Contacts of the helix formed by residues 297 - 304 (chain B) in PDB entry 2JDQ
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 VAL 297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 3.5 36.6 - - - +
263B LEU* 3.7 15.7 - - + +
278B LEU* 3.9 20.9 - - + -
292B VAL* 3.4 34.5 + - + +
293B ILE 4.5 0.2 + - - -
295B ALA* 4.1 9.9 - - + -
296B GLY* 1.3 75.8 - - - +
298B CYS* 1.3 69.5 + - - +
299B ARG 3.4 0.6 + - - -
300B ARG* 3.5 3.7 + - - -
301B LEU* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ILE* 4.0 22.2 + - + +
296B GLY 3.1 3.8 + - - -
297B VAL* 1.3 78.4 - - - +
299B ARG* 1.3 64.5 + - - +
301B LEU* 3.3 5.4 + - - +
302B VAL* 3.0 28.1 + - - +
323B ILE* 3.5 30.7 - - - -
333B VAL* 3.7 30.7 - - + -
334B ILE* 3.6 17.3 - - + -
337B CYS* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLY 4.1 5.9 + - - +
297B VAL 3.4 0.6 - - - -
298B CYS* 1.3 77.6 - - - +
300B ARG* 1.3 63.9 + - + +
302B VAL* 3.3 2.9 + - - +
303B GLU* 3.0 43.7 + - + +
336B ASN* 3.3 22.8 + - - +
337B CYS* 3.5 42.6 + - + +
338B SER* 5.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER 5.5 0.4 - - - +
263B LEU* 2.7 55.0 + - + -
264B PHE* 3.9 41.0 + - + +
265B VAL 4.6 4.0 + - - -
271B LEU* 4.5 4.6 - - - +
296B GLY 5.0 3.0 + - - +
297B VAL* 3.5 3.4 + - - +
298B CYS 3.4 0.2 - - - -
299B ARG* 1.3 78.0 - - + +
301B LEU* 1.3 57.2 + - - +
303B GLU* 3.0 43.4 + - - +
304B LEU* 2.9 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.9 9.9 - - + -
275B CYS* 3.9 22.9 - - - -
278B LEU* 3.7 24.2 - - + -
292B VAL* 5.3 0.7 - - + -
297B VAL* 3.0 39.6 + - + +
298B CYS* 3.4 5.4 - - - +
300B ARG* 1.3 77.0 - - - +
302B VAL* 1.3 60.1 + - - +
304B LEU* 3.4 14.6 + - - +
305B LEU* 3.5 12.1 + - - +
316B ALA* 3.9 9.6 - - - +
319B ALA* 3.8 31.0 - - + -
320B VAL* 4.1 12.1 - - + +
323B ILE* 4.0 17.3 - - + -
334B ILE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B CYS 3.0 19.6 + - - +
299B ARG 3.9 3.6 - - - +
301B LEU* 1.3 73.5 - - - +
303B GLU* 1.3 65.1 + - + +
305B LEU* 3.4 25.5 - - + +
306B MET* 4.5 1.2 + - - +
320B VAL* 4.1 9.9 - - + -
334B ILE* 3.7 25.1 - - + -
337B CYS* 3.6 29.6 - - + +
338B SER 4.2 2.5 - - - +
339B ALA* 3.6 37.7 - - + +
342B SER* 4.4 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG* 3.0 40.5 + - + +
300B ARG* 3.0 42.8 + - - +
302B VAL* 1.3 77.4 - - + +
304B LEU* 1.3 61.5 + - - +
306B MET* 3.3 20.6 + - - +
307B HIS 4.3 1.0 + - - -
337B CYS 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.1 17.7 - - + +
271B LEU* 3.9 25.6 - - + -
275B CYS* 3.8 25.6 - - - -
300B ARG* 2.9 41.5 + - - +
301B LEU* 3.4 6.9 + - - +
302B VAL 3.3 0.4 - - - -
303B GLU* 1.3 72.3 - - - +
305B LEU* 1.3 62.9 + - - +
306B MET 3.1 2.0 - - - -
307B HIS* 3.1 47.8 + - + +
312B VAL* 4.0 7.7 - - + +
313B VAL* 4.0 10.4 - - - +
316B ALA* 4.1 11.4 - - + -
----------------------------------------------------------
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