Contacts of the helix formed by residues 278 - 294 (chain A) in PDB entry 1K63
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 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.8 21.5 - - - -
269A ALA* 2.7 39.2 + - - +
274A ILE 3.0 7.1 + - - -
277A ASP* 1.3 80.2 + - - +
279A PRO* 1.4 64.6 - - - +
280A ASP 3.4 2.2 - - - -
281A GLU* 3.3 20.5 + - - +
282A ILE* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 4.1 6.5 - - - +
3A LEU* 3.6 29.8 - - + -
47A ASN* 3.6 30.3 - - + +
48A ILE* 3.6 22.9 - - + +
51A HIS* 4.0 2.3 - - - -
275A GLN 3.4 20.4 - - - +
277A ASP 3.4 8.1 - - - +
278A SER* 1.4 90.7 - - - +
280A ASP* 1.3 61.2 + - - +
281A GLU* 4.9 0.2 - - - +
283A GLY* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.6 47.7 + - - +
47A ASN 4.2 0.5 - - - +
51A HIS* 2.8 25.5 + - + +
278A SER 3.4 0.6 - - - -
279A PRO* 1.3 77.1 - - - +
281A GLU* 1.3 70.3 + - - +
284A ALA* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.8 7.1 - - + +
268A VAL* 4.0 18.6 - - + -
278A SER* 3.3 31.0 - - - +
279A PRO* 4.9 0.3 - - - +
280A ASP* 1.3 80.3 + - - +
282A ILE* 1.3 62.3 + - - +
284A ALA* 4.0 4.9 - - - +
285A ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.7 16.2 - - + -
131A MET* 4.2 7.0 - - - -
241A ILE* 3.8 27.3 - - + +
266A ILE* 4.7 6.3 - - - -
268A VAL* 4.1 10.3 - - + -
274A ILE* 3.6 46.2 - - + +
275A GLN* 3.9 11.2 - - + -
278A SER 3.1 20.0 + - - +
279A PRO 3.7 3.4 - - - +
281A GLU* 1.3 74.9 - - - +
283A GLY* 1.3 67.4 + - - +
285A ALA* 3.2 4.3 + - - +
286A ILE* 3.0 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.9 16.6 - - - +
51A HIS* 3.4 33.4 - - - +
52A CYS* 4.9 0.7 - - - -
279A PRO 2.8 19.3 + - - -
282A ILE* 1.3 75.5 - - - +
284A ALA* 1.3 56.4 + - - +
286A ILE* 3.3 4.3 + - - +
287A ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 3.5 13.9 - - + +
280A ASP 2.9 19.6 + - - +
281A GLU* 4.0 5.4 - - - +
283A GLY* 1.3 75.3 - - - +
285A ALA* 1.3 59.0 + - - +
287A ALA* 3.4 5.5 + - - +
288A ALA* 2.9 27.9 + - - +
291A ARG* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.6 14.3 - - + +
241A ILE* 5.2 0.9 - - + -
266A ILE* 3.5 44.0 - - + -
281A GLU 3.2 8.9 + - - +
282A ILE 3.8 2.9 - - - +
284A ALA* 1.3 76.5 - - - +
286A ILE* 1.3 65.8 + - - +
288A ALA* 3.3 7.4 + - - +
289A PHE* 3.0 23.6 + - - +
292A ARG* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.8 1.6 - - + -
34A PHE* 4.5 1.6 - - + -
48A ILE* 3.7 16.2 - - + -
52A CYS* 3.7 20.4 - - - -
103A VAL* 5.6 0.4 - - + -
105A VAL* 3.7 41.1 - - + -
129A ALA* 4.3 7.2 - - + -
239A LEU* 3.8 11.0 - - + -
241A ILE* 3.8 17.3 - - + -
282A ILE* 3.0 39.7 + - + +
283A GLY 3.7 4.3 - - - +
285A ALA* 1.3 76.2 - - - +
287A ALA* 1.3 57.0 + - - +
289A PHE* 3.2 3.7 + - + +
290A VAL* 2.9 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 3.4 27.6 - - + +
52A CYS* 4.3 3.1 - - - -
55A LEU* 3.7 15.3 - - + +
283A GLY 2.9 16.7 + - - +
284A ALA* 3.7 7.0 - - - +
286A ILE* 1.3 77.4 - - - +
288A ALA* 1.3 62.5 + - - +
290A VAL 3.2 0.7 + - - -
291A ARG* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA 2.9 17.9 + - - +
285A ALA* 3.7 6.3 - - - +
287A ALA* 1.3 75.3 - - - +
289A PHE* 1.3 63.6 + - - +
291A ARG* 3.3 15.5 + - - +
292A ARG* 3.1 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.5 4.9 - - + -
127A GLY 4.3 1.3 - - - -
128A ILE 3.9 18.2 - - - -
129A ALA* 4.3 6.3 - - + -
237A PRO* 3.6 31.6 - - + -
238A LYS 3.7 29.6 - - - -
239A LEU* 3.8 29.6 - - + -
264A THR* 5.1 1.8 - - - -
285A ALA 3.0 17.2 + - - +
286A ILE* 3.4 6.3 - - + +
288A ALA* 1.3 77.7 - - - +
290A VAL* 1.3 68.7 + - + +
292A ARG* 3.1 29.4 + - + +
293A LEU* 3.1 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.9 30.1 - - + -
52A CYS* 5.0 0.2 - - - -
55A LEU* 3.9 19.1 - - + -
103A VAL* 4.3 22.7 - - + -
286A ILE* 2.9 32.8 + - + +
287A ALA* 3.8 3.6 - - - +
289A PHE* 1.3 78.1 - - + +
291A ARG* 1.3 57.7 + - - +
293A LEU* 3.2 7.2 + - - +
294A ARG* 2.8 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS 4.3 8.3 + - - -
53A ALA 5.5 3.0 + - - -
55A LEU* 3.9 29.6 - - + +
284A ALA 5.1 0.8 + - - -
287A ALA* 2.9 48.5 + - - +
288A ALA* 3.7 11.9 - - - +
290A VAL* 1.3 75.5 - - - +
292A ARG* 1.3 61.9 + - + +
294A ARG* 3.4 6.5 - - - +
295A PRO* 3.4 22.9 - - - +
296A ALA 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 6.1 0.4 - - - +
264A THR* 3.8 31.7 + - - +
285A ALA* 4.9 1.8 + - - +
288A ALA* 3.1 41.1 + - - +
289A PHE* 3.1 33.1 + - + +
291A ARG* 1.3 78.6 - - + +
293A LEU* 1.3 64.4 + - + +
295A PRO* 3.4 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.9 23.3 - - + -
126A GLN* 3.6 37.8 + - + +
127A GLY* 4.1 0.4 - - - -
237A PRO* 3.5 35.0 - - + -
289A PHE* 3.1 46.4 + - + +
290A VAL* 3.6 8.3 - - - +
292A ARG* 1.3 80.4 - - + +
294A ARG* 1.3 58.7 + - + +
295A PRO* 3.3 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.0 36.4 + - - +
31A PRO 2.9 24.2 + - - -
32A ILE* 3.7 15.3 - - - +
55A LEU* 2.9 28.6 + - + +
56A GLY* 3.7 0.2 - - - -
101A ARG 3.0 21.0 + - - -
103A VAL* 3.8 8.0 - - - +
126A GLN* 2.7 25.9 + - - +
290A VAL* 2.8 28.6 + - + +
291A ARG* 3.4 9.4 - - - +
293A LEU* 1.3 84.0 - - + +
295A PRO* 1.4 66.0 - - - +
296A ALA* 3.1 8.8 + - - +
----------------------------------------------------------
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