Contacts of the helix formed by residues 302 - 311 (chain L) in PDB entry 2B4X
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 GLU 302 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L ARG* 3.6 23.5 + - - -
300L THR* 3.1 10.1 - - - +
301L PRO* 1.3 94.4 - - - +
303L VAL* 1.3 56.7 + - + +
305L GLN* 2.9 7.9 + - - +
306L GLU* 2.6 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298L GLU* 3.3 26.9 - - + +
299L LEU* 4.8 3.1 - - + -
300L THR* 3.1 26.9 + - + +
302L GLU* 1.3 75.2 - - + +
304L LEU* 1.3 59.3 + - - +
306L GLU* 2.9 25.3 + - + +
307L TRP* 3.0 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L THR* 5.8 1.3 - - + -
269L VAL* 6.3 0.2 - - + -
282L VAL* 5.1 6.1 - - + -
284L ILE* 3.9 28.5 - - + -
299L LEU* 4.2 8.5 - - + -
300L THR 3.0 13.7 + - - +
301L PRO* 4.2 7.6 - - + +
303L VAL* 1.3 80.1 - - - +
305L GLN* 1.3 58.3 + - - +
307L TRP* 4.0 12.7 - - + +
308L LEU* 3.0 49.4 + - + +
411L PHE* 3.9 35.2 - - + -
413L ARG* 4.7 11.0 - - - -
420L ILE* 5.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L PRO 3.1 20.4 + - - +
302L GLU* 2.9 10.4 + - - +
304L LEU* 1.3 77.5 - - - +
306L GLU* 1.3 67.1 + - - +
307L TRP 3.2 0.4 - - - -
308L LEU* 3.0 30.8 + - - +
309L ASP* 3.1 40.3 + - - +
413L ARG* 5.6 0.6 + - - +
418L ASN* 3.3 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L GLU* 2.6 18.5 + - - +
303L VAL* 3.2 13.9 - - + +
305L GLN* 1.3 71.3 - - - +
307L TRP* 1.3 67.1 + - + +
309L ASP* 3.0 20.6 + - - +
310L GLU* 3.3 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 307 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L ARG* 5.2 0.2 - - - +
263L VAL* 3.6 25.8 - - + +
264L ALA* 4.9 12.8 - - + +
267L THR* 5.0 5.6 - - + -
269L VAL* 4.2 19.7 - - + -
284L ILE* 3.5 39.3 - - + -
295L VAL* 3.9 29.2 - - + -
299L LEU* 4.6 9.0 - - + -
303L VAL* 3.0 34.6 + - + +
304L LEU* 4.0 20.6 - - + +
306L GLU* 1.3 82.6 - - + +
308L LEU* 1.3 63.8 + - + +
309L ASP 3.1 0.9 + - - -
310L GLU* 3.2 31.7 + - - +
311L LEU* 3.3 18.7 + - - +
409L LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ARG* 2.9 30.7 + - - +
269L VAL* 5.3 2.5 - - + -
271L GLU* 4.6 1.6 - - - +
282L VAL* 4.1 22.2 - - + -
304L LEU* 3.0 34.0 + - + +
305L GLN* 3.0 30.3 + - - +
307L TRP* 1.3 80.1 - - + +
309L ASP* 1.3 60.2 + - - +
311L LEU* 3.8 19.0 - - + +
413L ARG* 3.1 52.0 - - - +
418L ASN* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 309 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ARG* 4.2 2.8 + - - +
305L GLN* 3.1 39.4 + - - +
306L GLU* 3.0 11.4 + - - +
308L LEU* 1.3 79.0 - - - +
310L GLU* 1.3 65.0 + - + +
311L LEU 3.2 5.4 + - - +
312L GLU* 4.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L ARG* 3.7 35.5 + - + +
263L VAL* 3.5 28.2 - - - +
306L GLU* 3.5 20.2 - - + +
307L TRP* 3.2 25.4 + - - +
309L ASP* 1.3 74.9 - - + +
311L LEU* 1.3 60.3 + - - +
312L GLU* 2.8 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ARG* 2.8 56.6 + - + +
260L TYR 3.6 6.5 - - - +
261L ARG* 3.7 19.1 - - + -
269L VAL* 3.7 33.2 - - + +
270L LEU 4.9 0.2 - - - -
271L GLU* 3.7 31.4 - - + +
282L VAL* 5.2 0.2 - - + -
307L TRP 3.3 17.4 + - - +
308L LEU* 3.8 23.6 - - + +
309L ASP 3.2 3.3 - - - +
310L GLU* 1.3 74.9 - - - +
312L GLU* 1.3 62.2 + - - +
----------------------------------------------------------
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