Contacts of the helix formed by residues 287 - 301 (chain B) in PDB entry 3V9G
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 SER 287 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.4 11.6 - - - -
286B GLY* 1.3 72.8 - - - -
288B VAL* 1.3 65.6 + - - +
289B PRO* 3.7 11.3 - - - +
290B THR* 3.0 26.5 + - - -
291B PHE 3.1 17.7 + - - -
315B CYS* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 4.3 10.1 - - + -
286B GLY 3.9 1.0 + - - -
287B SER* 1.3 69.5 - - - +
289B PRO* 1.3 65.8 - - + +
291B PHE* 3.3 3.1 + - - +
292B LYS* 2.9 55.9 + - + +
315B CYS* 3.8 24.2 - - + +
316B GLY* 4.5 2.7 - - - +
447B GLU* 6.0 0.7 - - - +
476B TYR* 3.9 27.6 - - + +
525B ALA* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER* 3.4 15.7 - - - +
288B VAL* 1.3 97.0 - - + +
290B THR* 1.3 56.5 + - - +
292B LYS* 3.9 10.9 - - + +
293B HIS* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 6.2 0.7 - - + -
284B PHE* 3.8 22.0 - - + -
287B SER* 3.0 21.3 + - - -
288B VAL 3.3 0.4 - - - -
289B PRO* 1.3 77.6 - - - +
291B PHE* 1.3 59.2 + - - +
293B HIS* 3.3 9.1 + - + +
294B LEU* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.8 35.4 - + - -
282B ILE* 5.3 2.2 - - + -
284B PHE* 3.6 39.1 - + + -
287B SER 3.1 5.4 + - - +
288B VAL 3.3 6.7 + - - +
290B THR* 1.3 76.2 - - - +
292B LYS* 1.3 63.3 + - - +
294B LEU* 3.3 8.6 + - + +
295B TRP* 3.0 43.6 + + - +
311B LEU* 4.2 19.3 - - + -
312B ALA 3.7 11.2 - - - -
313B GLY* 3.5 29.8 - - - -
315B CYS* 3.9 11.9 - - - -
528B THR* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.8 40.6 - - + +
303A ASP* 3.5 39.3 + - - +
305A PHE 5.8 1.3 + - - -
308A PHE* 4.1 16.4 - - + -
288B VAL* 2.9 42.2 + - + +
289B PRO* 3.9 8.5 - - + +
291B PHE* 1.3 73.2 - - - +
293B HIS* 1.3 57.0 + - - +
295B TRP* 3.3 3.9 + - - +
296B LYS* 2.9 38.3 + - + +
525B ALA* 6.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PRO* 6.2 3.8 - - + -
271B ASP* 4.6 5.2 - - - -
289B PRO 3.0 20.0 + - - +
290B THR* 3.5 10.3 + - - +
292B LYS* 1.3 77.4 - - - +
294B LEU* 1.3 60.1 + - - +
296B LYS* 3.3 12.7 + - + +
297B GLN* 3.0 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.9 26.5 - - + -
270B GLY* 3.8 24.0 - - - -
273B VAL* 5.5 0.9 - - + -
274B THR* 4.2 10.8 - - + +
282B ILE* 4.4 21.1 - - + -
284B PHE* 3.9 21.1 - - + -
290B THR* 3.0 26.1 + - + +
291B PHE* 3.7 9.4 - - + +
293B HIS* 1.3 77.8 - - - +
295B TRP* 1.3 57.8 + - - +
297B GLN* 3.2 21.8 + - - +
298B VAL* 3.0 33.3 + - - +
311B LEU* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 4.8 16.2 + + - +
298A VAL* 4.5 13.8 - - + +
299A ALA* 3.8 29.6 - - + +
302A LEU* 3.5 23.2 - - + +
308A PHE* 3.9 29.2 - + + -
309A PRO* 3.7 25.1 - - + -
311A LEU* 5.5 3.4 - - + -
291B PHE* 3.0 39.8 + + - +
292B LYS 3.4 9.2 - - - +
294B LEU* 1.3 78.3 - - - +
296B LYS* 1.3 61.4 + - - +
298B VAL* 3.5 2.8 + - - +
299B ALA* 3.1 19.2 + - + +
311B LEU* 3.4 29.1 - - + +
528B THR* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 3.2 35.0 - - + +
300A GLN* 4.5 11.4 + - - +
302A LEU* 4.2 14.1 - - + -
303A ASP* 3.0 30.3 + - - -
292B LYS* 2.9 25.2 + - - +
293B HIS* 3.7 11.4 - - + +
295B TRP* 1.3 74.9 - - - +
297B GLN* 1.3 61.2 + - + +
299B ALA* 3.3 1.9 + - - +
300B GLN* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLY 3.8 4.3 - - - +
271B ASP* 2.9 29.7 + - - +
274B THR* 3.6 24.8 + - - +
293B HIS* 3.0 45.6 + - + +
294B LEU* 3.2 24.5 + - - +
296B LYS* 1.3 73.2 - - + +
298B VAL* 1.3 65.6 + - - +
300B GLN* 3.3 7.0 + - - +
301B ASN* 3.2 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 4.6 14.1 - - + +
274B THR* 3.8 19.7 - - + -
279B LEU* 3.8 19.7 - - + -
282B ILE* 4.1 9.6 - - + -
294B LEU 3.0 18.8 + - - +
295B TRP 3.8 4.5 - - - +
297B GLN* 1.3 77.0 - - - +
299B ALA* 1.3 62.9 + - - +
301B ASN 3.2 1.2 + - - -
302B LEU* 3.1 19.7 + - + +
305B PHE* 3.1 27.6 - - + -
309B PRO* 3.9 21.5 - - + -
311B LEU* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 3.8 27.1 - - + +
296A LYS* 3.2 25.6 - - - +
299A ALA* 3.4 34.1 - - + -
295B TRP 3.1 11.5 + - - +
296B LYS 3.7 2.9 - - - +
297B GLN 3.3 0.2 - - - -
298B VAL* 1.3 72.9 - - - +
300B GLN* 1.3 66.0 + - - +
301B ASN 3.0 2.8 + - - -
302B LEU* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS* 4.5 10.8 + - - +
296B LYS 2.9 17.6 + - - +
297B GLN* 3.3 8.7 + - - +
299B ALA* 1.3 75.7 - - - +
301B ASN* 1.3 65.8 + - - +
302B LEU 3.9 0.3 + - - -
303B ASP* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 3.0 30.0 + - - +
275B SER* 4.3 4.4 + - - -
297B GLN* 3.2 19.4 + - - +
298B VAL 3.2 2.9 + - - -
299B ALA 3.0 1.0 - - - -
300B GLN* 1.3 87.0 - - - +
302B LEU* 1.3 62.7 + - - +
303B ASP* 3.0 4.2 + - - -
304B ARG* 2.9 60.0 + - + +
305B PHE* 3.3 9.2 - - + -
----------------------------------------------------------
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