Contacts of the helix formed by residues 262 - 266 (chain D) in PDB entry 3DLX
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 PRO 262 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 4.0 14.8 - - + -
378C SER* 3.7 25.8 - - - +
379C PHE 5.8 0.2 - - - +
380C PHE* 4.2 18.2 - - + -
384C GLU* 5.7 2.7 - - + +
388C MET* 4.3 8.7 - - + -
219D GLY 4.5 0.2 - - - -
220D ASN* 3.6 7.4 - - - +
236D LYS* 5.9 0.4 - - - -
259D ILE* 3.8 8.3 - - + +
260D HIS 3.8 7.2 - - - +
261D ILE* 1.3 99.0 - - + +
263D GLN* 1.3 64.9 + - - +
264D ILE* 3.0 8.9 + - + -
265D TYR* 3.2 25.4 + - + +
266D VAL* 4.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C TYR* 2.7 32.6 + - + +
340C HIS* 3.4 31.0 + - - +
348C LEU* 4.2 11.1 - - + +
376C GLY 3.9 16.3 + - - +
40D THR* 3.9 2.6 + - - -
218D ALA* 3.3 44.5 - - - +
219D GLY* 3.5 16.8 - - - -
220D ASN* 3.0 13.7 + - - +
261D ILE 3.7 0.4 + - - -
262D PRO* 1.3 71.9 - - - +
264D ILE* 1.3 62.8 + - - +
265D TYR 3.1 2.8 + - - -
266D VAL* 3.2 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C TYR* 3.5 53.1 - - + -
342C GLN* 5.3 0.7 - - + -
348C LEU* 3.9 14.3 - - + +
388C MET* 4.0 38.8 - - + -
393C HIS* 3.6 34.7 + - + +
394C VAL* 4.3 7.0 - - + -
262D PRO* 4.2 2.2 - - + +
263D GLN* 1.3 80.3 - - - +
265D TYR* 1.3 82.0 + - + +
266D VAL 3.5 0.7 - - - -
267D HIS* 3.7 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C GLU* 2.7 29.1 + - - -
387C ALA* 4.4 3.5 - - - +
388C MET* 3.7 39.3 + - + +
393C HIS* 3.4 44.8 + + - -
149D GLY 5.1 0.7 + - - -
235D CYS* 3.3 12.3 - - + +
236D LYS* 3.6 36.8 - - + +
241D THR* 3.1 25.9 - - - +
261D ILE* 4.0 14.6 - - + -
262D PRO* 3.2 25.8 + - + +
263D GLN 3.1 0.4 - - - -
264D ILE* 1.3 82.1 - - + +
266D VAL* 1.3 60.3 + - - +
267D HIS* 3.8 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D THR* 3.1 36.3 + - + +
219D GLY 3.2 27.4 - - - +
221D VAL* 4.2 8.5 - - + -
241D THR* 4.3 3.8 - - + -
243D VAL* 3.9 26.2 - - + -
261D ILE* 3.6 28.3 - - + -
262D PRO 4.0 4.0 - - - +
263D GLN 3.2 8.9 + - - +
264D ILE 3.5 0.4 - - - -
265D TYR* 1.3 77.8 - - - +
267D HIS* 1.3 64.2 + - - +
268D ARG 4.1 7.9 - - - +
269D LEU* 4.4 8.5 - - + -
----------------------------------------------------------
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