Contacts of the helix formed by residues 301 - 315 (chain B) in PDB entry 2YTZ
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 ARG 301 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 6.1 1.2 - - - +
28B TYR* 5.5 1.2 + - - -
30B PRO* 3.4 34.8 + - - +
31B ARG* 4.9 5.1 + - - +
33B ALA* 3.7 22.0 - - + +
34B LEU* 4.2 15.5 - - + +
37B ASP* 2.9 21.5 + - - +
300B ALA* 1.3 86.0 + - - +
302B LYS* 1.3 65.5 + - - +
303B LYS* 2.8 32.6 + - - +
304B GLN* 3.0 18.1 + - + +
305B ALA* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA 3.0 26.9 - - - +
295B GLU* 3.1 20.7 + - - +
297B LEU 3.3 18.3 + - - +
298B SER* 5.8 0.4 - - - -
299B LEU* 3.4 31.1 + - + +
300B ALA 3.4 1.0 + - - -
301B ARG* 1.3 75.2 - - - +
303B LYS* 1.3 66.5 + - + +
305B ALA* 3.6 2.8 - - - +
306B LEU* 3.2 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA 4.8 2.0 - - - +
301B ARG* 2.8 36.6 + - - +
302B LYS* 1.3 74.5 - - + +
304B GLN* 1.3 96.5 + - + +
306B LEU* 3.1 16.8 + - - +
307B LYS* 3.2 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.9 25.9 - - + +
223B LYS* 4.7 14.5 - - - +
224B ASP* 5.1 4.8 + - - -
301B ARG* 3.0 21.2 + - - +
303B LYS* 1.3 102.6 + - + +
305B ALA* 1.3 62.2 + - - +
307B LYS* 3.8 16.5 - - - +
308B LEU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.4 23.9 - - + +
37B ASP* 4.6 3.8 - - + -
38B ILE* 4.3 10.7 - - + +
41B VAL* 5.8 0.2 - - + -
299B LEU* 3.9 24.9 - - + -
301B ARG 3.0 13.6 + - - +
302B LYS* 3.6 6.1 - - - +
304B GLN* 1.3 78.3 - - - +
306B LEU* 1.3 60.9 + - - +
308B LEU* 4.0 1.4 - - - +
309B LEU* 3.2 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 4.0 6.5 - - + +
294B ALA* 3.6 37.5 - - + -
295B GLU* 3.8 22.0 - - + -
302B LYS* 3.2 40.6 + - + +
303B LYS* 3.1 6.9 + - - +
305B ALA* 1.3 76.7 - - + +
307B LYS* 1.3 61.4 + - - +
309B LEU* 4.7 1.6 - - + -
310B LYS* 2.9 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LYS* 5.9 4.9 - - - +
303B LYS 3.2 12.7 + - - +
304B GLN* 3.8 19.1 - - - +
306B LEU* 1.3 77.8 - - - +
308B LEU* 1.3 57.6 + - - +
310B LYS* 3.9 4.4 - - - +
311B MET* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.6 8.5 - - + -
38B ILE* 4.5 16.4 - - + -
221B TYR* 4.1 21.1 - - + -
222B TYR 4.9 1.1 - - - +
223B LYS* 4.1 37.2 - - + +
226B TYR* 5.8 0.2 - - - +
304B GLN 3.1 17.0 + - - +
305B ALA* 4.0 4.0 - - - +
307B LYS* 1.3 75.5 - - - +
309B LEU* 1.3 67.8 + - + +
311B MET* 3.1 6.6 + - + +
312B ILE* 3.0 31.3 + - + +
356B HIS* 4.0 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.1 24.5 - - + -
41B VAL* 4.6 8.1 - - + -
219B LEU* 4.5 7.9 - - + -
221B TYR* 6.2 0.4 - - + -
287B VAL* 4.4 6.9 - - + +
290B MET* 4.0 42.2 - - + +
291B VAL* 4.0 15.9 - - + +
294B ALA* 3.7 29.8 - - + -
305B ALA* 3.2 19.7 + - + +
306B LEU* 4.2 2.7 - - - +
308B LEU* 1.3 79.0 - - + +
310B LYS* 1.3 54.9 + - - +
312B ILE* 3.1 9.2 + - + +
313B ASP* 2.6 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.7 20.9 - - + -
295B GLU* 3.6 24.8 + - - +
306B LEU* 2.9 41.4 + - + +
307B LYS* 4.0 4.3 - - - +
309B LEU* 1.3 76.8 - - - +
311B MET* 1.3 63.9 + - - +
313B ASP* 3.6 10.5 - - - +
314B GLN* 3.3 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LYS 3.0 16.3 + - - +
308B LEU* 3.2 12.6 - - + +
309B LEU 3.1 0.2 - - - -
310B LYS* 1.3 76.5 - - - +
312B ILE* 1.3 63.6 + - - +
314B GLN* 2.7 50.1 + - - +
315B GLU* 3.0 4.5 + - - +
354B ARG* 4.1 27.6 - - + -
355B THR* 4.0 20.9 - - - +
356B HIS* 3.6 27.8 - - + +
359B PRO* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.8 22.9 - - + -
220B ALA 4.8 0.7 - - - +
221B TYR* 3.6 34.1 - - + -
282B LYS* 2.5 50.4 + - + -
287B VAL* 3.9 11.9 - - + -
308B LEU* 3.0 25.7 + - + +
309B LEU* 3.7 9.4 - - + +
311B MET* 1.3 76.0 - - - +
313B ASP* 1.3 55.3 + - - +
315B GLU* 2.9 18.0 + - + +
356B HIS* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LYS* 3.2 11.6 + - - +
284B GLU* 4.5 4.2 - - - +
287B VAL* 3.7 11.7 - - + +
288B SER* 3.4 34.7 + - - -
291B VAL* 3.9 17.6 - - + +
292B LYS* 4.4 10.2 + - - -
309B LEU 2.6 20.8 + - - +
310B LYS* 3.6 8.4 - - - +
311B MET 3.3 0.2 - - - -
312B ILE* 1.3 74.2 - - - +
314B GLN* 1.3 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS 3.3 10.8 - - - +
311B MET* 2.7 38.4 + - - +
312B ILE 3.0 0.4 - - - -
313B ASP* 1.3 79.1 - - + +
315B GLU* 1.3 80.2 + - - +
316B LEU* 3.6 2.1 + - - +
353B THR* 3.6 24.6 - - - +
354B ARG* 3.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LYS* 3.0 22.1 + - + -
311B MET* 3.0 11.0 + - - +
312B ILE* 2.9 18.7 + - + +
314B GLN* 1.3 87.2 - - - +
316B LEU* 1.3 72.7 + - - +
317B ASP 3.5 1.2 + - - -
353B THR* 3.8 1.8 - - - -
354B ARG 3.4 13.9 - - - +
355B THR* 2.7 26.5 + - - +
356B HIS* 2.9 43.0 + - - +
357B PHE* 3.8 6.9 - - - -
363B LYS* 3.6 15.3 + - + -
----------------------------------------------------------
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