Contacts of the helix formed by residues 286 - 307 (chain A) in PDB entry 2ZV2
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 SER 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PRO 4.2 0.2 + - - -
285A LEU* 1.3 76.3 - - - +
287A GLU* 1.3 66.1 + - - +
288A ASP* 3.9 7.6 + - - +
289A GLN* 2.8 37.8 + - - +
290A ALA* 3.0 20.1 + - - +
385A VAL* 4.5 0.4 - - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 1.3 71.4 - - - +
288A ASP* 1.3 62.9 + - - +
290A ALA* 2.9 5.4 + - - +
291A ARG* 2.8 37.9 + - - +
385A VAL* 4.3 10.6 - - + +
415A ASP 4.6 1.7 - - - +
416A ILE* 3.3 17.2 - - + +
417A ALA* 2.7 33.6 + - - +
420A LEU* 4.1 14.7 - - + +
446A TRP* 3.2 27.6 + - - +
449A ARG* 3.7 13.3 + - - -
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Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 3.3 7.3 + - - +
287A GLU* 1.3 77.2 - - - +
289A GLN* 1.3 62.9 + - + +
291A ARG* 3.1 29.4 + - - +
292A PHE* 3.1 22.5 + - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 5.0 0.3 - - - +
285A LEU* 3.8 25.6 - - + +
286A SER* 2.8 40.8 + - - +
288A ASP* 1.3 76.2 - - + +
290A ALA* 1.3 66.6 + - - +
292A PHE* 3.1 8.0 + - - +
293A TYR* 3.1 43.7 + - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.4 5.8 - - + +
286A SER 3.0 10.9 + - - +
287A GLU 2.9 8.2 + - - +
289A GLN* 1.3 77.6 - - - +
291A ARG* 1.3 51.5 + - - +
293A TYR 3.3 0.5 + - - -
294A PHE* 2.7 38.3 + - - +
381A LEU* 4.2 2.0 - - + -
384A PHE* 3.8 28.4 - - + -
385A VAL* 3.7 23.8 - - + -
446A TRP* 3.9 10.8 - - + -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 2.8 18.5 + - - +
288A ASP* 3.1 35.8 + - - +
290A ALA* 1.3 71.9 - - - +
292A PHE* 1.3 64.4 + - - +
294A PHE* 3.7 0.9 - - - +
295A GLN* 2.9 52.4 + - + +
446A TRP* 2.6 90.5 + - + +
447A VAL* 3.7 7.9 - - - +
449A ARG* 3.8 38.2 + - - +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP 3.1 12.4 + - - +
289A GLN* 3.2 11.2 - - - +
291A ARG* 1.3 80.7 - - - +
293A TYR* 1.3 85.7 + + - +
295A GLN* 3.4 22.3 + - - +
296A ASP* 3.5 15.0 + - - +
324A ASP 5.4 1.3 - - - -
325A GLY* 3.3 26.9 - - - -
326A HIS* 3.5 34.8 - + - -
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 3.6 27.1 - - + +
285A LEU* 4.1 16.6 - - + -
289A GLN* 3.1 40.2 + - + +
292A PHE* 1.3 95.7 - + - +
294A PHE* 1.3 67.1 + - - +
296A ASP* 2.9 17.7 + - - +
297A LEU* 3.0 12.3 + - - +
319A LEU* 6.1 0.2 - - - +
321A VAL* 4.5 11.4 - - + +
325A GLY 3.6 17.9 + - - -
327A ILE* 3.4 28.0 - - + +
384A PHE* 3.6 22.2 - - + -
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Residues in contact with PHE 294 (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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290A ALA 2.7 24.7 + - - +
291A ARG* 3.7 6.7 - - - +
293A TYR* 1.3 72.6 - - - +
295A GLN* 1.3 58.9 + - + +
297A LEU* 3.2 15.6 + - + +
298A ILE* 2.8 65.1 + - + +
377A MET* 3.8 35.4 - - + -
381A LEU* 3.9 26.7 - - + -
384A PHE* 3.9 6.7 - + + -
423A LEU* 4.1 6.5 - - + -
427A MET* 3.5 31.2 - - + -
441A ILE* 3.6 14.1 - - + -
446A TRP* 4.2 7.9 - + + -
447A VAL* 4.0 16.2 - - + -
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Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 2.9 37.6 + - + +
292A PHE* 3.4 15.2 - - - +
293A TYR 3.1 0.2 - - - -
294A PHE* 1.3 78.0 - - - +
296A ASP* 1.3 62.8 + - - +
298A ILE* 3.4 9.2 + - + +
299A LYS* 3.1 42.5 + - - +
447A VAL* 3.2 38.7 + - + -
449A ARG 5.1 0.8 + - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASN* 3.4 30.9 + - - +
292A PHE* 3.5 17.9 + - - +
293A TYR* 2.9 8.1 + - - +
295A GLN* 1.3 79.2 - - - +
297A LEU* 1.3 56.8 - - - +
299A LYS* 3.1 12.1 + - - +
300A GLY* 2.9 26.5 + - - -
326A HIS* 3.0 32.6 + - - -
327A ILE* 3.1 33.6 + - + +
329A ILE* 6.2 0.2 - - - -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR 3.0 12.9 + - - +
294A PHE* 3.4 23.1 - - + +
296A ASP* 1.3 77.2 - - - +
298A ILE* 1.3 56.0 + - - +
300A GLY* 3.3 0.9 + - - +
301A ILE* 2.9 52.7 + - + +
314A ILE* 4.1 22.4 - - + -
319A LEU* 4.1 26.0 - - + -
327A ILE* 4.9 5.5 - - + +
329A ILE* 3.8 22.2 - - + -
377A MET* 4.0 25.4 - - + -
380A THR* 4.2 11.2 - - + -
384A PHE* 5.3 1.6 - - + -
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Residues in contact with ILE 298 (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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294A PHE* 2.8 54.4 + - + +
295A GLN* 3.6 7.4 - - + +
296A ASP 3.2 0.2 - - - -
297A LEU* 1.3 76.1 - - - +
299A LYS* 1.3 65.8 + - + +
301A ILE* 3.2 2.1 + - - +
302A GLU* 2.9 26.3 + - + +
377A MET* 4.2 15.7 - - + -
438A VAL* 4.4 18.9 - - + +
441A ILE* 3.9 11.9 - - + -
442A LYS* 4.5 26.9 - - + +
447A VAL* 4.0 22.4 - - + -
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Residues in contact with LYS 299 (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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246A HIS* 4.0 10.4 + - + +
248A ASN* 3.8 17.3 - - - +
295A GLN* 3.1 32.3 + - - +
296A ASP* 3.1 13.9 + - - +
298A ILE* 1.3 81.1 - - + +
300A GLY* 1.3 63.4 + - - +
302A GLU* 3.5 13.7 + - - +
303A TYR* 3.1 23.0 + - - +
442A LYS* 6.5 1.1 - - - -
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Residues in contact with GLY 300 (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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246A HIS* 4.3 7.0 - - - -
248A ASN* 4.0 16.5 - - - +
249A VAL* 4.5 1.7 - - - +
296A ASP 2.9 14.2 + - - -
297A LEU 3.8 2.2 - - - -
299A LYS* 1.3 77.2 - - - +
301A ILE* 1.3 57.2 + - - +
303A TYR* 3.3 4.9 + - - +
304A LEU* 2.9 31.5 + - - +
329A ILE* 3.8 16.8 - - - -
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Residues in contact with ILE 301 (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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297A LEU* 2.9 35.6 + - + +
298A ILE* 3.8 2.5 - - - +
300A GLY* 1.3 68.9 - - - +
302A GLU* 1.3 67.1 + - - +
304A LEU* 3.1 13.4 + - + +
305A HIS* 2.8 52.6 + - + +
311A HIS* 4.8 0.2 - - + -
314A ILE* 3.6 34.8 - - + -
329A ILE* 3.9 6.5 - - + +
373A ASP* 4.5 12.6 - - + +
377A MET* 3.9 27.4 - - + -
438A VAL* 4.3 7.9 - - + -
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Residues in contact with GLU 302 (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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298A ILE* 2.9 18.6 + - - +
299A LYS* 3.6 13.3 - - - +
301A ILE* 1.3 76.7 - - - +
303A TYR* 1.3 64.2 + - - +
305A HIS* 3.4 5.2 + - - +
306A TYR* 3.0 24.8 + - + +
438A VAL* 4.6 17.5 - - + +
439A PRO* 5.8 0.9 - - - +
442A LYS* 2.9 41.4 - - - +
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Residues in contact with TYR 303 (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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243A LYS 3.9 5.9 + - - -
244A LEU* 3.7 26.5 - - + -
245A ASP* 3.0 39.3 + - - +
246A HIS* 3.4 42.0 - + + +
249A VAL* 4.1 11.9 - - + -
299A LYS 3.1 10.7 + - - +
300A GLY 3.4 6.3 - - - +
301A ILE 3.2 0.2 - - - -
302A GLU* 1.3 80.8 - - - +
304A LEU* 1.3 60.7 + - + +
306A TYR* 3.2 10.7 + + - +
307A GLN* 2.9 61.9 + - + +
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Residues in contact with LEU 304 (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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244A LEU* 3.6 24.9 - - + -
249A VAL* 4.1 11.0 - - + -
300A GLY 2.9 22.3 + - - +
301A ILE* 3.6 9.9 - - + +
303A TYR* 1.3 78.2 - - + +
305A HIS* 1.3 58.3 + - + +
307A GLN* 3.2 8.9 + - - -
309A ILE* 2.7 47.4 + - + +
311A HIS* 4.2 21.8 - - + +
329A ILE* 4.1 17.7 - - + -
332A PHE* 3.4 41.1 - - + -
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Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 2.8 38.2 + - + +
302A GLU* 3.9 5.1 - - - +
304A LEU* 1.3 75.9 - - + +
306A TYR* 1.3 66.4 + - - +
308A LYS* 2.9 15.9 + - - +
309A ILE 3.3 21.3 - - - +
310A ILE* 4.3 7.8 - - + +
338A PHE* 3.9 9.3 - - - -
370A LYS* 3.7 58.9 + - + +
373A ASP* 2.9 26.2 + - + +
374A VAL* 5.2 0.2 - - + -
438A VAL* 4.2 15.9 - - + +
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Residues in contact with TYR 306 (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 GLU* 3.0 14.8 + - + +
303A TYR* 3.2 14.8 + + - +
305A HIS* 1.3 78.0 - - - +
307A GLN* 1.3 80.6 + - - +
308A LYS* 3.1 17.3 + - - +
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LYS* 2.8 57.8 + - - +
244A LEU* 4.3 6.1 - - + -
303A TYR* 2.9 55.5 + - + +
304A LEU 3.7 4.7 - - - +
305A HIS 3.2 0.4 - - - -
306A TYR* 1.3 104.2 - - - +
308A LYS* 1.3 67.0 + - - +
309A ILE* 3.3 11.0 + - + +
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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
------------------------------------------------------------
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