Contacts of the helix formed by residues 317 - 335 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B TYR* 4.7 1.3 - - + -
315B GLY 3.7 4.9 - - - +
316B LYS* 1.3 92.3 - - + +
318B MET* 1.3 66.8 + - - +
319B ILE* 4.5 4.7 - - + +
320B THR* 3.4 22.7 + - + +
321B SER* 2.9 25.6 + - - -
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Residues in contact with MET 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 3.6 40.6 - - + -
263B ILE* 4.0 2.9 - - + -
273B TYR* 3.5 48.2 - - + -
308B PHE* 3.7 9.6 - - + -
312B TYR* 4.5 11.4 - - + -
317B PRO* 1.3 72.0 - - - +
319B ILE* 1.3 62.2 + - + +
321B SER* 3.1 7.4 + - - -
322B LEU* 2.9 57.6 + - + +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR* 3.1 33.4 - - + +
284B PHE* 4.4 17.0 - - + -
317B PRO* 3.5 4.2 - - + +
318B MET* 1.3 82.8 - - + +
320B THR* 1.3 65.9 + - - +
322B LEU* 3.2 7.7 + - + +
323B HIS* 3.0 49.5 + - + +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASP* 4.3 6.1 - - - +
316B LYS* 4.1 26.0 - - + -
317B PRO* 3.4 29.3 + - + +
318B MET 3.3 0.4 - - - -
319B ILE* 1.3 80.3 - - - +
321B SER* 1.3 58.7 + - - +
323B HIS* 3.2 11.7 + - + +
324B ALA* 3.0 24.3 + - - +
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.6 35.3 - - - -
311B ASP* 4.2 9.0 - - - -
312B TYR* 3.3 27.2 + - - +
316B LYS* 3.4 7.6 + - - +
317B PRO 2.9 20.4 + - - -
318B MET 3.4 4.9 - - - -
320B THR* 1.3 74.4 - - - +
322B LEU* 1.3 59.5 + - - +
324B ALA* 3.1 4.2 + - - +
325B ALA* 2.8 27.7 + - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 4.1 6.7 - - + -
271B LEU* 4.3 10.8 - - + -
273B TYR* 3.7 29.6 - - + -
284B PHE* 3.7 28.5 - - + -
304B PHE* 4.1 20.2 - - + -
308B PHE* 3.7 19.7 - - + -
318B MET* 2.9 42.7 + - + +
319B ILE* 3.5 9.6 - - + +
321B SER* 1.3 74.3 - - - +
323B HIS* 1.3 57.0 + - - +
325B ALA* 3.2 6.0 + - - +
326B VAL* 3.0 31.5 + - - +
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.6 24.9 - + - -
319B ILE* 3.0 45.7 + - + +
320B THR* 3.4 11.0 - - + +
322B LEU* 1.3 76.0 - - - +
324B ALA* 1.3 58.0 + - - +
326B VAL* 3.5 7.4 + - + +
327B LYS* 3.0 27.4 + - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY* 3.6 18.3 - - - +
311B ASP* 3.5 34.8 - - - +
320B THR 3.0 9.4 + - - +
321B SER 3.1 8.3 + - - +
323B HIS* 1.3 76.7 - - - +
325B ALA* 1.3 61.8 + - - +
327B LYS* 3.4 11.5 + - + +
328B ALA* 3.2 17.7 + - - +
346B TYR* 4.3 2.9 + - - -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.2 51.8 - - + +
307B GLY* 3.8 1.5 - - - -
308B PHE* 3.6 21.1 - - + +
321B SER 2.8 12.4 + - - +
322B LEU* 3.3 11.7 - - - +
323B HIS 3.2 0.2 - - - -
324B ALA* 1.3 74.0 - - - +
326B VAL* 1.3 64.8 + - - +
328B ALA* 3.3 2.6 + - - +
329B ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 4.2 18.6 - - + -
286B VAL* 4.3 12.3 - - + -
287B GLU* 4.2 28.3 - - + +
289B PHE* 4.8 6.6 - - + -
294B ILE* 4.2 13.9 - - + -
304B PHE* 4.1 17.5 - - + -
322B LEU 3.0 18.3 + - - +
323B HIS* 3.9 7.9 - - + +
325B ALA* 1.3 74.0 - - - +
327B LYS* 1.3 59.5 + - - +
329B ALA* 3.3 5.5 + - - +
330B ALA* 2.8 29.1 + - + +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B HIS 3.0 18.6 + - - +
324B ALA* 3.6 10.5 - - - +
325B ALA 3.2 0.2 - - - -
326B VAL* 1.3 79.7 - - - +
328B ALA* 1.3 56.3 + - - +
330B ALA* 3.4 7.9 + - - +
331B TYR* 3.1 25.8 + - - +
346B TYR* 3.7 45.6 + - + +
347B SER* 3.1 28.9 + - - -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.7 15.3 - - + +
76B ILE* 4.6 0.4 - - + -
303B ALA* 3.2 31.8 - - - +
307B GLY* 3.8 10.1 - - - +
324B ALA 3.2 11.8 + - - +
325B ALA 3.6 5.2 - - - +
327B LYS* 1.3 74.6 - - - +
329B ALA* 1.3 65.0 + - - +
331B TYR* 3.2 4.3 + - - +
332B ILE* 3.2 19.2 + - - +
346B TYR* 3.4 20.1 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.7 30.5 - - + +
300B ALA* 3.6 25.6 - - + +
303B ALA* 4.0 4.8 - - - +
304B PHE* 4.3 4.0 - - + -
325B ALA 3.1 10.6 + - - +
326B VAL* 3.7 7.6 - - - +
328B ALA* 1.3 78.6 - - - +
330B ALA* 1.3 57.8 - - - +
332B ILE* 3.4 2.8 + - - +
333B ILE* 3.0 35.5 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 6.1 0.2 - - + -
289B PHE* 3.5 33.3 - - + -
326B VAL* 2.8 19.3 + - + +
327B LYS* 3.5 10.1 - - - +
328B ALA 3.2 0.2 - - - -
329B ALA* 1.3 77.9 - - - +
331B TYR* 1.3 60.8 + - - +
333B ILE* 3.4 3.5 + - - +
334B CYS* 3.0 30.6 + - - -
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B MET* 4.1 11.0 - - + -
75B TRP* 3.7 25.6 - + - -
327B LYS 3.1 13.9 + - - +
328B ALA 3.2 8.0 + - - +
330B ALA* 1.3 74.1 - - - +
332B ILE* 1.3 75.5 + - + +
334B CYS* 3.3 8.1 + - + +
335B ARG* 3.2 49.6 + - + +
339B SER 3.9 9.4 - - - -
340B LEU* 4.2 7.6 - - + -
341B GLY* 2.9 30.1 + - - -
342B SER 4.3 1.9 + - - -
345B SER* 3.9 23.7 - - - -
346B TYR* 3.8 23.8 - + + -
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 4.2 3.8 - - + -
297B THR* 4.6 6.9 - - - -
299B GLY* 4.0 24.2 - - - +
300B ALA* 4.2 4.0 - - - +
303B ALA* 3.5 27.1 - - + -
328B ALA 3.2 5.0 + - - +
329B ALA 3.4 6.5 + - - +
331B TYR* 1.3 80.7 - - + +
333B ILE* 1.3 57.8 + - - +
335B ARG* 2.8 25.8 + - - +
337B GLY 3.3 17.2 - - - +
338B PHE* 4.1 18.2 - - + -
339B SER 4.0 28.0 - - - +
340B LEU* 4.1 19.3 - - + -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.7 41.3 - - + -
292B ASP* 3.6 32.9 - - + +
293B GLN 3.2 35.4 - - - +
294B ILE* 4.0 3.4 - - - +
297B THR* 4.9 7.2 - - - -
300B ALA* 4.2 8.3 - - + -
329B ALA 3.0 23.9 + - - +
330B ALA* 3.6 6.5 - - - +
331B TYR 3.3 0.2 - - - -
332B ILE* 1.3 77.3 - - - +
334B CYS* 1.3 64.4 + - - +
335B ARG 3.1 8.4 + - - +
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Residues in contact with CYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 5.3 8.5 - - - -
330B ALA* 3.0 23.2 + - - +
331B TYR* 3.3 8.2 + - + +
333B ILE* 1.3 81.2 - - - +
335B ARG* 1.3 62.0 + - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR* 3.2 46.6 + - + +
332B ILE* 2.8 17.7 + - - +
333B ILE 3.1 8.3 - - - +
334B CYS* 1.3 82.9 - - + +
336B SER* 1.3 60.8 + - - +
337B GLY 3.1 9.3 + - - +
339B SER* 2.9 45.7 + - - +
341B GLY* 3.6 26.7 - - - +
345B SER* 6.3 0.8 - - - -
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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
------------------------------------------------------------
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