Contacts of the helix formed by residues 273 - 283 (chain B) in PDB entry 3NMV
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 ARG 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 3.3 36.6 + - - +
268B ASP 3.0 30.0 + - - -
269B HIS* 3.6 5.4 - - - -
270B LYS* 3.0 20.0 + - + +
272B ASP* 1.3 79.2 + - - +
274B ASP* 1.3 58.3 + - - +
275B ASP* 3.0 37.4 + - - +
276B GLU* 3.0 20.5 + - + +
277B ALA* 2.7 33.3 + - - +
303B ARG* 5.1 1.4 - - - +
319B GLU* 2.9 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP 3.2 7.6 + - - +
273B ARG* 1.3 72.0 - - - +
275B ASP* 1.3 63.8 + - - +
277B ALA* 3.5 5.8 + - - +
278B ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 3.0 45.2 + - - +
274B ASP* 1.3 74.6 + - - +
276B GLU* 1.3 67.2 + - - +
278B ALA* 3.2 8.0 + - - +
279B ARG* 2.8 26.9 + - - +
303B ARG* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B HIS* 3.9 4.9 - - + -
270B LYS 3.5 21.1 - - - +
271B PRO 4.2 0.9 - - - +
273B ARG* 3.0 27.9 + - + +
275B ASP* 1.3 79.9 + - - +
277B ALA* 1.3 65.2 + - - +
279B ARG* 2.9 31.4 + - - +
280B ILE* 2.9 29.5 + - - +
302B SER* 2.4 36.2 + - - +
303B ARG* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO 3.4 19.9 + - - +
272B ASP* 4.6 5.2 - - - +
273B ARG 2.7 18.4 + - - +
274B ASP* 3.8 7.9 - - - +
276B GLU* 1.3 72.4 - - - +
278B ALA* 1.3 62.6 + - - +
280B ILE* 3.4 6.2 + - - +
281B GLU* 3.1 30.5 + - + +
287B VAL* 4.5 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASP 3.1 15.3 + - - +
275B ASP* 3.5 10.8 - - - +
276B GLU 3.1 0.2 - - - -
277B ALA* 1.3 75.2 - - - +
279B ARG* 1.3 66.1 + - - +
281B GLU* 3.4 9.0 + - - +
282B ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP 2.8 17.1 + - - +
276B GLU* 2.9 39.6 + - - +
278B ALA* 1.3 74.1 - - - +
280B ILE* 1.3 65.0 + - - +
282B ALA* 3.4 7.6 + - + +
283B ALA* 2.9 37.7 + - - +
302B SER 3.2 18.4 + - - -
303B ARG* 3.6 12.3 - - - +
312B PRO 4.3 5.5 + - - -
313B SER 3.0 28.9 + - - -
315B ILE* 3.8 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 4.9 1.6 - - + +
276B GLU 2.9 20.5 + - - +
277B ALA 3.6 4.7 - - - +
279B ARG* 1.3 85.2 - - - +
281B GLU* 1.3 68.6 + - - +
283B ALA* 3.0 13.6 + - - +
284B GLY 3.2 0.2 + - - -
285B GLY 2.9 43.1 + - - +
286B LYS* 3.6 7.4 - - - +
287B VAL* 4.0 26.2 - - + -
295B VAL* 4.5 10.5 - - + -
302B SER* 4.3 13.7 - - - -
313B SER* 3.4 40.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 3.1 20.0 + - + +
278B ALA* 3.7 7.4 - - - +
280B ILE* 1.3 77.0 - - - +
282B ALA* 1.3 62.7 + - - +
284B GLY* 2.9 17.7 + - - -
285B GLY 3.2 24.5 - - - +
286B LYS* 3.9 13.5 - - - +
287B VAL* 4.4 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.0 17.2 + - - +
279B ARG* 3.6 7.9 - - + +
281B GLU* 1.3 76.4 - - - +
283B ALA* 1.4 58.1 + - - +
284B GLY 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ARG* 2.9 23.9 + - - +
280B ILE* 3.0 6.4 + - - +
282B ALA* 1.4 74.4 - - - +
284B GLY* 1.3 57.6 + - - +
285B GLY 3.6 0.2 - - - -
312B PRO* 3.7 49.2 - - + +
313B SER* 4.2 7.7 + - - +
----------------------------------------------------------
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