Contacts of the helix formed by residues 249 - 264 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP 4.5 0.2 - - - -
241B PHE* 2.9 38.0 + - - -
243B THR* 3.0 22.1 + - + +
245B GLU 3.1 12.1 + - - +
246B LEU 3.1 5.7 + - - +
247B GLU 3.4 0.6 - - - -
248B GLU* 1.3 79.5 - - - +
250B PRO* 1.4 64.4 - - - +
251B ALA* 3.1 21.5 + - - +
252B TYR* 3.1 34.6 + - + -
253B GLN* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL 5.3 5.8 - - - +
6B THR* 5.2 3.6 - - + -
7B PHE* 3.8 22.1 - - + +
240B ASP* 4.6 2.2 - - + +
241B PHE* 3.7 26.9 - - + -
248B GLU 3.4 11.0 - - - +
249B ASN* 1.4 85.6 - - - +
251B ALA* 1.3 60.7 + - - +
253B GLN* 3.3 20.0 + - - +
254B TYR* 3.0 23.9 + - - +
400B PHE* 3.7 13.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 3.8 22.2 - - + -
249B ASN* 3.1 11.1 + - - +
250B PRO* 1.3 78.5 - - - +
252B TYR* 1.3 65.0 + - + +
254B TYR* 3.4 1.9 + - - +
255B ALA 3.1 17.0 + - - -
400B PHE* 3.6 34.6 - - + +
403B LYS* 4.2 5.4 - - + -
404B ALA* 3.2 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.6 19.7 - - + -
32B HIS* 2.8 32.7 + - + +
35B ILE* 4.3 5.0 - - + +
36B HIS* 4.2 0.5 + - - -
243B THR 3.3 11.4 - - - -
244B SER* 4.5 2.5 - - - -
246B LEU* 3.7 14.8 - - + -
249B ASN* 3.1 41.3 + - + +
251B ALA* 1.3 77.0 - - + +
253B GLN* 1.3 61.3 + - - +
255B ALA* 3.3 5.9 + - - +
256B VAL* 2.9 33.8 + - - +
403B LYS* 2.8 39.3 + - + -
407B MSE 3.5 42.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.8 21.7 - - + +
9B TYR* 3.8 25.2 - - + +
21B ILE* 5.1 6.3 - - + -
246B LEU* 3.1 38.3 + - + +
247B GLU* 3.4 22.1 + - - +
249B ASN 3.0 17.8 + - - +
250B PRO* 3.3 18.3 + - - +
252B TYR* 1.3 75.0 - - - +
254B TYR* 1.3 65.1 + - - +
256B VAL* 3.3 2.7 + - - +
257B VAL* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.5 34.5 - + + -
250B PRO 3.0 12.9 + - - +
251B ALA 3.6 6.7 - - - +
253B GLN* 1.3 77.3 - - - +
255B ALA* 1.3 61.2 + - - +
257B VAL* 3.3 0.7 + - - -
258B ARG* 3.0 48.4 + - + +
269B GLU* 2.5 35.1 + - - -
285B TRP* 3.4 17.5 + - - -
289B PHE* 3.8 13.5 - + - -
328B THR* 3.8 17.4 + - + +
382B LEU* 4.2 4.9 - - + -
384B VAL* 5.5 0.4 - - + -
400B PHE* 4.0 15.9 - + + -
401B PHE* 3.6 26.4 - + - -
404B ALA* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA 3.1 10.2 + - - +
252B TYR 3.6 3.1 - - - +
253B GLN 3.3 0.2 - - - -
254B TYR* 1.3 78.2 - - - +
256B VAL* 1.3 61.9 + - - +
258B ARG* 3.5 5.0 + - - +
259B ASN* 3.1 31.0 + - - -
404B ALA* 3.4 25.1 - - - +
407B MSE 3.5 28.0 - - + -
408B SER* 3.5 16.2 - - - +
411B LEU* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 4.2 2.5 - - - +
21B ILE* 3.8 36.8 - - + +
24B LEU* 3.8 22.6 - - + +
28B VAL* 3.5 30.7 - - + -
246B LEU* 3.7 12.1 - - + -
252B TYR 2.9 21.1 + - - +
253B GLN 3.8 3.4 - - - +
255B ALA* 1.3 74.4 - - - +
257B VAL* 1.3 59.4 + - - +
259B ASN* 3.3 3.9 + - - +
260B ALA* 3.0 28.5 + - + +
411B LEU* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.4 4.3 - - + -
9B TYR* 4.2 18.2 - - + -
16B ILE* 3.7 19.7 - - + -
21B ILE* 3.9 31.2 - - + -
253B GLN* 2.9 21.2 + - - +
254B TYR 3.8 3.1 - - - +
256B VAL* 1.3 76.2 - - - +
258B ARG* 1.3 62.3 + - - +
260B ALA* 3.2 7.0 + - - +
261B LEU* 2.9 27.4 + - + +
382B LEU* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.0 57.1 + - + +
255B ALA* 3.7 5.6 - - - +
257B VAL* 1.3 75.0 - - - +
259B ASN* 1.3 58.7 + - - +
261B LEU* 3.3 3.6 + - - +
262B TYR* 2.9 28.4 + - - +
269B GLU* 2.8 29.1 + - - +
285B TRP* 4.8 2.4 - - - -
289B PHE* 3.5 27.1 - - - +
293B GLU* 2.7 31.1 + - - -
300B ILE* 3.6 39.2 + - + +
302B PRO* 5.9 1.2 - - - +
326B PHE* 4.2 14.1 - - + -
382B LEU* 5.2 0.2 - - + -
408B SER* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.2 7.2 - - + -
255B ALA 3.1 23.4 + - - +
256B VAL* 3.8 5.4 - - - +
257B VAL 3.3 0.2 - - - -
258B ARG* 1.3 78.9 - - - +
260B ALA* 1.3 63.3 + - - +
262B TYR* 3.4 10.7 + - - +
263B ASN* 3.0 34.5 + - - +
293B GLU* 5.4 0.4 - - - +
300B ILE* 6.1 1.3 - - - -
408B SER* 3.3 35.9 + - - +
411B LEU* 3.8 15.7 - - + +
412B LEU* 3.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 5.1 7.0 - - + -
20B GLU* 3.9 33.0 - - + +
21B ILE* 6.2 1.3 - - + -
24B LEU* 5.8 3.9 - - + +
256B VAL* 3.0 14.4 + - + +
257B VAL* 3.2 10.7 + - - +
259B ASN* 1.3 75.1 - - - +
261B LEU* 1.3 64.1 + - - +
263B ASN* 3.1 17.4 + - - +
264B LYS* 3.2 18.2 + - - +
298C LYS* 3.7 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.8 0.9 - - + -
16B ILE* 3.3 32.5 - - + -
257B VAL* 2.9 35.4 + - + +
258B ARG 3.7 3.6 - - - +
260B ALA* 1.3 74.3 - - - +
262B TYR* 1.3 63.6 + - - +
264B LYS* 3.1 21.6 + - + +
265B GLY 3.4 0.3 + - - -
266B LYS* 3.0 28.1 + - + +
326B PHE* 3.7 47.3 - - + -
380B PRO* 4.0 27.1 - - + -
382B LEU* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 2.9 26.1 + - - -
258B ARG 2.9 17.3 + - - +
259B ASN* 3.6 11.9 - - - +
260B ALA 3.3 0.2 - - - -
261B LEU* 1.3 74.8 - - - +
263B ASN* 1.3 60.9 + - - +
265B GLY* 3.1 20.3 + - - -
266B LYS 3.4 13.3 + - - -
267B THR* 4.1 11.1 - - + +
299B GLY* 3.1 40.1 + - - -
300B ILE* 3.4 28.2 - - + +
412B LEU* 3.8 18.8 - - + -
262C TYR 5.5 0.2 - - - -
263C ASN* 2.6 52.4 + - - -
322D ARG* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.0 22.8 + - - +
260B ALA* 3.1 10.6 + - - +
262B TYR* 1.3 80.6 - - - +
264B LYS* 1.3 56.5 + - - +
265B GLY 3.2 1.7 + - - -
262C TYR* 2.6 42.8 + - + -
263C ASN* 3.4 22.2 - - - +
298C LYS* 3.5 24.1 - - + +
411C LEU 5.6 0.6 + - - -
412C LEU* 3.7 28.7 + - + +
322D ARG* 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.0 26.8 + - + +
16B ILE* 3.5 12.1 - - - -
20B GLU* 2.9 36.0 + - - -
260B ALA 3.5 9.2 - - - +
261B LEU* 3.1 25.4 + - + +
263B ASN* 1.3 75.8 - - - +
265B GLY* 1.3 59.1 + - - +
266B LYS* 4.8 13.6 + - + +
296C ASP 2.7 33.1 + - - +
297C GLN* 3.3 28.5 + - + +
298C LYS* 4.0 3.8 - - - +
322D ARG* 3.5 15.0 + - - -
323D ARG 5.4 2.1 + - - -
----------------------------------------------------------
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