Contacts of the helix formed by residues 312 - 324 (chain A) in PDB entry 1VEP
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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A GLN* 2.7 36.3 + - - +
310A TYR 5.5 0.2 - - - -
311A ASN* 1.3 81.5 - - - +
313A TYR* 1.3 57.4 + - - +
314A SER* 3.1 13.2 + - - -
315A HIS* 2.9 35.0 + - + +
316A LEU* 3.0 11.3 + - - +
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Residues in contact with TYR 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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288A ILE* 4.9 8.7 - - + -
289A ALA 5.5 1.8 + - - -
291A VAL* 5.4 0.5 + - - +
295A TYR* 5.6 0.7 - + - -
302A HIS* 5.9 1.3 - + - -
305A GLU* 2.5 41.1 + - - +
310A TYR* 3.6 42.2 - + + +
311A ASN 5.5 2.5 - - - -
312A ASP* 1.3 72.0 + - - +
314A SER* 1.3 60.7 + - - +
316A LEU* 3.5 15.2 - - + +
317A LEU* 2.8 36.7 + - + +
329A PHE* 5.8 1.6 - + - -
349A LEU* 3.7 22.5 - - + +
352A ASN* 4.1 12.6 - - - +
353A ILE* 3.5 25.6 - - + -
356A LEU* 3.7 19.5 - - + -
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Residues in contact with SER 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 ASP* 3.1 8.6 + - - -
313A TYR* 1.3 77.7 - - - +
315A HIS* 1.3 64.3 + - - +
318A ASP* 3.1 28.3 + - - -
356A LEU* 3.8 21.0 - - - +
360A LYS* 3.0 31.8 + - - +
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Residues in contact with HIS 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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255A GLU* 6.2 4.6 - - + +
258A GLN* 3.9 3.1 + - - +
262A GLU* 2.6 41.9 + - - +
266A LYS* 6.3 0.9 - - - -
312A ASP* 2.9 29.0 + - + +
314A SER* 1.3 77.0 - - - +
316A LEU* 1.3 62.6 + - - +
318A ASP* 3.4 25.6 + - + +
319A ALA 3.6 3.8 + - - -
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Residues in contact with LEU 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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173A LEU* 3.9 24.2 - - + -
258A GLN* 3.5 15.7 - - + +
261A LEU* 5.2 2.7 - - + -
262A GLU* 3.6 23.1 - - + +
288A ILE* 4.2 23.8 - - + -
310A TYR* 3.8 34.5 - - + -
312A ASP 3.0 15.2 + - - +
313A TYR* 3.2 18.4 + - + +
315A HIS* 1.3 78.5 - - - +
317A LEU* 1.3 62.4 + - + +
319A ALA* 3.1 18.5 + - + +
320A PHE* 3.6 9.2 + - + -
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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
----------------------------------------------------------
288A ILE* 3.7 30.3 - - + -
313A TYR* 2.8 25.5 + - + +
314A SER 3.8 0.2 - - - +
316A LEU* 1.3 71.9 - - + +
318A ASP* 1.3 61.9 + - - +
320A PHE* 2.8 25.1 + - + +
321A LYS 3.0 9.9 + - - -
327A VAL* 4.2 18.4 - - + -
353A ILE* 4.0 17.9 - - + +
356A LEU* 3.6 34.8 - - + -
357A ALA* 3.8 15.9 - - + +
360A LYS* 3.8 14.4 - - + -
362A ILE* 3.5 13.7 - - + +
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Residues in contact with ASP 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 SER* 3.1 15.8 + - - +
315A HIS* 3.5 22.0 - - + +
316A LEU 3.2 0.4 - - - -
317A LEU* 1.3 74.8 - - - +
319A ALA* 1.3 62.7 + - - +
321A LYS* 3.8 9.4 - - - +
322A SER* 3.0 25.2 + - - -
360A LYS* 2.7 30.4 + - - +
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Residues in contact with ALA 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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262A GLU* 3.8 42.2 - - + +
265A THR* 4.0 9.7 - - + +
266A LYS* 4.2 17.1 - - - +
315A HIS 3.6 3.1 + - - +
316A LEU* 3.1 14.7 + - + +
317A LEU 3.0 0.2 - - - -
318A ASP* 1.3 79.5 - - - +
320A PHE* 1.3 55.9 + - - +
322A SER* 3.4 2.6 + - - -
323A ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 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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173A LEU* 3.8 28.5 - - + -
265A THR* 4.0 15.7 - - + -
286A ALA* 3.7 37.0 - - + -
287A LYS 4.9 1.1 - - - -
288A ILE* 3.9 28.3 - - + -
316A LEU* 3.6 15.7 - - + -
317A LEU* 2.8 18.0 + - + +
319A ALA* 1.3 77.0 - - - +
321A LYS* 1.3 65.7 + - - +
323A ALA* 3.2 2.0 + - - -
324A LYS 2.9 18.9 + - - -
325A LEU* 3.1 27.6 + - + +
326A ASP 3.7 22.7 - - - -
327A VAL* 4.3 9.2 - - + -
362A ILE* 4.4 8.7 - - + -
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Residues in contact with LYS 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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317A LEU 3.0 10.0 + - - +
318A ASP* 3.8 11.7 - - - +
320A PHE* 1.3 75.5 - - - +
322A SER* 1.3 63.6 + - - +
324A LYS* 3.2 18.9 + - - +
325A LEU 5.2 1.1 - - - -
360A LYS* 2.9 36.4 + - + +
361A GLY* 3.9 12.1 + - - -
362A ILE* 4.1 16.2 - - + +
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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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266A LYS* 4.1 19.4 - - - +
318A ASP 3.0 18.1 + - - -
319A ALA* 3.4 8.7 - - - -
320A PHE 3.1 0.2 - - - -
321A LYS* 1.3 79.5 - - - +
323A ALA* 1.3 60.3 + - - +
324A LYS* 3.2 8.7 + - - +
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Residues in contact with ALA 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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265A THR* 3.7 24.9 - - + +
266A LYS* 3.9 14.6 - - - +
269A GLY* 4.3 8.1 - - - +
273A HIS* 3.5 15.2 - - - -
319A ALA 2.9 16.7 + - - +
320A PHE 3.2 1.3 + - - +
322A SER* 1.3 74.8 + - - +
324A LYS* 1.3 74.8 + - - +
325A LEU* 3.9 17.0 - - + +
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Residues in contact with LYS 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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273A HIS* 2.8 41.4 + - + +
277A ASP* 5.5 2.6 + - - -
284A ILE 4.0 4.0 + - - +
320A PHE 2.9 5.2 + - - -
321A LYS* 3.2 13.6 + - - +
322A SER 3.2 7.2 - - - +
323A ALA* 1.3 85.1 - - - +
325A LEU* 1.3 61.1 + - - +
326A ASP* 4.5 1.9 + - - +
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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