Contacts of the helix formed by residues 257 - 274 (chain F) in PDB entry 1NZB
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 257 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F GLN* 3.4 6.4 + - - +
256F LEU* 1.3 74.7 - - - +
258F THR* 1.3 59.3 + - - +
259F ARG* 3.1 11.7 + - - +
260F ALA* 2.9 30.0 + - - +
261F LEU* 3.2 10.5 + - - +
107G UMP 2.9 34.5 + - - -
108G T 4.0 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ILE* 3.4 21.6 - - + +
175F ALA* 3.6 37.9 - - + +
178F ALA* 4.5 7.4 - - + -
255F GLN* 5.6 3.7 - - - +
256F LEU 3.7 1.0 + - - -
257F SER* 1.3 72.4 - - - +
259F ARG* 1.3 58.6 + - - +
261F LEU* 3.4 7.5 + - - +
262F GLU* 2.9 33.0 + - - +
125H T 4.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 259 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F SER* 2.9 10.2 - - - +
258F THR* 1.3 79.0 + - - +
260F ALA* 1.3 59.4 + - - +
262F GLU* 3.2 27.8 + - - +
263F GLY* 2.8 29.8 + - - +
266F GLU* 5.2 7.3 + - - -
344F IOD 4.2 1.5 - - - +
107G UMP 5.0 6.7 - - + +
108G T 3.8 27.4 - - + +
109G C 4.2 5.4 - - - +
127H C 3.5 27.7 - - - +
128H G 2.7 50.3 + - - -
129H A 4.2 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F ARG* 6.1 0.9 - - - +
256F LEU* 3.4 27.4 - - + -
257F SER* 2.9 14.9 + - - +
259F ARG* 1.3 76.7 - - - +
261F LEU* 1.3 57.6 + - - +
263F GLY* 2.9 2.6 + - - -
264F ILE* 2.9 31.9 + - + +
344F IOD 3.9 12.7 - - + +
106G C 4.1 18.4 - - - +
107G UMP 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F PHE* 3.3 42.8 - - + -
174F ILE* 3.9 21.8 - - + +
177F ILE* 4.5 2.2 - - + -
178F ALA* 3.9 34.5 - - + +
239F PHE* 5.3 4.0 - - + -
256F LEU* 3.7 28.5 - - + +
257F SER 3.2 10.6 + - - +
258F THR* 3.7 9.9 - - - +
259F ARG 3.1 0.6 - - - -
260F ALA* 1.3 74.6 - - - +
262F GLU* 1.3 61.0 + - - +
263F GLY 2.9 5.1 + - - -
264F ILE* 3.2 23.1 + - + +
265F PHE* 3.5 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ILE* 3.5 17.5 - - + +
258F THR* 2.9 23.3 + - - +
259F ARG* 3.2 27.0 + - - +
261F LEU* 1.3 76.2 - - - +
263F GLY* 1.3 61.9 + - - +
265F PHE* 3.4 10.9 + - - +
266F GLU* 3.3 21.3 + - - +
286F TRP 4.6 1.4 - - - +
287F SER* 5.0 3.2 - - - -
288F GLY* 4.5 7.6 - - - +
125H T 3.7 3.0 - - - +
126H A 2.2 54.1 + - - +
127H C 3.4 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 2.8 17.9 + - - -
260F ALA* 2.9 7.4 + - - -
261F LEU 2.9 0.4 - - - -
262F GLU* 1.3 74.9 - - - +
264F ILE* 1.3 65.9 + - - +
265F PHE 2.9 2.8 + - - -
266F GLU* 3.0 7.2 + - - +
267F ALA* 2.8 26.0 + - - +
344F IOD 4.6 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F ARG* 3.6 19.1 - - - +
160F ASN* 3.2 54.9 + - + +
163F PHE* 4.0 28.5 - - + -
164F LEU* 4.6 3.3 - - + +
239F PHE* 6.1 0.2 - - + -
256F LEU* 4.9 1.3 - - + -
260F ALA* 2.9 14.5 + - + +
261F LEU* 3.5 31.4 - - + +
263F GLY* 1.3 73.5 - - - +
265F PHE* 1.3 59.6 + - - +
267F ALA* 4.0 3.7 - - - +
268F THR* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F PHE* 4.4 14.4 - + - -
163F PHE* 3.3 28.5 - + - -
164F LEU* 3.5 26.5 - - + -
167F ALA* 4.1 14.8 - - + -
174F ILE* 4.6 2.5 - - + -
261F LEU 3.5 17.6 + - - -
262F GLU* 3.4 5.7 + - - +
263F GLY 2.9 1.8 + - - -
264F ILE* 1.3 75.0 - - - +
266F GLU* 1.3 68.2 + - - +
267F ALA 3.0 1.6 + - - -
268F THR* 3.0 6.7 + - - -
269F HIS* 2.8 23.0 + - - +
286F TRP* 3.1 36.2 - + + +
287F SER 3.2 25.1 - - - +
288F GLY* 4.0 17.3 - - - -
290F SER* 4.2 9.6 - - - -
291F ALA* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 5.2 9.0 + - - -
262F GLU 3.3 9.5 + - - +
263F GLY* 3.0 8.8 + - - +
265F PHE* 1.3 78.4 - - - +
267F ALA* 1.3 62.6 + - - +
269F HIS* 3.4 6.2 + - - +
270F ARG* 3.0 34.3 + - + +
276F LYS* 3.6 34.5 + - + +
285F ALA* 4.6 11.7 - - + +
286F TRP 3.3 10.6 + - - +
127H C 5.1 10.2 + - - +
128H G 4.4 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ASN* 5.7 4.3 - - - +
263F GLY 2.8 17.3 + - - +
264F ILE* 4.0 6.1 - - - +
266F GLU* 1.3 73.0 - - - +
268F THR* 1.3 57.0 + - - +
269F HIS 2.9 3.4 - - - -
270F ARG* 2.6 46.9 + - - +
271F LEU* 2.8 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F VAL* 3.6 33.6 - - + +
149F MET* 5.0 9.0 - - - +
160F ASN* 5.2 4.0 + - - +
164F LEU* 3.6 21.4 - - + +
264F ILE* 2.9 22.6 + - - +
265F PHE* 3.0 5.6 + - - -
267F ALA* 1.3 77.1 - - - +
269F HIS* 1.3 61.3 + - - +
271F LEU* 3.6 19.4 - - + +
272F ILE* 3.7 11.1 - - + +
286F TRP* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F LEU* 4.4 7.6 - - + +
265F PHE 2.8 9.2 + - - +
266F GLU 3.6 7.9 - - - +
267F ALA 2.7 4.0 + - - -
268F THR* 1.3 72.6 - - - +
270F ARG* 1.3 67.7 + - - +
272F ILE 3.0 3.8 + - - -
273F TYR* 3.0 61.5 + + + +
274F GLY 5.1 4.2 + - - -
276F LYS* 5.8 4.8 - - + +
284F LEU 3.7 22.7 + - - -
285F ALA* 3.4 20.6 - - + +
286F TRP* 3.5 50.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLU* 3.0 24.6 + - + +
267F ALA* 2.6 29.3 + - - +
269F HIS* 1.3 74.1 + - - +
271F LEU* 1.3 53.9 + - - +
272F ILE 2.6 9.9 + - - -
273F TYR 2.8 0.2 + - - -
274F GLY* 2.5 59.5 + - - +
275F ALA* 3.8 8.4 - - - +
276F LYS 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F VAL* 6.2 1.6 - - + -
148F LEU* 3.8 29.2 - - + +
149F MET* 5.3 14.1 - - + -
267F ALA 2.8 10.6 + - - +
268F THR* 3.6 17.0 - - + +
270F ARG* 1.3 78.3 - - - +
272F ILE* 1.3 71.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F GLN* 3.4 36.1 - - + +
145F VAL* 3.6 31.9 - - + -
148F LEU* 4.3 12.6 - - + -
268F THR 3.7 8.7 - - - +
269F HIS 3.0 2.7 + - - +
270F ARG 2.6 5.1 + - - -
271F LEU* 1.3 93.6 - - + +
273F TYR* 1.3 85.7 + - + +
274F GLY 3.9 0.2 - - - -
286F TRP* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F ASP* 4.1 13.7 + - - -
144F GLN* 4.6 7.1 + - - -
269F HIS* 3.0 50.3 + + + +
270F ARG 2.8 1.6 + - - -
272F ILE* 1.3 116.5 - - + +
274F GLY* 1.3 70.9 + - - +
275F ALA 3.8 4.3 - - - +
286F TRP* 4.7 11.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F HIS* 5.1 3.1 + - - -
270F ARG* 2.5 41.6 + - - +
272F ILE 3.9 0.2 - - - -
273F TYR* 1.3 84.0 - - - +
275F ALA* 1.3 67.8 + - - +
276F LYS* 3.4 2.9 + - - +
----------------------------------------------------------
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