 1.3 63.0 - - - +
320A GLU* 3.3 12.0 + - - +
321A ARG* 3.0 61.7 + - + +
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Residues in contact with PHE 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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277A ILE* 4.1 24.0 - - + -
283A MET* 3.8 19.4 - - + +
286A ALA* 3.9 8.1 - - + -
287A VAL* 3.7 31.8 - - + +
290A ALA* 3.6 26.2 - - + -
308A THR* 3.9 14.4 - - + -
310A VAL* 3.5 32.1 - - + -
314A ILE 2.9 19.7 + - - +
315A TYR 3.5 3.1 - - - +
317A GLU* 1.3 78.5 - - - +
319A VAL* 1.3 55.3 + - - +
321A ARG* 3.3 3.3 + - - +
322A SER* 2.7 52.2 + - - -
405A MET* 5.2 1.6 - - + -
407A ILE* 4.6 9.4 - - + -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 2.8 62.4 + - + +
316A ASP* 3.8 4.5 - - - +
318A PHE* 1.3 72.9 - - + +
320A GLU* 1.3 63.2 + - - +
322A SER* 3.2 6.6 + - - -
323A VAL* 2.9 31.4 + - + +
368A LEU* 3.3 36.6 - - + -
407A ILE* 4.0 19.1 - - + -
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Residues in contact with GLU 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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316A ASP 3.0 17.4 + - - +
317A GLU* 3.5 13.4 - - - +
319A VAL* 1.3 78.9 - - - +
321A ARG* 1.3 71.0 + - - +
323A VAL* 3.3 5.9 + - - +
324A ALA* 3.1 22.3 + - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 3.4 31.7 - - - +
284A ASP* 2.9 37.0 + - - +
287A VAL* 3.8 19.5 - - + +
317A GLU* 3.0 49.4 + - - +
318A PHE 3.7 3.1 - - - +
320A GLU* 1.3 86.7 + - - +
322A SER* 1.3 57.6 + - - +
324A ALA* 3.5 6.7 + - - +
325A ARG* 3.0 28.9 + - - +
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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
----------------------------------------------------------
287A VAL* 4.2 12.6 + - - +
290A ALA* 5.7 0.2 - - - +
291A HIS* 4.9 3.9 + - - -
318A PHE* 2.7 48.7 + - - -
319A VAL 3.6 5.6 - - - -
321A ARG* 1.3 75.6 - - - +
323A VAL* 1.3 60.6 + - - +
325A ARG* 3.3 4.3 + - - +
326A ALA* 2.9 29.5 + - - +
385A VAL* 4.7 0.9 - - - +
405A MET* 3.4 28.9 - - - +
407A ILE* 4.2 4.5 - - - -
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Residues in contact with VAL 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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319A VAL* 2.9 23.5 + - + +
320A GLU* 3.7 6.1 - - - +
322A SER* 1.3 71.1 - - - +
324A ALA* 1.3 66.9 + - - +
326A ALA* 3.3 6.8 + - - +
327A LYS* 3.0 50.5 + - + +
368A LEU* 3.7 48.9 - - + +
369A CYS* 4.0 6.1 - - + -
385A VAL* 4.4 8.5 - - + -
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Residues in contact with ALA 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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320A GLU* 3.1 19.0 + - - +
321A ARG* 3.7 11.0 - - - +
323A VAL* 1.3 78.2 - - - +
325A ARG* 1.3 61.2 + - - +
327A LYS* 3.3 9.7 + - - +
328A SER* 3.1 24.1 + - - -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 4.7 8.3 - - + -
288A GLU* 2.8 45.7 + - - +
291A HIS* 3.2 53.9 + - + +
321A ARG 3.0 17.1 + - - +
322A SER* 3.6 7.6 - - - +
324A ALA* 1.3 76.9 - - - +
326A ALA* 1.3 59.5 + - - +
328A SER* 2.9 31.7 + - - -
329A ARG* 3.2 11.2 + - - +
340A GLU* 2.8 39.8 + - - -
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Residues in contact with ALA 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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291A HIS* 3.9 10.3 - - - -
295A PHE* 4.3 8.7 - - + -
322A SER 2.9 17.2 + - - +
323A VAL 3.3 4.2 + - - +
325A ARG* 1.3 77.2 - - - +
327A LYS* 1.3 62.4 + - - +
329A ARG* 3.2 17.5 + - - +
369A CYS* 3.8 9.0 - - - -
383A PRO* 3.4 23.9 - - + +
385A VAL* 3.6 26.7 - - + -
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Residues in contact with LYS 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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323A VAL* 3.0 39.3 + - + +
324A ALA* 3.3 8.9 + - - +
326A ALA* 1.3 75.6 - - - +
328A SER* 1.3 59.8 + - - +
329A ARG 3.5 4.2 + - - +
368A LEU 4.4 4.0 + - - -
369A CYS* 3.9 22.7 - - + +
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Residues in contact with SER 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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324A ALA 3.1 12.2 + - - -
325A ARG* 2.9 32.4 + - - -
327A LYS* 1.3 76.4 - - - +
329A ARG* 1.3 63.9 + - - +
330A VAL* 3.1 14.9 + - - +
340A GLU* 3.9 4.8 - - - +
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Residues in contact with ARG 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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291A HIS* 3.0 39.6 + - + +
292A PHE* 6.0 0.6 - - - +
295A PHE* 3.6 35.8 + - - +
296A PHE* 4.5 4.4 - - - +
297A ASN 5.0 2.0 - - - +
298A GLN* 5.1 1.4 + - - +
325A ARG* 3.2 11.4 + - - +
326A ALA 3.2 16.9 + - - +
327A LYS 3.3 3.7 - - - +
328A SER* 1.3 74.7 - - - +
330A VAL* 1.3 63.6 + - - +
331A VAL* 3.4 10.6 + - - +
340A GLU* 3.1 51.7 + - + +
341A GLN* 3.1 35.7 + - + +
383A PRO* 3.9 14.0 - - + +
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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