Contacts of the helix formed by residues 249 - 264 (chain D) in PDB entry 3IFS
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 ASN 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ASP 4.8 0.2 - - - -
241D PHE* 3.0 37.8 + - - -
243D THR* 3.0 22.3 + - + +
245D GLU 3.6 12.1 - - - +
246D LEU 3.0 5.9 + - - +
247D GLU 3.5 0.4 - - - -
248D GLU* 1.3 80.5 - - - +
250D PRO* 1.3 64.4 - - - +
251D ALA* 3.0 21.7 + - - +
252D TYR* 3.1 31.8 + - + -
253D GLN* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D THR* 4.0 25.4 - - + +
5D VAL 5.1 1.6 - - - +
6D THR* 5.5 0.2 - - - -
7D PHE* 4.0 26.7 - - + +
240D ASP 5.0 1.3 - - - +
241D PHE* 3.8 26.5 - - + -
248D GLU 3.5 10.5 - - - +
249D ASN* 1.3 85.6 - - - +
251D ALA* 1.3 61.1 + - - +
253D GLN* 3.3 17.5 + - - +
254D TYR* 3.1 19.8 + - - +
400D PHE* 3.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D PHE* 3.8 22.9 - - + -
249D ASN* 3.0 10.5 + - - +
250D PRO* 1.3 77.4 - - - +
252D TYR* 1.3 66.6 + - + +
254D TYR* 3.4 1.7 + - - +
255D ALA* 3.1 16.5 + - - +
400D PHE* 3.5 35.1 - - + +
403D LYS* 4.3 4.7 - - + -
404D ALA* 3.3 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 3.5 22.9 - - + -
32D HIS* 2.9 28.4 + + + +
35D ILE* 4.4 3.8 - - + +
36D HIS* 4.0 0.5 + - - -
243D THR 3.3 13.5 - - - -
244D SER* 4.5 2.7 - - - -
246D LEU* 3.5 17.9 - - + -
249D ASN* 3.1 40.0 + - + +
251D ALA* 1.3 76.4 - - + +
253D GLN* 1.3 60.1 + - - +
255D ALA* 3.3 5.7 + - - +
256D VAL* 2.9 32.6 + - - +
403D LYS* 3.1 41.5 + - + -
407D MSE 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 3.9 18.8 - - + +
9D TYR* 3.9 24.8 - - + +
21D ILE* 4.9 7.4 - - + -
246D LEU* 3.0 34.3 + - + +
247D GLU* 3.2 23.4 + - - +
248D GLU 4.4 0.4 - - - -
249D ASN 3.0 20.9 + - - +
250D PRO* 3.5 18.3 - - - +
252D TYR* 1.3 77.4 - - - +
254D TYR* 1.3 57.3 + - - +
256D VAL* 3.2 3.3 + - - +
257D VAL* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 3.5 35.6 - + + -
250D PRO 3.1 12.7 + - - +
251D ALA 3.7 6.1 - - - +
253D GLN* 1.3 77.7 - - - +
255D ALA* 1.3 61.5 + - - +
257D VAL* 3.9 0.5 - - - +
258D ARG* 2.9 52.4 + - + +
269D GLU* 2.6 34.0 + - - -
285D TRP* 3.4 17.7 + - - -
289D PHE* 3.9 7.4 - + - -
328D THR* 3.7 18.5 + - + +
382D LEU* 4.2 5.2 - - + -
384D VAL* 5.6 0.4 - - + -
400D PHE* 4.0 16.8 - + + -
401D PHE* 3.5 26.0 - + - -
404D ALA* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ALA 3.1 11.6 + - - +
252D TYR 3.5 8.3 - - - +
254D TYR* 1.3 77.2 - - - +
256D VAL* 1.3 62.8 + - - +
258D ARG* 3.5 4.2 + - - +
259D ASN* 3.1 30.2 + - - -
404D ALA* 3.5 20.9 - - - +
407D MSE 3.5 26.9 - - + -
408D SER* 3.6 15.7 - - - +
411D LEU* 4.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU 4.1 3.8 - - - +
21D ILE* 3.9 33.7 - - + -
24D LEU* 3.9 22.7 - - + +
28D VAL* 3.6 29.4 - - + -
246D LEU* 4.0 10.5 - - + -
252D TYR 2.9 19.1 + - - +
253D GLN* 3.2 4.0 + - - +
255D ALA* 1.3 73.8 - - - +
257D VAL* 1.3 60.4 + - - +
259D ASN* 3.3 3.5 + - - +
260D ALA* 2.9 29.1 + - + +
411D LEU* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 4.3 13.2 - - + -
9D TYR* 4.3 13.7 - - + -
16D ILE* 4.0 24.9 - - + -
21D ILE* 4.0 24.2 - - + -
253D GLN 2.9 22.8 + - - +
254D TYR 3.9 2.7 - - - +
256D VAL* 1.3 73.4 - - - +
258D ARG* 1.3 65.6 + - - +
260D ALA* 3.2 2.1 + - - +
261D LEU* 2.9 30.4 + - + +
382D LEU* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D TYR* 2.9 61.5 + - + +
255D ALA* 3.7 5.4 - - - +
257D VAL* 1.3 75.7 - - - +
259D ASN* 1.3 60.1 + - - +
261D LEU* 3.4 2.0 + - - +
262D TYR* 2.9 28.6 + - - +
269D GLU* 2.9 28.5 + - - +
285D TRP* 4.7 1.6 - - - -
289D PHE* 3.4 33.6 - - - +
293D GLU* 2.8 28.3 + - - -
300D ILE* 3.5 44.8 + - + +
302D PRO* 5.9 0.8 - - - +
326D PHE* 4.2 13.4 - - + -
382D LEU* 5.3 0.2 - - + -
408D SER* 2.8 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 5.4 5.4 - - + -
255D ALA 3.1 19.5 + - - +
256D VAL* 3.8 5.6 - - - +
258D ARG* 1.3 81.3 - - - +
260D ALA* 1.3 56.5 + - - +
262D TYR* 3.3 10.6 + - - +
263D ASN* 3.1 34.8 + - - +
293D GLU* 4.6 0.4 + - - -
300D ILE* 5.3 1.8 - - - -
408D SER* 2.9 41.9 + - - +
411D LEU* 4.0 16.5 - - + +
412D LEU* 3.6 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS* 3.7 12.4 - - - +
16D ILE* 3.8 21.5 - - + -
20D GLU* 3.8 18.8 - - + +
24D LEU* 5.9 3.7 - - + +
256D VAL* 2.9 20.7 + - + +
257D VAL 3.7 3.8 - - - +
259D ASN* 1.3 73.0 - - - +
261D LEU* 1.3 66.1 + - - +
263D ASN* 3.2 16.6 + - - +
264D LYS* 3.2 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 6.1 0.2 - - + -
15D PHE* 4.7 3.4 - - + -
16D ILE* 4.4 16.2 - - + -
257D VAL* 2.9 35.3 + - + +
258D ARG 3.8 3.6 - - - +
260D ALA* 1.3 72.8 - - - +
262D TYR* 1.3 67.5 + - - +
264D LYS* 3.0 35.8 + - + +
265D GLY 3.4 0.3 + - - -
266D LYS* 3.0 24.8 + - + +
326D PHE* 3.6 49.6 - - + -
380D PRO* 4.2 25.6 - - + -
382D LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 2.6 52.0 + - - -
322B ARG* 4.9 2.1 + - - -
322C ARG* 2.9 27.8 + - - -
258D ARG 2.9 13.8 + - - +
259D ASN* 3.3 14.8 - - - +
260D ALA 3.3 0.2 - - - -
261D LEU* 1.3 76.1 - - - +
263D ASN* 1.3 61.5 + - - +
265D GLY* 2.9 21.1 + - - -
266D LYS 3.4 14.2 + - - -
267D THR* 4.1 10.4 - - + +
299D GLY* 3.1 39.1 + - - -
300D ILE* 3.5 26.0 - - + +
412D LEU* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 2.6 44.7 + - + -
263A ASN* 3.3 25.3 + - - +
298A LYS* 3.7 23.5 - - + +
411A LEU 5.6 0.2 - - - +
412A LEU* 3.6 26.2 - - + +
322B ARG* 3.6 2.7 + - - -
259D ASN* 3.1 21.0 + - - +
260D ALA* 3.5 10.7 - - - +
261D LEU 3.2 0.4 - - - -
262D TYR* 1.3 79.8 - - - +
264D LYS* 1.3 57.9 + - - +
265D GLY 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP 2.7 35.3 + - - +
297A GLN* 3.3 27.4 + - + +
298A LYS* 3.9 4.5 - - + -
322B ARG* 3.7 11.8 + - - -
323B ARG 5.5 2.3 + - - -
15D PHE* 3.0 25.9 + - + +
16D ILE* 4.2 8.7 - - - -
20D GLU* 2.7 41.2 + - - -
260D ALA 3.3 13.7 - - - +
261D LEU* 3.0 24.0 + - + +
263D ASN* 1.3 75.8 - - - +
265D GLY* 1.3 59.7 + - - +
266D LYS* 4.8 14.8 + - + +
----------------------------------------------------------
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