Contacts of the helix formed by residues 297 - 314 (chain B) in PDB entry 6E8Y
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 LEU 297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 4.8 3.1 - - + -
269B ARG* 4.1 22.4 - - + +
270B ASN* 3.4 38.6 - - - +
273B VAL* 3.6 31.0 - - + -
274B ALA 5.4 0.2 - - - +
284B ILE* 4.6 5.2 - - + -
288B GLU* 2.7 26.0 + - + +
292B LEU* 3.6 24.0 - - + -
296B LYS* 1.3 71.4 - - - +
298B GLN* 1.3 63.5 + - - +
299B GLY 3.5 0.2 - - - -
300B PRO* 3.6 28.2 - - + +
301B GLU* 3.8 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 3.9 26.5 + - - -
121B GLY* 5.3 4.6 - - - -
122B VAL* 4.6 14.8 - - - +
205B ASN* 4.2 17.9 - - - +
269B ARG* 5.4 6.0 - - - +
270B ASN* 4.2 4.0 + - - +
296B LYS* 3.6 11.8 + - - +
297B LEU* 1.3 76.5 - - - +
299B GLY* 1.3 64.8 + - - +
301B GLU* 3.0 28.5 + - - +
302B THR* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 3.7 25.7 - - - +
206B VAL* 3.4 12.4 - - - +
209B VAL* 4.3 4.3 - - - -
270B ASN* 2.9 20.0 + - - -
298B GLN* 1.3 78.0 - - - +
300B PRO* 1.3 66.5 - - - +
302B THR* 3.4 0.6 + - - -
303B ALA* 3.0 20.1 + - - +
325B VAL* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 4.1 7.9 - - + -
270B ASN* 3.9 0.9 - - - +
284B ILE* 4.4 15.7 - - + -
297B LEU* 3.6 40.2 - - + +
299B GLY* 1.3 89.4 - - - +
301B GLU* 1.3 60.7 + - + +
303B ALA* 3.2 7.2 + - + +
304B ARG 3.0 18.2 + - - -
325B VAL* 4.9 1.3 - - + -
329B CYS* 3.9 33.0 - - + -
330B TYR* 3.3 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 6.0 0.7 - - - +
296B LYS* 3.6 20.7 - - - +
297B LEU 3.8 11.0 - - - +
298B GLN* 3.0 31.0 + - - +
299B GLY 3.3 0.6 - - - -
300B PRO* 1.3 77.9 - - - +
302B THR* 1.3 63.8 + - - +
304B ARG* 3.2 23.4 + - - +
305B GLU* 3.1 27.2 + - + +
330B TYR* 3.6 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 4.0 15.4 - - - +
129B LEU* 4.5 12.8 - - + -
202B ALA* 4.0 22.9 + - + +
203B LEU* 4.4 9.9 - - + -
206B VAL* 3.7 17.7 - - + -
298B GLN* 2.9 23.9 + - - +
299B GLY 3.7 4.3 - - - -
301B GLU* 1.3 75.7 - - - +
303B ALA* 1.3 65.0 + - - +
305B GLU* 3.1 9.5 + - - +
306B LEU* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.9 5.8 - - + +
299B GLY 3.0 14.2 + - - +
300B PRO* 3.2 8.5 + - + +
302B THR* 1.3 74.9 - - - +
304B ARG* 1.3 65.0 + - - +
306B LEU* 3.0 15.3 + - - +
307B TYR* 2.8 23.0 + - - +
322B PHE 4.1 6.7 - - - +
323B MET* 4.0 3.5 - - - +
325B VAL* 3.9 13.7 - - + -
326B TYR* 3.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO 3.0 12.9 + - - +
301B GLU* 3.4 25.6 + - - +
303B ALA* 1.3 75.8 - - - +
305B GLU* 1.3 71.9 + - - +
307B TYR* 3.1 15.3 + - + +
308B SER* 3.2 11.9 + - - -
326B TYR* 3.6 27.3 - - + -
330B TYR* 3.4 38.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.6 38.6 + - + +
301B GLU* 3.1 17.1 + - + +
302B THR* 3.1 6.3 + - - +
304B ARG* 1.3 84.0 + - - +
306B LEU* 1.3 61.7 + - - +
308B SER* 3.2 12.7 + - - -
309B ILE* 3.1 27.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
129B LEU* 3.9 13.5 - - + -
203B LEU* 4.0 16.2 - - + -
206B VAL* 4.2 11.4 - - + -
238B PHE* 3.3 42.8 - - + -
302B THR* 2.9 20.7 + - + +
303B ALA* 3.3 14.4 - - - +
305B GLU* 1.3 74.8 - - - +
307B TYR* 1.3 65.5 + - - +
309B ILE* 3.3 3.6 + - - +
310B LEU* 2.8 34.2 + - + +
322B PHE* 3.7 30.7 - - + -
323B MET* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 2.8 12.6 + - - +
304B ARG* 3.1 9.2 + - + +
306B LEU* 1.3 75.2 - - - +
308B SER* 1.3 59.4 + - - +
310B LEU* 3.8 0.5 - - - +
311B GLN* 2.9 77.9 + - + +
316B VAL* 4.1 14.8 - - + -
323B MET* 3.5 28.4 - - - +
326B TYR* 3.3 43.1 - + + -
327B LYS* 3.6 26.9 + - - -
331B GLU* 4.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 3.2 8.1 + - - -
305B GLU* 3.2 17.1 + - - -
306B LEU 3.2 1.0 - - - -
307B TYR* 1.3 81.2 - - - +
309B ILE* 1.3 63.3 + - - +
311B GLN* 3.5 12.2 + - - +
312B HIS* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 39.7 - - + +
238B PHE* 4.1 30.7 - - + -
242B PHE* 4.2 14.1 - - + -
305B GLU* 3.1 17.1 + - - +
306B LEU 3.8 3.6 - - - +
308B SER* 1.3 77.7 - - - +
310B LEU* 1.3 63.3 + - - +
312B HIS* 3.2 10.4 + - + +
313B LYS* 3.1 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 4.0 22.7 - - + -
241B LEU* 4.5 8.7 - - + -
306B LEU* 2.8 25.9 + - + +
307B TYR* 3.9 2.9 - - - +
309B ILE* 1.3 75.3 - - - +
311B GLN* 1.3 58.2 + - - +
313B LYS* 3.3 4.0 + - + +
314B GLY 2.8 23.9 + - - -
315B LEU* 2.9 21.6 + - + +
316B VAL* 3.7 16.3 + - + +
319B PHE* 3.7 49.8 - - + -
322B PHE* 5.0 1.3 - - + -
323B MET* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 2.9 66.8 + - + +
308B SER* 3.8 9.6 - - - +
309B ILE 3.2 0.2 - - - -
310B LEU* 1.3 76.3 - - - +
312B HIS* 1.3 64.8 + - - +
314B GLY* 2.9 14.8 + - - +
316B VAL* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER 3.3 9.8 + - - +
309B ILE* 3.2 12.0 + - + +
311B GLN* 1.3 79.5 - - - +
313B LYS* 1.3 75.3 + - + +
314B GLY 3.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.6 45.9 + - + +
242B PHE* 5.2 5.4 - - - +
309B ILE* 3.1 32.2 + - + +
310B LEU* 3.9 5.6 - - + +
312B HIS* 1.3 89.4 - - + +
314B GLY* 1.3 61.2 + - - +
315B LEU* 3.5 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 2.8 5.5 + - - -
311B GLN* 2.9 13.8 + - - -
312B HIS 3.2 0.8 + - - -
313B LYS* 1.3 78.3 - - - +
315B LEU* 1.3 63.6 + - - +
316B VAL* 3.7 2.9 + - - -
317B ASP* 4.6 5.7 - - - +
----------------------------------------------------------
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