Contacts of the helix formed by residues 295 - 306 (chain B) in PDB entry 3ECS
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 ALA 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A SER* 4.3 4.5 - - - +
291B LEU* 4.4 10.1 - - + -
292B THR* 3.0 28.5 + - + +
294B SER* 1.3 79.5 + - - +
296B VAL* 1.3 63.8 + - - +
297B SER 3.3 0.2 - - - -
298B ASP* 3.2 21.6 + - + +
299B GLU* 3.3 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.9 23.1 - - + -
201B VAL 3.6 25.4 - - - +
202B GLU 3.9 3.6 - - - +
204B GLY* 3.9 5.2 - - - -
235B PHE* 4.2 13.7 - - + -
284B LEU* 4.1 13.7 - - + -
291B LEU* 3.7 27.1 - - + -
292B THR 3.6 5.1 + - - +
293B PRO 2.9 17.1 + - - +
295B ALA* 1.3 78.4 - - - +
297B SER* 1.3 59.1 + - - +
299B GLU* 3.2 2.0 + - - +
300B LEU* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU 5.0 0.4 - - - -
203A ASN* 4.3 14.7 + - - -
239A PHE* 3.7 25.9 - - - -
294A SER* 4.1 8.7 + - - -
297A SER* 4.5 6.6 + - - -
202B GLU 3.6 19.3 + - - -
293B PRO 4.4 0.2 + - - -
294B SER 3.3 16.0 + - - -
296B VAL* 1.3 78.2 - - - +
298B ASP* 1.3 70.5 + - - +
300B LEU* 3.8 2.0 - - - +
301B ILE* 3.3 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASN 5.6 0.4 - - - -
278A PRO* 4.1 24.9 - - - +
279A SER* 4.9 3.1 + - - -
293A PRO* 4.9 1.7 - - - +
294A SER* 2.8 37.7 + - - -
295B ALA* 3.2 8.5 + - - +
296B VAL 3.2 0.4 - - - -
297B SER* 1.3 79.8 + - - +
299B GLU* 1.3 71.2 + - - +
301B ILE* 3.2 18.5 + - - +
302B LYS* 3.4 17.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 4.0 6.7 - - + -
288B LEU* 3.8 35.1 - - + +
291B LEU* 3.6 36.4 - - + +
295B ALA* 3.3 9.6 + - + +
296B VAL 3.2 7.0 + - - +
298B ASP* 1.3 82.3 - - - +
300B LEU* 1.3 58.3 + - - +
302B LYS* 3.5 23.5 + - - +
303B LEU* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 4.4 16.8 - - + -
241A LEU* 4.7 2.0 - - + -
200B VAL 4.7 2.0 - - - +
202B GLU* 4.1 22.9 - - + +
235B PHE* 3.7 34.9 - - + -
236B VAL 3.9 21.5 - - - +
237B ARG* 4.5 11.0 - - - -
296B VAL* 2.8 19.3 + - + +
297B SER* 3.8 7.2 - - - +
298B ASP 3.2 0.2 - - - -
299B GLU* 1.3 76.1 - - - +
301B ILE* 1.3 61.1 + - - +
303B LEU* 3.9 1.1 - - - -
304B TYR* 2.9 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASN* 4.1 14.8 - - + +
239A PHE* 3.8 16.2 - - + -
240A PRO 5.3 0.2 - - - +
241A LEU* 4.3 17.5 - - + +
275A TYR* 4.6 2.9 - - - +
277A ALA* 5.5 6.3 - - + -
278A PRO* 3.4 38.6 - - + -
297B SER 3.3 18.4 + - - +
298B ASP* 3.2 7.7 + - - +
300B LEU* 1.3 74.3 - - - +
302B LYS* 1.3 61.4 + - + +
304B TYR 3.2 1.9 + - - -
305B LEU* 2.8 57.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
298B ASP* 3.4 12.2 + - + +
299B GLU* 3.7 28.7 - - - +
301B ILE* 1.3 78.5 - - + +
303B LEU* 1.3 64.7 + - - +
305B LEU* 4.8 3.6 - - - -
306B ALA* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.1 52.7 - - + +
100B PHE* 6.5 0.7 - - + -
103B ARG* 4.2 16.4 - - - +
232B SER* 3.9 33.4 - - - +
235B PHE* 4.5 9.2 - - + -
288B LEU* 4.2 9.2 - - + -
299B GLU 2.8 19.3 + - - +
300B LEU* 3.4 7.4 - - - +
302B LYS* 1.3 81.5 - - - +
304B TYR* 1.3 68.1 + - + +
305B LEU 3.2 2.4 + - - -
306B ALA* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 3.8 20.4 - - + -
67B SER* 3.4 16.3 - - - -
70B GLU* 3.3 33.2 + - + -
71B LEU* 3.6 23.6 - - + -
74B ARG* 3.2 45.6 + - - +
235B PHE 2.7 30.7 + - - -
236B VAL* 4.0 3.8 - - - -
237B ARG* 3.8 15.4 + - + +
300B LEU* 2.9 46.7 + - + +
301B ILE 3.2 2.4 + - - +
303B LEU* 1.3 84.5 - - + +
305B LEU* 1.3 62.8 + - - +
306B ALA 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 3.7 33.9 - - + +
242A ASN* 5.2 4.9 - - + +
74B ARG* 4.8 7.0 - - - +
301B ILE* 2.8 43.3 + - + +
302B LYS* 3.6 2.7 - - - +
304B TYR* 1.3 82.8 - - + +
306B ALA* 1.3 68.2 + - - +
307B ALA 3.2 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.3 15.1 - - + -
302B LYS 2.8 17.5 + - - +
303B LEU* 3.5 9.5 + - - +
304B TYR 3.7 1.1 - - - +
305B LEU* 1.3 76.1 - - - +
307B ALA* 1.3 75.6 + - + +
----------------------------------------------------------
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