Contacts of the helix formed by residues 317 - 334 (chain A) in PDB entry 3VAS
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 PRO 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 5.0 0.9 - - + -
315A GLY 3.8 6.1 - - - +
316A LYS* 1.3 92.9 - - + +
318A MET* 1.3 67.4 + - - +
319A ILE* 3.4 4.5 - - + +
320A THR* 3.3 21.6 + - - +
321A SER* 3.0 19.8 + - - -
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Residues in contact with MET 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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261A LEU* 3.8 26.9 - - + -
263A ILE* 4.0 12.6 - - + -
273A TYR* 3.6 52.5 - - + -
308A PHE* 3.9 8.1 - - - -
312A TYR* 4.8 12.4 - - + -
317A PRO* 1.3 73.7 - - - +
319A ILE* 1.3 61.8 + - + +
321A SER* 3.3 7.1 + - - -
322A LEU* 3.0 57.5 + - + +
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Residues in contact with ILE 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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273A TYR* 3.4 30.5 - - + +
284A PHE* 4.0 22.0 - - + -
317A PRO* 3.4 2.7 - - + +
318A MET* 1.3 75.5 - - + +
320A THR* 1.3 67.4 + - - +
322A LEU* 3.2 8.0 + - + +
323A HIS* 3.1 38.8 + - + +
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP* 4.1 9.0 - - - +
316A LYS* 3.9 22.9 - - + +
317A PRO* 3.3 29.0 + - + +
319A ILE* 1.3 77.4 - - - +
321A SER* 1.3 58.3 + - - +
323A HIS* 3.3 11.4 + - - +
324A ALA* 3.0 24.9 + - - +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.6 37.0 - - - -
311A ASP* 3.8 12.3 - - - +
312A TYR* 3.4 18.7 + - - +
316A LYS* 3.3 13.3 + - - +
317A PRO 3.0 14.3 + - - -
318A MET 3.5 8.7 - - - -
320A THR* 1.3 74.1 - - - +
322A LEU* 1.3 59.2 + - - +
324A ALA* 3.1 3.8 + - - +
325A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 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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263A ILE* 4.2 8.5 - - + -
271A LEU* 4.2 13.0 - - + -
273A TYR* 3.6 36.3 - - + -
284A PHE* 3.6 33.2 - - + -
304A PHE* 4.3 10.5 - - + -
308A PHE* 3.8 14.8 - - + -
318A MET* 3.0 39.6 + - + +
319A ILE* 3.2 12.1 + - + +
321A SER* 1.3 77.0 - - - +
323A HIS* 1.3 56.7 + - - +
325A ALA* 3.1 5.0 + - - +
326A VAL* 3.0 32.9 + - - +
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Residues in contact with HIS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.5 29.0 - + - -
285A MET 5.5 1.0 + - - -
319A ILE* 3.1 33.8 + - + +
320A THR* 3.6 10.6 - - - +
321A SER 3.3 0.2 - - - -
322A LEU* 1.3 76.3 - - - +
324A ALA* 1.3 58.1 + - - +
326A VAL* 3.4 6.9 + - + +
327A LYS* 2.9 29.1 + - - +
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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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307A GLY* 3.6 12.8 - - - +
311A ASP* 3.3 37.0 - - - +
320A THR 3.0 9.3 + - - +
321A SER 3.1 9.6 + - - +
323A HIS* 1.3 75.9 - - - +
325A ALA* 1.3 57.2 + - - +
327A LYS* 3.6 9.5 - - - +
328A ALA* 3.0 26.7 + - - +
346A TYR* 4.2 2.8 + - - -
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Residues in contact with ALA 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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304A PHE* 3.2 54.2 - - + +
307A GLY* 3.8 0.9 - - - -
308A PHE* 3.5 17.3 - - + +
321A SER 2.9 12.4 + - - +
322A LEU* 3.1 10.1 + - - +
324A ALA* 1.3 76.9 - - - +
326A VAL* 1.3 63.8 + - - +
328A ALA* 3.3 4.0 + - - +
329A ALA* 3.0 19.1 + - - +
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Residues in contact with VAL 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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271A LEU* 4.6 0.4 - - + -
284A PHE* 4.0 21.1 - - + -
286A VAL* 4.2 30.5 - - + -
287A GLU* 4.7 16.2 - - + +
289A PHE* 6.0 2.9 - - + -
304A PHE* 4.2 17.7 - - + -
322A LEU 3.0 20.3 + - - +
323A HIS* 3.8 8.3 - - + +
325A ALA* 1.3 72.3 - - - +
327A LYS* 1.3 61.7 + - - +
329A ALA* 3.3 4.5 + - - +
330A ALA* 2.8 33.2 + - + +
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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 HIS 2.9 18.5 + - - +
324A ALA* 3.6 9.6 - - - +
325A ALA 3.3 0.2 - - - -
326A VAL* 1.3 76.9 - - - +
328A ALA* 1.3 63.1 + - - +
330A ALA* 3.3 6.6 + - - +
331A TYR* 3.0 23.2 + - - +
346A TYR* 3.6 48.6 - - + +
347A SER* 2.9 29.4 + - - -
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Residues in contact with ALA 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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72A MET* 3.7 17.4 - - + +
76A ILE* 4.6 0.4 - - + -
303A ALA* 3.2 32.6 - - - +
307A GLY* 3.6 11.7 - - - -
324A ALA 3.0 15.3 + - - +
325A ALA 3.5 6.3 - - - +
327A LYS* 1.3 75.5 - - - +
329A ALA* 1.3 62.6 + - - +
331A TYR* 3.3 4.3 + - - +
332A ILE 3.2 16.1 + - - -
346A TYR* 3.3 16.3 + - - +
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Residues in contact with ALA 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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300A ALA* 3.5 26.8 - - + +
303A ALA* 3.8 10.7 - - - +
304A PHE* 4.2 9.4 - - + +
325A ALA 3.0 16.4 + - - +
326A VAL* 3.7 7.4 - - + +
328A ALA* 1.3 77.1 - - - +
330A ALA* 1.3 56.9 + - - +
332A ILE* 3.2 3.6 + - - +
333A ILE* 2.8 39.2 + - + +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 6.5 0.4 - - + -
289A PHE* 3.6 30.5 - - + -
326A VAL* 2.8 21.7 + - + +
327A LYS* 3.6 7.0 - - - +
329A ALA* 1.3 74.7 - - - +
331A TYR* 1.3 64.5 + - - +
333A ILE* 3.4 4.8 + - - +
334A CYS* 3.3 29.9 + - - -
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Residues in contact with TYR 331 (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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72A MET* 4.2 10.5 - - + -
75A TRP* 3.7 20.2 - + - -
327A LYS 3.0 13.6 + - - +
328A ALA 3.5 8.1 - - - +
329A ALA 3.3 0.2 - - - -
330A ALA* 1.3 76.9 - - - +
332A ILE* 1.3 72.8 + - + +
334A CYS* 3.5 6.7 + - - +
335A ARG* 3.3 53.8 + - - +
339A SER 3.8 9.9 - - - -
340A LEU* 4.1 8.5 - - + -
341A GLY* 2.8 32.2 + - - -
342A SER 4.6 1.4 + - - -
345A SER* 4.4 16.4 - - - -
346A TYR* 3.7 31.4 - + + -
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Residues in contact with ILE 332 (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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72A MET* 4.3 4.0 - - - -
296A ASP 3.4 1.9 - - - +
298A ASN 3.8 22.0 - - - +
299A GLY 4.0 15.9 - - - -
300A ALA* 4.0 2.9 - - - +
303A ALA* 3.5 24.7 - - + -
328A ALA 3.2 4.8 + - - +
329A ALA 3.2 7.6 + - - +
331A TYR* 1.3 85.8 - - + +
333A ILE* 1.3 59.5 + - - +
335A ARG* 2.9 32.0 + - + +
337A GLY 4.4 5.4 - - - +
338A PHE* 4.0 18.8 - - + -
339A SER 3.7 33.0 - - - +
340A LEU* 4.3 9.2 - - + -
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Residues in contact with ILE 333 (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 PHE* 4.1 36.3 - - + -
294A ILE* 4.3 18.2 - - + -
295A ILE 3.1 3.8 + - - -
296A ASP 2.9 33.6 + - - -
297A THR* 4.1 27.1 - - + +
300A ALA* 3.9 24.0 - - + -
329A ALA* 2.8 27.3 + - + +
330A ALA* 3.7 6.1 - - - +
331A TYR 3.4 0.2 - - - -
332A ILE* 1.3 75.3 - - - +
334A CYS* 1.3 58.1 + - - +
335A ARG 3.2 0.4 + - - -
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Residues in contact with CYS 334 (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 PHE* 4.0 20.0 - - - -
293A GLN* 3.9 21.3 - - - +
295A ILE* 3.6 20.9 - - + +
330A ALA* 3.3 16.6 + - - +
331A TYR* 3.5 4.9 + - - +
332A ILE 3.1 1.2 - - - -
333A ILE* 1.3 75.6 - - - +
335A ARG* 1.3 63.7 + - + +
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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