Contacts of the helix formed by residues 298 - 313 (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 ASN 298 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 4.9 8.7 + - - +
132B ARG* 4.6 9.5 - - + +
134B MET* 3.7 24.3 - - + -
295B ILE 5.0 0.2 - - - +
296B ASP* 3.3 15.2 - - + -
297B THR 1.3 76.0 + - - +
299B GLY* 1.3 58.1 + - - +
300B ALA 3.2 1.6 + - - -
301B GLY* 3.7 8.3 + - - -
302B ASP* 4.3 2.3 + - - +
401B ADN 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 5.0 0.2 - - - -
132B ARG* 6.0 0.2 - - - +
297B THR* 3.3 6.5 - - - -
298B ASN* 1.3 76.9 - - - +
300B ALA* 1.3 62.2 + - - +
301B GLY 3.3 0.7 - - - -
302B ASP* 3.4 4.4 + - - -
303B ALA* 3.2 17.8 + - - +
332B ILE* 4.1 3.6 - - - -
337B GLY 6.2 0.4 - - - -
338B PHE* 3.4 34.2 - - - -
401B ADN 3.6 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLN 3.5 24.9 - - - +
294B ILE* 3.4 13.7 - - - +
297B THR* 3.2 20.4 - - - +
298B ASN 3.2 0.6 - - - -
299B GLY* 1.3 75.8 - - - +
301B GLY* 1.3 61.0 + - - +
303B ALA* 3.2 5.0 + - - +
304B PHE* 2.8 28.2 + - - +
329B ALA* 3.6 8.8 - - + +
332B ILE* 4.3 7.2 - - + -
333B ILE* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASN* 4.8 7.4 + - - -
265B THR* 6.2 0.2 - - - -
294B ILE 3.4 13.0 + - - -
295B ILE* 4.0 13.8 + - - -
298B ASN 3.7 7.0 + - - -
299B GLY 3.3 0.4 - - - -
300B ALA* 1.3 76.9 - - - +
302B ASP* 1.3 64.6 + - - +
304B PHE* 3.4 7.1 + - - +
305B ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.7 24.4 - - - +
68B ASN* 3.3 30.2 + - + -
69B THR* 2.9 32.1 + - - +
165B TYR* 4.8 4.9 + - - -
195B ASN* 5.0 4.2 + - - -
298B ASN 4.4 1.2 + - - +
299B GLY* 3.4 7.9 + - - +
300B ALA 3.3 0.4 - - - -
301B GLY* 1.3 77.2 - - - +
303B ALA* 1.3 61.6 + - - +
305B ALA* 3.5 2.2 + - - -
306B ALA* 3.2 13.9 + - - +
338B PHE* 4.2 1.1 - - + -
401B ADN 2.5 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.6 18.6 - - - -
299B GLY 3.2 8.8 + - - +
300B ALA 3.5 7.9 - - - +
301B GLY 3.2 0.2 - - - -
302B ASP* 1.3 76.1 - - - +
304B PHE* 1.3 59.9 + - - +
306B ALA* 3.2 2.2 + - - +
307B GLY 2.9 25.1 + - - -
328B ALA* 3.2 23.3 - - - +
329B ALA* 4.0 1.3 - - - -
332B ILE* 3.5 32.1 - - + -
338B PHE* 4.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 4.1 20.0 - + - -
263B ILE* 4.0 18.8 - - + -
265B THR* 3.9 14.8 - - + -
271B LEU* 3.6 32.8 - - + -
294B ILE* 3.7 26.5 - - + +
300B ALA 2.8 17.0 + - - +
301B GLY* 3.5 11.2 - - - +
303B ALA* 1.3 77.7 - - - +
305B ALA* 1.3 62.9 + - - +
308B PHE* 3.1 20.1 + - + +
322B LEU* 4.1 12.6 - - + -
325B ALA* 3.2 50.4 + - + +
326B VAL* 4.1 8.5 - - + -
329B ALA* 4.3 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 4.1 0.9 - - + -
165B TYR* 3.6 36.3 - - + +
195B ASN* 4.6 1.8 - - - +
220B PHE* 4.0 26.2 - - + -
301B GLY 3.2 9.4 + - - +
302B ASP 3.8 8.1 - - - +
303B ALA 3.3 0.2 - - - -
304B PHE* 1.3 81.1 - - - +
306B ALA* 1.3 60.9 + - - +
308B PHE* 3.8 0.9 - - - +
309B ILE* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 3.3 27.3 - - + +
72B MET* 3.8 22.4 - - + -
73B ILE* 3.7 17.3 - - + +
76B ILE* 4.2 2.0 - - - -
302B ASP 3.2 11.7 + - - +
303B ALA 3.2 8.8 + - - +
305B ALA* 1.3 79.1 - - - +
307B GLY* 1.3 57.0 + - - +
309B ILE 3.4 0.3 + - - -
310B ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.9 11.0 - - - -
303B ALA 2.9 14.5 + - - -
304B PHE 4.0 0.9 - - - -
306B ALA* 1.3 73.5 - - - +
308B PHE* 1.3 67.1 + - - +
310B ALA* 4.1 1.4 - - - +
311B ASP* 3.4 13.5 + - - +
324B ALA* 3.6 30.6 - - - +
325B ALA* 3.8 6.3 - - - -
328B ALA* 3.8 8.4 - - - +
346B TYR* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 4.0 10.5 - - + -
220B PHE* 4.0 23.3 - + + -
261B LEU* 3.5 30.5 - - + -
263B ILE* 3.7 8.1 - - + -
304B PHE* 3.1 18.1 + + + +
305B ALA 3.8 3.6 - - - +
307B GLY* 1.3 78.0 - - - +
309B ILE* 1.3 62.2 + - + +
312B TYR* 2.9 59.4 + + + +
318B MET* 3.7 13.7 - - - -
321B SER* 3.6 36.5 - - - -
322B LEU* 3.7 28.3 - - + -
325B ALA* 3.6 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 4.7 0.4 - - + -
73B ILE* 3.9 23.3 - - + -
163B VAL* 4.1 14.8 - - + -
165B TYR* 3.5 34.1 - - + -
191B LEU* 5.4 0.4 - - + -
193B CYS* 3.9 23.1 - - + -
218B ILE* 5.4 1.3 - - + -
220B PHE* 4.0 14.8 - - + -
305B ALA 3.1 19.3 + - - +
306B ALA 4.0 2.2 - - - +
308B PHE* 1.3 82.1 - - + +
310B ALA* 1.3 64.5 + - - +
312B TYR* 4.4 3.1 - - - -
313B ILE* 3.0 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.4 7.8 - - + +
76B ILE* 3.8 32.5 - - + -
77B ILE* 4.1 17.4 - - + +
306B ALA 2.9 19.6 + - - +
307B GLY 4.1 3.4 - - - +
309B ILE* 1.3 78.6 - - - +
311B ASP* 1.3 57.4 + - - +
313B ILE* 3.9 6.6 - - - +
314B ARG* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 5.2 2.1 - - - +
307B GLY 3.4 10.6 + - - +
308B PHE 3.4 1.8 + - - +
309B ILE 3.1 0.4 - - - -
310B ALA* 1.3 80.1 - - - +
312B TYR* 1.3 65.9 + - - +
313B ILE 3.3 0.4 - - - -
314B ARG* 3.1 31.4 + - - +
315B GLY 3.5 0.2 + - - -
316B LYS* 3.1 44.3 + - + +
320B THR* 4.3 8.1 - - - +
321B SER* 3.7 13.7 - - - +
324B ALA* 3.5 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 4.5 21.3 - - + -
218B ILE* 4.1 24.0 - - + -
261B LEU* 4.8 12.7 - - + +
308B PHE* 2.9 43.5 + + + +
309B ILE* 4.0 3.4 - - - +
311B ASP* 1.3 77.8 - - - +
313B ILE* 1.3 61.2 + - + +
315B GLY* 3.3 13.3 + - - -
316B LYS 3.7 17.4 + - - +
317B PRO* 4.6 1.6 - - + -
318B MET* 4.5 13.9 - - + -
321B SER* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.8 34.0 - - + +
8B TYR* 4.2 14.2 + - + -
9B VAL* 3.7 29.6 - - + -
73B ILE* 5.1 0.7 - - + -
77B ILE* 4.3 7.9 - - + -
163B VAL* 3.7 23.6 - - + -
191B LEU* 3.9 16.8 - - + -
309B ILE* 3.0 38.1 + - + +
310B ALA* 3.9 7.4 - - - +
312B TYR* 1.3 76.8 - - + +
314B ARG* 1.3 58.8 + - - +
315B GLY 3.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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