Contacts of the helix formed by residues 260 - 272 (chain Y) in PDB entry 2CKV
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 260 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y THR* 5.6 0.2 - - - -
219Y PHE* 5.8 0.8 - - + -
258Y PHE* 3.7 0.8 - - - +
259Y SER* 1.3 80.3 + - - +
261Y PRO* 1.4 80.1 - - - +
262Y ASN* 3.4 13.0 + - - +
263Y ALA* 3.5 15.1 + - + +
264Y ALA* 3.2 21.7 + - - +
359Y TRP* 2.8 52.5 + - - +
390Y GLN* 5.6 1.2 - - - +
394Y SER* 3.4 25.7 + - - +
1411Y B12 3.7 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y THR* 4.9 18.4 - - + +
20Y MET* 3.4 30.0 - - + +
23Y SER* 5.3 13.0 - - - +
34Y VAL* 5.8 3.1 - - + -
259Y SER 3.5 6.9 - - - +
260Y ASN* 1.4 97.9 - - - +
262Y ASN* 1.3 64.2 + - - +
264Y ALA* 3.4 1.3 + - + -
265Y ALA* 3.0 24.5 + - - +
359Y TRP 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y ALA* 4.3 7.1 - - - +
33Y ASN* 2.7 24.7 + - - +
34Y VAL* 5.6 1.8 - - - +
260Y ASN* 3.3 12.1 + - - +
261Y PRO* 1.3 83.6 - - - +
263Y ALA* 1.3 63.8 + - - +
265Y ALA* 3.3 14.4 + - - +
266Y GLN* 3.3 21.3 + - - +
358Y SER* 2.7 50.7 + - - +
359Y TRP* 3.3 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Y PHE* 3.7 36.3 - - + +
258Y PHE* 3.5 21.7 - - + -
260Y ASN* 3.2 28.9 + - + +
262Y ASN* 1.3 80.8 - - - +
264Y ALA* 1.3 58.8 + - - +
266Y GLN* 3.6 10.9 + - - +
267Y VAL* 3.6 6.4 + - - +
359Y TRP* 4.4 4.4 - - - +
1411Y B12 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y LEU* 4.0 27.8 - - + +
19Y THR* 5.2 2.7 - - + -
20Y MET* 3.7 19.7 - - + -
258Y PHE* 4.0 11.4 - - + +
260Y ASN 3.2 9.3 + - - +
261Y PRO* 3.8 3.4 - - + +
263Y ALA* 1.3 77.8 - - - +
265Y ALA* 1.3 58.3 + - - +
266Y GLN 3.2 0.9 - - - -
267Y VAL* 3.9 8.7 - - - -
268Y LEU* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y MET* 3.7 14.5 - - + +
33Y ASN* 3.7 27.4 - - + +
34Y VAL* 4.8 0.9 - - - -
37Y SER* 2.7 35.4 + - - +
261Y PRO 3.0 16.7 + - - +
262Y ASN 3.6 7.6 - - - +
263Y ALA 3.3 0.4 - - - -
264Y ALA* 1.3 76.6 - - - +
266Y GLN* 1.3 58.2 + - + +
267Y VAL 3.5 0.2 - - - -
268Y LEU* 4.9 0.9 - - - -
269Y PRO* 3.1 16.5 - - - +
276Y PHE* 5.2 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 266 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y ASN* 5.7 7.5 - - + +
122Y TYR* 3.5 17.0 + - - -
167Y MET* 5.3 0.8 - - - +
219Y PHE 4.5 9.4 - - - +
222Y GLY* 3.3 13.6 - - - +
223Y GLU* 3.3 24.9 + - + +
226Y GLN* 2.6 31.1 + - - +
262Y ASN 3.3 12.4 + - - +
263Y ALA* 3.6 6.0 + - - +
264Y ALA 3.2 0.4 - - - -
265Y ALA* 1.3 78.8 - - + +
267Y VAL* 1.3 58.6 + - - +
268Y LEU 3.7 0.2 - - - -
269Y PRO* 3.8 0.4 - - - -
276Y PHE* 4.9 13.2 - - + -
359Y TRP* 3.2 35.4 + - + -
1411Y B12 3.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y GLU* 6.0 2.0 - - - +
16Y LEU* 4.0 17.0 - - + -
221Y THR* 5.5 0.7 - - - -
222Y GLY* 4.0 19.5 - - - +
225Y MET* 6.4 1.6 - - + -
249Y VAL* 4.8 14.8 - - + -
258Y PHE* 3.9 29.8 - - + -
263Y ALA 3.6 12.9 + - - +
264Y ALA* 3.5 15.3 - - - +
266Y GLN* 1.3 79.5 - - - +
268Y LEU* 1.3 65.9 + - - +
269Y PRO* 3.4 2.7 - - - -
270Y ALA* 3.3 18.9 + - + +
271Y LEU* 3.7 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y LEU* 3.8 31.9 - - + +
16Y LEU* 3.8 37.7 - - + +
17Y LEU* 3.8 22.2 - - + -
20Y MET* 3.7 24.2 - - + -
37Y SER* 5.7 1.1 - - - -
38Y LEU* 5.5 1.8 - - + -
41Y VAL* 3.6 22.6 - - + +
264Y ALA 2.9 24.8 + - - +
265Y ALA* 4.9 1.8 - - - -
267Y VAL* 1.3 76.4 - - - +
269Y PRO* 1.3 68.3 - - + +
271Y LEU* 3.1 22.6 + - + +
272Y MET 4.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 269 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y SER* 4.0 18.2 - - - +
40Y LEU* 4.1 19.3 - - + -
41Y VAL* 4.1 8.7 - - + +
226Y GLN* 4.2 15.5 - - - +
265Y ALA 3.1 26.9 - - - +
266Y GLN 3.8 1.1 - - - -
267Y VAL 3.4 7.0 - - - +
268Y LEU* 1.3 94.3 - - + +
270Y ALA* 1.3 58.4 + - - +
271Y LEU 3.4 0.2 + - - -
272Y MET* 3.8 3.1 + - - +
273Y GLY 3.4 3.5 + - - -
274Y LYS* 3.0 39.6 + - - +
275Y THR* 5.1 0.7 - - - +
276Y PHE* 5.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Y GLU* 5.4 0.2 - - - -
5Y VAL* 3.4 21.0 + - + +
222Y GLY 4.4 3.1 - - - +
225Y MET* 3.8 32.5 - - + -
226Y GLN* 4.4 13.3 - - + +
267Y VAL* 3.3 16.3 + - + +
268Y LEU 3.2 0.8 - - - -
269Y PRO* 1.3 76.5 - - - +
271Y LEU* 1.3 64.8 + - - +
273Y GLY* 3.4 11.9 + - - +
274Y LYS 3.9 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Y VAL* 4.0 23.6 - - + +
8Y GLU* 3.6 46.0 - - + +
9Y ASN 5.4 3.4 - - - +
13Y LEU* 3.9 37.7 - - + -
41Y VAL* 5.1 4.9 - - + -
42Y GLY* 5.5 2.5 - - - +
267Y VAL 3.7 4.3 + - - +
268Y LEU* 3.1 20.2 + - + +
270Y ALA* 1.3 79.2 - - - +
272Y MET* 1.3 70.6 + - + +
273Y GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 272 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Y GLU* 5.2 2.1 - - - +
5Y VAL 5.6 1.6 - - - +
40Y LEU 3.4 28.0 - - - +
41Y VAL* 3.9 2.7 - - - +
42Y GLY* 3.4 32.3 - - - +
268Y LEU 4.1 1.0 + - - -
269Y PRO 3.8 4.3 + - - +
270Y ALA 3.5 0.2 - - - -
271Y LEU* 1.3 86.2 - - + +
273Y GLY* 1.3 59.3 + - - +
274Y LYS* 4.2 26.8 - - + +
287Y SER* 4.7 12.6 - - - +
288Y ALA 5.5 4.0 - - - +
289Y SER* 6.0 0.7 - - - +
----------------------------------------------------------
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