Contacts of the helix formed by residues 306 - 316 (chain B) in PDB entry 1EJD
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 MET 306 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG 4.9 0.2 - - - +
233B ILE* 3.7 30.5 - - + +
236B GLY* 3.4 33.9 - - - +
237B THR 3.9 0.9 - - - +
240B VAL* 3.9 6.1 - - + -
259B LEU* 5.4 0.9 - - + -
262B VAL* 3.9 11.2 - - + -
302B PHE* 3.7 17.3 - - + -
303B PRO* 3.0 29.2 + - + +
305B ASP* 1.3 76.1 - - - +
307B GLN* 1.3 63.9 + - - +
309B GLN* 3.2 33.6 - - + +
310B PHE* 3.1 45.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 4.0 9.9 - - + -
302B PHE* 4.3 7.2 - - - -
303B PRO 3.6 2.6 + - - -
304B THR 3.0 14.9 + - - +
306B MET* 1.3 77.2 - - - +
308B ALA* 1.3 67.5 + - - +
310B PHE* 3.1 4.0 + - - +
311B THR* 2.8 53.0 + - - -
323B ILE* 3.6 25.6 - - + +
325B GLU* 2.9 30.3 + - - +
331B ARG* 3.0 33.3 + - - +
332B PHE* 3.6 15.1 - - + -
334B HIS* 3.5 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR 4.6 1.2 + - - -
307B GLN* 1.3 90.0 + - - +
309B GLN* 1.3 69.6 + - - +
311B THR 3.3 0.9 + - - -
312B LEU* 3.1 20.3 + - - +
331B ARG* 5.7 1.0 - - - +
334B HIS* 3.5 28.3 - - + +
369B ASP* 5.2 0.7 - - - +
371B ARG* 3.9 4.5 - - + +
372B ALA* 3.8 22.7 - - + +
375B SER* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 3.9 4.4 - - - +
237B THR* 3.2 35.6 + - + +
240B VAL* 3.6 25.3 - - + +
305B ASP 3.1 27.9 + - - +
306B MET* 3.2 36.9 - - + +
308B ALA* 1.3 84.3 + - - +
310B PHE* 1.3 56.9 + - - +
312B LEU* 3.4 6.6 + - - +
313B LEU 3.0 20.3 + - - -
371B ARG* 3.9 10.4 - - - +
375B SER* 3.3 19.1 - - - +
378B LEU* 5.0 4.3 - - + -
399B TYR* 4.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 3.7 16.8 - - + -
262B VAL* 4.1 12.1 - - + -
265B LYS* 3.6 33.7 - - + -
266B LEU* 3.6 35.4 - - + -
269B ALA* 5.7 0.2 - - + -
292B VAL* 4.3 9.6 - - + -
294B VAL* 4.3 8.1 - - + -
302B PHE* 3.4 33.4 - + + -
306B MET* 3.1 30.6 + - + +
307B GLN* 3.9 3.1 - - - +
309B GLN* 1.3 75.6 - - - +
311B THR* 1.3 65.9 + - - +
313B LEU* 3.5 15.7 - - + +
314B ASN* 2.9 22.3 + - - +
323B ILE* 3.4 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLN* 2.8 32.0 + - - -
308B ALA 3.3 9.2 + - - -
310B PHE* 1.3 76.3 - - - +
312B LEU* 1.3 65.0 + - - +
314B ASN* 3.2 3.3 + - - +
315B LEU* 2.9 45.9 + - + +
323B ILE* 3.2 19.0 - - - +
334B HIS* 3.9 6.3 - - + -
335B VAL* 4.0 24.2 - - + -
352B VAL* 3.9 9.8 - - + +
354B CYS* 4.2 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 5.4 0.4 - - + -
244B ILE* 3.6 29.8 - - + -
308B ALA 3.1 12.7 + - - +
309B GLN* 3.5 10.1 - - - +
310B PHE 3.2 0.2 - - - -
311B THR* 1.3 77.5 - - - +
313B LEU* 1.3 64.6 + - - +
315B LEU* 3.0 12.9 + - + -
316B VAL* 3.2 16.0 + - + +
338B LEU* 4.1 22.4 - - + +
360B LEU* 4.0 17.9 - - + -
375B SER* 3.4 29.8 - - - +
378B LEU* 3.8 8.5 - - + -
379B ALA* 3.7 26.7 - - + +
382B ILE* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 4.6 5.6 - - + -
243B ALA* 4.2 16.8 - - + -
244B ILE* 3.7 22.2 - - + -
266B LEU* 4.1 25.8 - - + -
269B ALA* 4.3 13.9 - - + -
289B PRO* 4.1 13.1 - - + +
290B LYS 4.2 16.4 - - - +
292B VAL* 4.5 8.1 - - + -
309B GLN 3.0 14.0 + - - +
310B PHE* 3.2 19.9 + - + +
312B LEU* 1.3 78.5 - - - +
314B ASN* 1.3 78.1 + - - +
316B VAL* 3.2 4.3 + - - +
317B ALA* 3.1 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 3.4 6.9 - - + +
292B VAL* 2.9 53.1 + - - +
310B PHE 2.9 13.0 + - - +
311B THR 3.7 5.6 - - - +
313B LEU* 1.3 79.1 - - - +
315B LEU* 1.3 62.2 + - - +
317B ALA* 3.1 16.4 + - - +
319B GLY 4.5 2.3 - - - +
321B GLY* 3.5 21.4 + - - -
323B ILE* 3.7 20.0 - - - +
354B CYS* 3.6 19.2 - - + +
356B GLY* 3.4 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B THR* 2.9 32.4 + - + +
312B LEU* 3.0 8.2 + - + +
314B ASN* 1.3 75.3 - - - +
316B VAL* 1.3 63.2 + - + +
335B VAL* 5.0 4.5 - - + -
338B LEU* 3.5 31.2 - - + -
343B ALA* 4.1 22.1 - - + +
344B HIS 3.4 28.3 - - - +
345B ALA* 3.7 15.9 - - + -
354B CYS* 3.5 21.5 - - + -
355B HIS 4.2 2.2 - - - +
356B GLY* 3.4 3.6 - - - -
357B VAL* 2.9 29.6 + - - +
360B LEU* 4.9 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.0 20.2 - - + +
288B ARG* 3.0 26.2 + - - +
289B PRO* 4.1 4.5 - - + +
312B LEU* 3.2 17.2 + - + +
313B LEU 3.5 6.3 - - - +
314B ASN 3.1 0.2 - - - -
315B LEU* 1.3 80.7 - - - +
317B ALA* 1.3 60.9 + - - +
357B VAL* 3.3 15.3 - - + +
358B GLU 4.9 6.0 - - - +
359B LYS* 5.8 0.2 - - - -
360B LEU* 3.7 37.5 - - + +
382B ILE* 3.9 25.4 - - + -
----------------------------------------------------------
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