Contacts of the helix formed by residues 262 - 274 (chain A) in PDB entry 3NJ8
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 HIS 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 5.5 2.0 + - - -
227A LEU* 4.6 2.3 - - - +
259A ARG* 5.4 2.0 - - - +
260A ASP* 3.6 7.5 + - + +
261A LEU* 1.3 76.4 - - - +
263A SER* 1.3 92.2 + - - +
264A ASP* 3.0 40.6 + - + -
265A ASP* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS 4.6 8.3 + - - -
22A GLY 4.7 1.2 + - - -
23A TYR* 4.0 17.1 - - - -
25A TRP* 5.9 1.2 - - - -
26A ALA* 3.7 21.7 - - - +
227A LEU* 3.9 30.2 - - - +
262A HIS* 1.3 90.3 + - - +
264A ASP* 1.3 66.3 + - - +
265A ASP 2.9 1.2 + - - -
266A VAL* 3.0 8.3 + - - +
267A GLY 2.8 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.2 10.3 - - - +
29A LYS* 4.1 24.5 + - - +
30A HIS* 3.2 30.4 + - + +
262A HIS* 3.0 32.9 + - + -
263A SER* 1.3 81.9 + - - +
265A ASP* 1.3 55.7 + - - +
267A GLY 3.4 0.7 - - - +
268A GLY* 2.6 32.9 + - - -
279B ARG* 5.0 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 2.8 44.8 + - - -
261A LEU* 2.9 22.6 - - + +
262A HIS* 2.9 27.6 + - - +
263A SER 2.9 0.8 + - - -
264A ASP* 1.3 81.4 - - - +
266A VAL* 1.3 57.5 + - - +
268A GLY* 3.1 1.4 + - - -
269A ALA* 2.9 22.9 + - - +
288A VAL* 4.3 4.0 - - - +
277B LEU 3.7 7.7 - - - +
279B ARG* 3.4 23.0 + - + +
280B ALA* 3.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.2 43.7 - - + +
27A ILE* 5.0 5.2 - - + -
177A LEU* 4.3 15.3 - - + -
222A ILE* 3.7 26.2 - - + -
224A ALA* 3.9 15.7 - - + -
261A LEU* 4.9 3.1 - - + -
263A SER 3.0 1.2 + - - -
265A ASP* 1.3 74.6 - - + +
267A GLY* 1.3 60.8 + - - +
269A ALA* 3.8 6.7 - - - -
270A ALA* 2.8 30.7 + - - +
288A VAL* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 5.2 0.2 - - - -
26A ALA* 3.8 16.1 - - - +
27A ILE* 4.2 7.3 - - - +
30A HIS* 3.2 29.5 - - - +
263A SER 2.8 14.0 + - - -
264A ASP 2.9 5.4 + - - -
266A VAL* 1.3 78.9 - - - +
268A GLY* 1.3 60.5 + - - +
270A ALA* 3.4 3.1 + - - +
271A LEU 3.1 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.5 17.0 + - - -
264A ASP 2.6 15.6 + - - -
265A ASP 3.7 2.5 - - - -
267A GLY* 1.3 69.7 - - - -
269A ALA* 1.3 64.5 + - - +
271A LEU* 3.3 6.5 + - - +
272A PHE* 3.2 20.8 + - - +
277B LEU* 4.1 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 3.8 6.3 - - + -
265A ASP 2.9 13.2 + - - +
266A VAL* 3.0 8.5 + - - +
268A GLY* 1.3 78.8 - - - +
270A ALA* 1.3 62.6 + - - +
272A PHE* 3.4 16.1 + - - +
273A LEU* 3.4 12.0 + - - +
286A LEU* 4.6 3.0 - - + +
288A VAL* 3.6 33.7 - - + -
272B PHE* 4.0 20.9 - - + -
277B LEU 3.9 2.2 + - - +
281B VAL* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.9 32.1 - - + -
175A VAL* 4.7 4.5 - - + -
222A ILE* 3.3 20.7 - - + +
266A VAL 2.8 19.0 + - - +
267A GLY 3.7 4.3 - - - +
269A ALA* 1.3 70.7 - - - +
271A LEU* 1.3 67.6 + - - +
273A LEU* 2.8 17.0 + - - +
274A LEU* 3.0 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.0 28.9 - - + -
7A LEU* 3.6 29.2 - - + -
30A HIS* 3.2 42.4 - - + +
31A LEU* 3.9 12.9 - - + +
33A SER* 5.3 2.0 - - - +
34A ALA* 3.8 7.2 - - + -
267A GLY 3.1 12.1 + - - +
268A GLY* 3.5 8.3 - - - +
270A ALA* 1.3 77.8 - - - +
272A PHE* 1.3 64.4 + - - +
274A LEU* 3.4 2.1 + - - +
275A SER* 3.2 21.3 + - - -
4B PRO* 5.5 7.4 - - + -
277B LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.8 8.0 - - + +
268A GLY 3.2 4.7 + - - +
269A ALA 3.4 8.5 - - - +
270A ALA 2.9 0.4 + - - -
271A LEU* 1.3 79.7 - - - +
273A LEU* 1.3 90.7 + - + +
275A SER* 2.8 30.5 + - - -
277A LEU* 4.0 17.7 - - + -
278A ALA* 3.2 36.6 - - + +
281A VAL* 4.2 6.7 - - + -
286A LEU* 5.3 0.2 - - + -
269B ALA* 3.9 35.7 - - + -
272B PHE* 3.5 55.9 - + + -
277B LEU* 5.4 0.7 - - + -
286B LEU* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER* 3.6 2.6 + - - -
175A VAL* 4.2 5.8 - - + -
218A ARG* 2.6 34.7 + - - -
220A ASN* 4.0 36.8 + - + +
221A ALA 4.6 1.8 - - - +
222A ILE* 3.3 37.9 - - + -
269A ALA 3.4 5.8 + - - +
270A ALA* 2.8 11.9 + - - +
272A PHE* 1.3 99.3 - - + +
274A LEU* 1.3 55.9 + - + +
275A SER 3.3 0.4 - - - -
278A ALA* 3.7 4.3 - - + -
281A VAL* 4.1 13.9 - - + -
284A VAL* 4.6 5.6 - - + -
286A LEU* 3.9 19.3 - - + -
286B LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.3 1.9 - - - +
10A GLN* 4.7 2.3 - - - +
27A ILE* 4.4 0.2 - - + -
31A LEU* 3.5 26.5 - - + -
123A ILE* 3.4 46.1 - - + +
124A LEU 3.9 4.9 - - - +
125A VAL* 3.7 18.8 - - + -
173A SER* 3.7 32.2 - - - +
174A ALA 4.1 0.9 - - - -
175A VAL* 3.7 30.3 - - + +
218A ARG* 4.1 3.6 - - - -
270A ALA* 3.0 23.6 + - + +
271A LEU 3.8 3.8 - - - +
273A LEU* 1.3 77.9 - - - +
275A SER* 1.3 58.9 + - - +
276A PRO* 4.7 0.5 - - - +
----------------------------------------------------------
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