Contacts of the helix formed by residues 279 - 286 (chain B) in PDB entry 2XFN
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 PRO 279 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PRO 3.7 2.2 - - - +
278B LEU* 1.3 91.2 - - + +
280B MET* 1.3 67.5 + - - +
281B MET* 3.2 5.0 + - + +
282B ARG* 3.2 10.0 + - + +
283B ASN* 2.9 19.2 + - - +
416B GLN* 6.0 2.0 - - - +
418B VAL* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ALA 4.4 5.2 - - - +
350A ARG* 4.6 4.0 - - + -
353A ALA* 3.5 26.9 - - + -
387A ASN* 2.8 34.1 - - - +
389A CYS* 3.6 32.9 - - + +
390A GLU* 4.2 22.7 - - + +
278B LEU 3.6 1.4 + - - -
279B PRO* 1.3 70.9 - - - +
281B MET* 1.3 86.8 + - - +
283B ASN* 3.2 5.3 + - - +
284B GLN* 3.0 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.6 36.8 - - + +
279B PRO* 3.2 3.2 + - + +
280B MET* 1.3 91.2 - - + +
282B ARG* 1.3 59.5 + - - +
285B MET* 2.8 28.6 + - - +
409B GLN 3.1 27.8 - - - +
410B TYR* 3.5 25.3 - - + -
413B VAL* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B SER* 5.3 1.0 + - - -
266B PRO* 4.6 14.6 + - - +
269B GLY* 6.0 1.4 - - - -
274B PHE* 6.1 1.4 - - - -
278B LEU* 4.1 22.1 - - + +
279B PRO* 3.2 15.6 + - + +
281B MET* 1.3 77.5 - - - +
283B ASN* 1.3 65.5 + - - +
285B MET* 3.1 26.6 + - + +
286B ILE* 3.1 32.3 + - + +
413B VAL* 3.4 31.2 + - + +
414B LEU 3.3 23.6 + - - -
418B VAL* 4.0 14.4 - - + -
423B PHE* 3.3 50.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A CYS 2.9 22.7 + - - +
390A GLU 3.7 4.2 - - - +
391A GLU 3.2 26.7 + - - -
392A GLN* 3.7 21.9 - - - +
395A GLY* 4.4 10.1 - - - +
270B MET* 4.8 4.0 - - - +
278B LEU* 4.1 24.7 + - + +
279B PRO 2.9 13.4 + - - +
280B MET* 3.4 10.1 - - - +
282B ARG* 1.3 75.7 - - - +
284B GLN* 1.3 60.8 + - - +
286B ILE* 3.5 15.8 - - - +
287B THR* 3.8 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU 3.6 6.5 + - - -
292A GLY 3.0 25.3 + - - -
293A SER* 2.8 20.0 + - - -
350A ARG* 4.4 1.9 - - - +
389A CYS* 3.4 35.1 - - + +
395A GLY 2.9 27.5 + - - +
396A GLY* 3.5 5.1 - - - -
280B MET* 3.0 11.3 + - - +
283B ASN* 1.3 77.1 - - - +
285B MET* 1.3 64.8 + - - +
286B ILE 3.2 0.4 - - - -
287B THR* 2.7 25.3 + - - -
288B ARG* 3.4 19.0 - - - +
410B TYR* 3.0 21.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PRO* 4.3 2.5 - - + -
281B MET 2.8 22.9 + - - +
282B ARG* 3.1 43.2 + - + +
284B GLN* 1.3 72.0 - - - +
286B ILE* 1.3 67.9 + - + +
288B ARG* 2.9 23.7 + - - +
289B VAL* 3.3 30.3 - - + +
402B PHE* 5.5 1.8 - - + -
406B ILE* 5.6 0.2 - - + -
410B TYR* 3.8 38.3 - - + +
413B VAL* 3.9 11.9 - - + -
414B LEU* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 5.7 2.0 - - - +
266B PRO 3.4 22.4 - - - +
267B THR* 2.8 29.5 + - - -
269B GLY* 3.9 8.5 - - - +
270B MET* 3.5 43.7 - - + +
274B PHE* 5.2 0.4 - - + -
278B LEU* 3.8 24.9 - - + -
282B ARG* 3.4 29.4 - - + +
283B ASN* 3.5 13.2 - - - +
285B MET* 1.3 96.7 - - + +
287B THR* 1.3 54.0 + - - +
288B ARG 3.5 0.7 - - - -
289B VAL* 4.0 6.3 - - - -
----------------------------------------------------------
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