Contacts of the strand formed by residues 299 - 306 (chain D) in PDB entry 1XPM
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 299 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ASN* 4.3 1.5 + - - +
222D LYS* 5.6 6.2 + - - +
226D ASP 4.5 12.5 + - - -
227D PHE* 3.7 13.2 - - + -
228D ALA* 2.9 31.3 + - - +
297D GLY 3.8 5.0 + - - -
298D GLU* 1.3 75.4 - - - +
300D ILE* 1.3 65.2 - - - +
315D SER* 3.6 28.5 - - - +
316D ALA 3.3 14.1 - - - +
317D THR* 3.4 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 4.2 20.2 - - + -
227D PHE* 3.7 2.7 - - - -
228D ALA* 5.5 0.4 - - + -
229D SER* 3.3 14.1 - - - +
231D CYS* 4.1 8.1 - - + -
285D LEU* 4.3 8.5 - - + -
288D LEU* 3.9 24.2 - - + -
289D LEU* 4.3 14.8 - - + -
294D LEU* 3.8 30.1 - - + -
298D GLU 5.5 0.2 - - - -
299D THR* 1.3 76.8 - - - +
301D GLY* 1.3 68.8 + - - +
302D LEU* 3.6 15.9 - - + +
315D SER* 3.2 6.9 - - - -
316D ALA* 2.9 35.5 + - + +
318D LEU* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D PHE* 3.4 24.1 - - - -
229D SER 3.0 9.9 + - - -
230D LEU* 3.1 9.2 - - - +
231D CYS 2.8 25.1 + - - -
300D ILE* 1.3 73.3 - - - +
302D LEU* 1.3 60.1 + - - -
313D PHE* 3.8 14.8 - - - -
314D TYR 3.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 6.0 0.2 - - + -
231D CYS* 3.1 13.9 - - + +
281D LEU* 4.3 19.1 - - + -
282D TYR* 4.7 0.7 - - + -
285D LEU* 4.3 31.2 - - + -
300D ILE* 3.6 26.7 - - + +
301D GLY* 1.3 75.3 - - - +
303D PHE* 1.3 61.2 + - - +
304D SER 4.2 0.4 - - - -
312D GLU 3.6 0.9 - - - +
313D PHE* 3.2 10.1 - - - -
314D TYR* 2.8 82.4 + - + +
316D ALA* 4.2 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D TYR* 4.2 23.1 - + - -
208D SER* 3.7 13.7 - - - -
209D PHE* 3.4 68.9 - + + -
212D SER* 3.8 15.3 - - - -
231D CYS 3.0 8.1 + - - -
232D PHE* 3.4 12.6 - + + -
233D HIS 3.3 24.7 + - - -
281D LEU* 3.8 5.1 - - - +
301D GLY 4.3 0.2 + - - -
302D LEU* 1.3 75.2 - - - +
304D SER* 1.3 74.0 + - - +
305D TYR* 3.7 20.4 - - + -
311D GLY* 3.8 0.9 - - - -
312D GLU 3.3 23.6 - - - -
313D PHE* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SCY 4.3 2.8 + - - -
112D TYR* 3.5 23.9 + - - -
115D THR* 2.7 37.4 + - - -
233D HIS* 4.8 1.8 - - - -
281D LEU* 3.6 16.1 - - - +
282D TYR* 5.2 0.9 - - - -
302D LEU 4.2 0.4 - - - -
303D PHE* 1.3 77.4 - - - +
305D TYR* 1.3 61.6 + - - +
311D GLY* 3.2 4.9 - - - -
312D GLU 2.9 35.1 + - - -
314D TYR* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SCY 3.1 29.1 + - - +
112D TYR* 3.9 4.3 - - - -
184D ASP* 2.9 18.6 + - - -
204D ALA* 3.4 16.5 - - - +
205D TYR* 3.5 36.8 - + + -
208D SER* 3.5 38.8 - - - -
233D HIS* 4.1 12.8 - + + +
303D PHE* 3.7 15.5 - + + -
304D SER* 1.3 76.5 + - - +
306D GLY* 1.3 72.9 + - - +
307D SER* 3.8 12.1 - - - -
309D SER* 3.3 25.5 - - - -
310D VAL 3.6 4.3 - - - -
4402D CAA 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLU* 3.5 1.6 - - - -
110D ALA* 3.8 4.0 - - - -
111D SCY 3.3 6.3 - - - -
112D TYR* 3.6 22.4 - - - +
305D TYR* 1.3 80.0 - - - +
307D SER* 1.3 69.9 + - - -
309D SER* 3.1 4.7 - - - -
310D VAL 2.9 29.5 + - - +
----------------------------------------------------------
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