Contacts of the helix formed by residues 284 - 301 (chain A) in PDB entry 6DWY
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 LEU 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A PHE* 5.1 5.8 - - + -
281A THR* 3.1 23.5 + - + +
282A PRO 3.0 0.8 - - - -
283A GLU* 1.3 75.7 - - - +
285A ASN* 1.3 64.8 + - - +
286A MET 3.2 2.9 - - - -
287A PRO* 3.1 18.8 - - + +
288A ILE* 3.2 18.3 - - + +
356A ILE* 4.3 14.8 - - + -
360A MET* 4.0 23.8 - - + -
405A ASP* 3.3 45.5 - - + +
406A ILE* 4.3 13.2 - - + -
409A LEU* 3.7 24.2 - - + -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 4.2 14.8 + - - +
279A GLU* 5.4 2.4 + - - +
281A THR 4.6 0.7 - - - +
282A PRO* 2.8 39.6 + - - +
284A LEU* 1.3 80.2 - - - +
286A MET* 1.3 57.3 + - - +
288A ILE* 3.8 7.8 - - - +
289A LEU* 2.8 35.6 + - + +
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Residues in contact with MET 286 (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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282A PRO 4.4 1.0 + - - -
283A GLU 4.4 5.2 + - - +
285A ASN* 1.3 78.0 - - - +
287A PRO* 1.3 76.2 - - + +
289A LEU* 4.2 3.8 - - - +
290A ALA* 3.3 24.1 + - - +
351A HIS* 4.0 34.5 - - + +
352A ILE* 5.6 0.2 - - - -
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Residues in contact with PRO 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU 4.2 4.5 - - - +
284A LEU* 3.1 30.3 - - + +
286A MET* 1.3 98.9 - - + +
288A ILE* 1.3 66.8 + - + +
290A ALA* 4.0 3.9 - - + +
291A CYS* 3.3 25.3 + - - -
352A ILE* 4.2 10.2 - - + +
353A ASN* 5.3 10.5 - - + +
356A ILE* 5.1 17.3 - - + -
357A ILE* 4.2 20.5 - - + +
360A MET* 5.5 2.2 - - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 5.1 8.7 - - + -
284A LEU* 3.2 17.3 - - + +
285A ASN* 3.3 12.0 + - - +
287A PRO* 1.3 77.9 - - + +
289A LEU* 1.3 65.8 + - - +
291A CYS* 3.1 9.1 + - - +
292A LYS* 3.0 28.3 + - + +
314A GLU* 4.8 4.9 - - - +
322A THR* 4.6 10.3 - - - +
325A MET* 4.1 19.1 - - + -
326A LEU* 3.8 20.4 - - + -
357A ILE* 5.0 2.0 - - + -
360A MET* 3.7 37.0 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 2.8 24.5 + - + +
286A MET* 4.3 4.0 - - - +
288A ILE* 1.3 74.6 - - - +
290A ALA* 1.3 58.1 + - - +
292A LYS* 3.1 25.0 + - + +
293A ASN* 2.8 46.6 + - - +
296A LYS* 5.9 2.7 - - - -
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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
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286A MET* 3.3 21.9 + - + +
287A PRO 4.0 0.4 - - - +
289A LEU* 1.3 76.9 - - - +
291A CYS* 1.3 52.0 + - - +
293A ASN* 3.0 10.4 + - - +
294A ILE* 2.7 37.2 + - - +
348A ARG 4.2 8.6 - - - +
351A HIS* 5.8 4.0 - - + -
352A ILE* 3.6 28.3 - - + -
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Residues in contact with CYS 291 (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 PRO 3.3 15.8 + - - -
288A ILE* 3.1 11.5 + - - +
290A ALA* 1.3 76.8 - - - +
292A LYS* 1.3 57.3 + - - +
294A ILE* 2.8 9.5 + - - +
295A VAL* 2.8 33.1 + - - +
325A MET* 3.8 17.0 - - - -
326A LEU* 4.6 6.5 - - + -
329A ILE* 4.3 25.7 - - + +
333A TRP* 5.7 0.2 - - - -
352A ILE* 3.7 16.1 - - - +
357A ILE* 3.5 25.4 - - - -
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Residues in contact with LYS 292 (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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288A ILE* 3.0 17.4 + - + +
289A LEU* 3.1 25.4 + - + +
291A CYS* 1.3 74.9 - - - +
293A ASN* 1.3 57.0 + - - +
295A VAL* 3.3 9.3 + - + +
296A LYS* 2.9 59.4 + - - +
314A GLU* 3.5 48.1 + - + +
316A PRO* 5.7 1.4 - - - +
325A MET* 3.6 21.3 - - + -
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Residues in contact with ASN 293 (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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289A LEU* 2.8 48.4 + - - +
290A ALA* 3.0 12.4 + - - +
292A LYS* 1.3 71.8 - - - +
294A ILE* 1.3 64.8 + - - +
296A LYS* 3.9 17.3 - - - +
297A TYR* 3.3 11.4 + - - +
348A ARG* 3.2 39.1 + - + +
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Residues in contact with ILE 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 17.2 + - - +
291A CYS* 2.8 10.6 + - - +
293A ASN* 1.3 71.7 - - - +
295A VAL* 1.3 63.9 + - - +
297A TYR* 3.1 16.2 + - - +
298A PHE* 3.3 14.9 + - + +
311A LEU* 4.1 12.3 - - + -
329A ILE* 4.5 12.6 - - + -
336A VAL* 4.0 25.8 - - + -
340A LEU* 4.6 10.3 - - + -
348A ARG* 3.5 30.3 - - + +
349A ILE* 3.8 23.1 - - + -
352A ILE* 3.7 23.6 - - + -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A CYS 2.8 25.9 + - - +
292A LYS* 3.7 7.4 - - - +
294A ILE* 1.3 72.6 - - - +
296A LYS* 1.3 64.7 + - + +
297A TYR 3.2 0.3 + - - -
298A PHE* 3.4 2.8 + - - +
299A LYS* 3.2 26.0 + - + +
304A GLN* 5.4 0.4 - - - +
311A LEU* 3.8 24.7 - - + +
312A LYS 3.2 27.4 - - - +
313A SER* 3.4 22.9 - - - +
325A MET* 4.1 9.2 - - + -
329A ILE* 3.6 23.1 - - + -
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Residues in contact with LYS 296 (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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289A LEU* 5.9 2.5 - - - -
292A LYS* 2.9 57.7 + - - +
293A ASN* 3.9 20.4 - - - +
294A ILE 3.3 0.2 - - - -
295A VAL* 1.3 76.7 - - + +
297A TYR* 1.3 58.2 + - - +
299A LYS* 3.5 7.4 + - - +
300A LYS* 3.0 30.0 + - - +
313A SER* 6.2 0.2 - - - +
314A GLU* 5.8 1.6 - - - +
348A ARG* 5.6 1.6 - - - +
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Residues in contact with TYR 297 (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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293A ASN 3.3 11.0 + - - +
294A ILE* 3.1 10.6 + - - +
296A LYS* 1.3 77.6 - - - +
298A PHE* 1.3 75.2 + + - +
300A LYS* 3.0 9.9 + - + +
301A ALA* 2.8 49.6 + - + +
303A LEU* 4.2 16.2 - - + +
340A LEU* 4.7 10.5 - - + -
343A ALA* 3.5 28.4 + - + +
345A GLU* 3.6 21.8 - - + +
348A ARG* 3.9 36.5 - - - +
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Residues in contact with PHE 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 ILE* 3.3 9.1 + - + +
295A VAL 4.0 6.1 - - - +
297A TYR* 1.3 84.7 - + - +
299A LYS* 1.3 60.5 + - - +
303A LEU* 2.9 67.9 + - + +
304A GLN* 4.1 25.6 - - + -
307A LEU* 4.3 14.6 - - + -
311A LEU* 3.4 27.1 - - + -
336A VAL* 3.5 38.6 - - + -
339A ILE* 4.0 19.7 - - + -
340A LEU* 3.6 20.9 - - + -
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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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295A VAL* 3.2 17.8 + - + +
296A LYS* 3.9 6.3 - - - +
297A TYR 3.1 0.6 - - - -
298A PHE* 1.3 79.3 - - - +
300A LYS* 1.3 60.9 + - - +
301A ALA 3.6 0.2 + - - -
302A ASN* 3.7 8.3 + - - -
303A LEU 5.3 0.4 - - - -
304A GLN* 4.1 19.1 - - - +
311A LEU 4.2 15.9 - - - -
312A LYS* 6.0 0.2 - - - +
313A SER* 3.3 31.0 + - - +
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Residues in contact with LYS 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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296A LYS 3.0 17.5 + - - +
297A TYR* 3.0 10.3 + - + +
299A LYS* 1.3 77.6 - - - +
301A ALA* 1.3 59.8 + - - +
302A ASN 3.2 2.4 + - - -
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Residues in contact with ALA 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 TYR* 2.8 35.8 + - + +
298A PHE 3.8 0.2 + - - -
299A LYS 3.4 0.2 - - - -
300A LYS* 1.3 75.7 - - - +
302A ASN* 1.3 65.2 + - - +
303A LEU* 3.0 37.8 + - + +
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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
------------------------------------------------------------
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