Contacts of the strand formed by residues 298 - 307 (chain B) in PDB entry 3VAG
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 LEU 298 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 3.6 26.5 - - + +
292B LYS* 4.0 2.2 - - - -
293B ASP* 2.8 33.0 + - + +
296B THR* 3.1 25.8 + - + +
297B GLY* 1.3 75.7 - - - +
299B SER* 1.3 79.3 + - - +
300B LYS* 4.3 0.2 - - - +
403B DIO 3.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 5.7 0.5 - - - +
267B PRO 4.8 1.7 + - - -
268B ASN* 3.6 27.0 - - - +
270B LEU 4.2 6.6 + - - -
290B LEU* 3.7 18.8 - - - +
291B VAL 3.6 7.2 - - - -
292B LYS* 4.1 1.8 - - - -
298B LEU* 1.3 83.6 - - - +
300B LYS* 1.3 59.2 + - - +
301B GLY* 3.0 20.8 + - - -
403B DIO 2.9 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 5.9 0.7 - - - -
291B VAL* 2.9 29.8 + - + +
292B LYS 3.9 4.7 - - - -
293B ASP* 3.7 42.9 + - + +
294B SER 5.3 0.2 - - - +
298B LEU 4.3 0.7 - - - +
299B SER* 1.3 72.3 - - - +
301B GLY* 1.3 60.0 + - - +
302B TYR* 3.5 31.6 + - + +
2P C 3.9 8.7 + - - -
5P U 2.7 31.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
265B GLY 3.5 7.8 + - - -
266B LEU* 3.3 47.1 + - - +
268B ASN* 5.2 5.4 - - - -
299B SER* 3.0 17.3 + - - -
300B LYS* 1.3 78.7 - - - +
302B TYR* 1.3 62.3 + - - +
2P C 3.8 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.7 27.6 - + + -
263B ILE 3.2 14.1 - - - +
264B GLY* 4.1 2.2 - - - -
266B LEU* 4.3 2.4 - - - +
290B LEU* 3.5 7.5 - - - +
291B VAL* 3.1 54.3 + - + +
300B LYS* 3.7 26.8 + - + +
301B GLY* 1.3 78.6 - - - +
303B ALA* 1.3 61.3 + - - +
304B PHE* 4.0 5.2 - + - -
2P C 3.4 32.8 - - - +
3P BRU 3.5 21.4 + - - -
4P U 3.3 31.8 - - - -
5P U 4.5 0.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
262B PHE* 3.6 4.0 - - - -
263B ILE* 2.8 39.4 + - + +
266B LEU* 4.2 11.0 - - + -
275B VAL* 4.5 1.6 - - + -
288B PHE* 4.1 19.3 - - + -
289B ASN 3.3 15.0 - - - +
290B LEU* 4.1 12.8 - - + -
302B TYR* 1.3 77.3 - - - +
304B PHE* 1.3 72.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
260B LYS* 3.8 18.4 - - - -
261B LEU 3.2 16.4 - - - +
262B PHE* 3.6 20.4 - + + -
263B ILE* 4.3 2.7 - - - -
288B PHE* 3.5 3.8 - - - -
289B ASN* 3.0 45.5 + - - +
291B VAL* 3.9 15.3 - - + -
302B TYR* 4.0 10.1 - + - -
303B ALA* 1.3 78.1 - - - +
305B CYS* 1.3 63.7 + - - +
335B ALA* 4.2 7.2 - - + -
3P BRU 3.5 36.6 - + - -
4P U 3.4 55.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B HIS 4.2 0.2 - - - +
260B LYS* 3.5 4.1 - - - +
261B LEU* 2.9 51.0 + - - +
263B ILE* 3.8 11.7 - - - -
279B LEU* 3.8 23.6 - - + -
285B LEU* 4.0 17.5 - - + -
287B ALA* 3.3 17.7 - - - +
288B PHE* 4.0 13.9 - - + -
304B PHE* 1.3 76.4 - - - +
306B GLU* 1.3 64.9 + - - +
307B TYR* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 5.8 0.2 - - - -
143B GLY* 5.8 0.2 - - - -
144B PRO* 3.5 30.3 - - - +
233B GLN* 4.3 4.7 + - - +
237B GLY* 4.1 9.9 - - - -
259B HIS* 3.8 12.0 - - - +
260B LYS* 3.5 34.1 - - + +
285B LEU* 3.6 7.4 - - - -
286B LYS* 2.8 59.2 + - + +
287B ALA* 3.0 20.5 + - + +
305B CYS* 1.3 78.7 - - - +
307B TYR* 1.3 61.2 + - - +
310B ILE* 5.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B HIS 5.1 2.8 + - - -
261B LEU* 3.9 18.6 - - + -
279B LEU* 2.8 38.0 + - + +
282B PHE* 3.8 6.1 - - + -
283B GLY 3.5 27.4 - - - -
284B PRO 3.7 7.6 - - - +
285B LEU* 3.7 17.5 - - + -
286B LYS* 3.2 21.1 + - - -
305B CYS* 4.4 4.3 - - - -
306B GLU* 1.3 74.4 - - - +
308B VAL* 1.3 64.8 + - - +
309B ASP 3.6 21.7 + - - +
310B ILE* 4.3 3.9 + - - +
312B VAL* 3.8 23.3 - - + -
313B THR* 4.4 17.6 + - - +
316B ALA* 3.5 33.3 - - + +
----------------------------------------------------------
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