Contacts of the helix formed by residues 281 - 290 (chain B) in PDB entry 2VXO
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 GLN 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.8 27.8 - - + +
279B GLU 3.2 1.0 - - - +
280B SER* 1.3 83.1 + - - +
282B SER* 1.3 52.0 + - - +
283B VAL 3.1 4.3 - - - -
284B GLU* 3.1 10.2 + - - +
285B GLU* 2.7 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG 3.7 16.4 + - - -
279B GLU* 4.0 6.8 - - - +
281B GLN* 1.3 79.1 - - - +
283B VAL* 1.3 58.7 + - - +
285B GLU* 4.0 12.2 - - - +
286B ALA* 3.3 24.4 + - - +
432B LEU* 4.4 2.6 - - - +
435B ARG* 3.6 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 4.3 19.7 - - + -
245B GLY* 4.0 25.4 - - - +
250B THR* 4.1 20.2 - - + +
269B HIS* 6.5 0.7 - - + -
279B GLU 3.3 21.2 + - - +
280B SER* 4.8 3.8 - - - -
281B GLN 3.1 0.6 - - - -
282B SER* 1.3 78.8 + - - +
284B GLU* 1.3 63.7 + - - +
285B GLU 3.3 0.2 - - - -
286B ALA* 4.3 0.9 - - - +
287B LEU* 3.3 27.7 + - + +
432B LEU* 4.1 14.3 - - + +
435B ARG* 3.4 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 5.9 0.4 - - - -
280B SER 3.7 15.5 + - - +
281B GLN* 3.1 14.8 + - - +
283B VAL* 1.3 80.3 - - - +
285B GLU* 1.3 58.7 + - + +
287B LEU* 3.9 1.4 - - - +
288B LYS* 2.9 42.0 + - + +
292B ILE 4.7 0.9 - - - +
293B GLN* 4.9 5.0 - - - +
294B VAL* 3.3 40.4 + - + +
296B VAL* 3.5 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 2.7 38.5 + - + +
282B SER* 4.3 9.3 + - - -
284B GLU* 1.3 76.2 - - + +
286B ALA* 1.3 59.2 + - - +
288B LYS* 3.3 8.0 + - - +
289B LYS* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER 3.3 18.8 + - - +
283B VAL 3.8 1.3 + - - +
285B GLU* 1.3 78.0 - - - +
287B LEU* 1.3 62.6 + - - +
289B LYS* 3.7 6.4 + - - +
290B LEU* 3.5 28.7 + - - +
428B LEU* 5.0 1.6 - - + -
429B PRO* 4.2 20.7 - - + +
432B LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.5 32.8 - - + -
250B THR* 4.1 32.1 - - + +
253B THR* 4.7 6.1 - - + -
254B ALA* 4.6 4.0 - - + +
283B VAL* 3.3 24.3 + - + +
284B GLU 4.0 2.9 - - - +
285B GLU 3.2 0.6 - - - -
286B ALA* 1.3 77.6 - - - +
288B LYS* 1.3 63.2 + - - +
290B LEU* 3.1 12.4 + - + +
291B GLY 3.3 0.2 + - - -
292B ILE* 2.8 59.2 + - + +
294B VAL* 3.8 10.5 - - + -
428B LEU* 4.3 11.0 - - + -
432B LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 2.9 32.9 + - + +
285B GLU* 3.3 8.3 + - - +
287B LEU* 1.3 75.0 - - - +
289B LYS* 1.3 55.7 + - - +
291B GLY* 2.7 24.9 + - - -
292B ILE 3.2 14.7 + - - +
293B GLN* 3.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU 2.9 17.8 + - - +
286B ALA* 3.8 8.5 - - - +
287B LEU 3.3 0.2 - - - -
288B LYS* 1.3 77.1 - - - +
290B LEU* 1.3 59.9 + - + +
291B GLY 3.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA* 5.6 1.6 - - + -
257B ASN* 5.0 1.6 - - - +
286B ALA 3.5 16.8 + - - +
287B LEU* 3.1 11.1 + - + +
288B LYS 3.1 1.2 - - - -
289B LYS* 1.3 77.4 - - + +
291B GLY* 1.3 61.4 + - - +
292B ILE* 3.4 17.4 + - + +
426B LEU 4.3 8.5 - - - +
427B GLY* 3.4 40.8 - - - +
428B LEU* 4.0 22.9 - - + +
429B PRO* 5.0 1.1 - - + -
----------------------------------------------------------
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