Contacts of the helix formed by residues 264 - 270 (chain D) in PDB entry 3T79
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 THR 264 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D TYR* 1.3 81.4 - - - +
265D LYS* 1.3 65.2 + - - +
266D LYS* 3.2 4.5 - - - -
267D HIS* 3.0 60.4 + - + +
268D TRP* 3.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU* 3.1 30.7 + - - +
246D LEU* 6.0 1.8 - - - +
249D GLY* 4.4 17.5 - - - +
263D TYR* 3.3 33.9 - - + +
264D THR* 1.3 69.3 - - - +
266D LYS* 1.3 67.9 + - - +
267D HIS 3.0 0.9 + - - -
268D TRP* 3.1 2.8 + - - -
269D PHE* 2.9 47.5 + - + +
270D GLN* 4.9 3.9 - - - +
5E T 3.7 53.2 + - + +
6E T 5.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D THR* 3.2 3.3 - - - -
265D LYS* 1.3 79.3 - - - +
267D HIS* 1.3 72.2 + - + +
270D GLN* 3.0 55.0 + - + +
271D VAL 4.4 12.8 - - - +
272D ASN* 5.4 0.6 - - - +
273D GLN* 5.2 4.3 - - - -
5E T 3.6 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU* 6.4 0.6 - - - +
146D LYS* 2.7 34.0 + - - -
264D THR* 3.0 39.0 + - + +
265D LYS 3.0 1.0 - - - -
266D LYS* 1.3 85.8 - - + +
268D TRP* 1.3 73.9 + + + +
270D GLN 3.2 5.4 - - - +
272D ASN* 4.1 30.9 + - - +
274D GLU* 6.1 2.6 - - - -
275D TRP* 6.2 2.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 4.7 8.7 - - + -
143D PHE* 3.7 34.1 - + - -
146D LYS* 3.7 27.2 - - + +
147D PHE* 3.9 31.6 - + + -
156D ARG* 2.1 39.4 + - - -
252D TYR* 4.1 21.5 - + + +
256D PHE* 3.8 23.5 - + - -
263D TYR* 3.9 20.5 - + - +
264D THR 3.3 21.1 + - - +
265D LYS 3.1 2.4 + - - -
267D HIS* 1.3 94.2 - + + +
269D PHE* 1.3 62.0 - - + +
270D GLN 3.5 1.1 - - - -
275D TRP* 4.3 18.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ASP* 5.3 0.7 - - - -
152D SER* 4.3 2.9 + - - -
153D PHE* 3.3 40.9 + + + +
154D GLU 4.9 0.2 + - - -
156D ARG* 3.6 3.8 - - - +
245D GLU* 3.5 43.1 - - + +
248D LEU* 3.6 17.3 - - + -
249D GLY* 3.3 26.0 - - - -
252D TYR* 3.7 25.8 - + - -
263D TYR* 4.1 11.7 - - - -
265D LYS* 2.9 34.5 + - + +
268D TRP* 1.3 85.7 - - + +
270D GLN* 1.3 78.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LYS* 3.5 7.6 - - - -
152D SER* 4.6 7.9 - - - +
245D GLU* 5.5 2.0 + - - -
265D LYS* 4.9 4.9 - - - +
266D LYS* 3.0 64.9 + - + +
267D HIS 3.2 12.1 - - - +
268D TRP 3.5 0.6 + - - -
269D PHE* 1.3 94.8 - - - +
271D VAL* 1.3 71.9 + - - +
272D ASN 3.3 0.3 + - - -
5E T 4.3 16.5 + - - -
----------------------------------------------------------
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