Contacts of the helix formed by residues 369 - 386 (chain D) in PDB entry 2XLR
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 369 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D VAL* 1.3 81.8 - - + +
370D ALA* 1.3 65.8 + - - +
371D GLU* 3.7 11.3 + - - +
372D GLU* 2.7 58.1 + - - +
373D MET* 3.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D TRP* 4.0 26.4 - - + -
368D VAL 4.2 0.4 + - - -
369D THR* 1.3 71.8 - - - +
371D GLU* 1.3 63.7 + - - +
373D MET* 3.1 5.7 + - - +
374D TYR* 3.0 25.1 + - - +
403D LEU* 5.4 3.1 - - + -
406D LYS* 4.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D THR* 3.1 11.0 + - - +
370D ALA* 1.3 79.1 - - - +
372D GLU* 1.3 57.6 + - + +
374D TYR* 3.7 3.2 + - - +
375D THR* 2.7 39.8 + - - +
400D LYS* 5.5 4.0 - - - +
403D LEU* 4.0 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D THR* 4.6 12.3 - - - +
367D LEU* 4.0 20.4 - - + +
368D VAL* 3.1 19.3 + - - +
369D THR* 2.7 50.5 + - - +
371D GLU* 1.3 77.2 - - + +
373D MET* 1.3 59.0 + - - +
375D THR* 3.6 7.2 + - - -
376D TYR* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 3.7 28.3 - - + +
324D TRP* 3.7 35.4 - - + -
367D LEU* 3.9 29.2 - - + +
368D VAL 3.6 26.0 - - - +
369D THR 3.1 10.7 + - - +
370D ALA* 3.1 7.2 + - - +
372D GLU* 1.3 73.7 - - - +
374D TYR* 1.3 66.5 + - - +
375D THR 3.0 1.1 - - - -
376D TYR* 2.9 15.1 + - - +
377D GLN* 3.0 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D TRP* 4.2 26.0 - - + -
325D TYR* 3.6 5.5 - - + -
370D ALA 3.0 14.4 + - - +
371D GLU* 4.3 4.3 - - - +
373D MET* 1.3 74.8 - - - +
375D THR* 1.3 57.5 + - - +
377D GLN* 3.4 1.1 + - - +
378D GLY 3.0 22.3 + - - -
399D ASN* 3.5 22.6 - - + +
402D PHE* 4.4 25.1 - - + -
403D LEU* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D GLU* 2.7 30.5 + - - +
372D GLU* 3.6 8.1 - - - -
373D MET 3.0 0.8 - - - -
374D TYR* 1.3 75.5 - - - +
376D TYR* 1.3 60.0 + - - +
378D GLY* 3.3 0.9 + - - -
379D ASP* 2.8 48.9 + - - +
399D ASN* 3.8 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 3.9 39.9 - - + -
299D TRP* 3.3 20.1 - + - +
360D TRP* 2.9 56.0 + + - -
363D LYS* 3.7 31.4 - - + -
364D GLU* 3.7 9.6 - - + +
367D LEU* 3.7 18.2 - - + -
372D GLU 3.0 14.8 + - - +
373D MET 2.9 7.7 + - - +
375D THR* 1.3 77.0 - - - +
377D GLN* 1.3 63.0 + - + +
379D ASP* 3.0 12.4 + - + +
380D TYR* 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 3.8 19.7 + - + +
321D GLN* 4.2 7.7 - - - +
322D ASP 2.9 22.2 + - - -
324D TRP* 2.7 37.0 + - + +
325D TYR* 2.8 23.0 + - + +
329D MET* 3.5 32.0 - - - +
373D MET 3.0 13.8 + - - +
374D TYR 3.9 4.0 - - - +
376D TYR* 1.3 80.7 - - + +
378D GLY* 1.3 55.9 + - - +
380D TYR* 3.0 11.7 + - + +
381D ILE* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.9 10.9 - - - -
374D TYR 3.0 14.6 + - - -
375D THR 3.6 4.3 - - - -
376D TYR 3.2 0.2 - - - -
377D GLN* 1.3 74.5 - - - +
379D ASP* 1.3 58.5 + - - +
381D ILE* 3.3 5.1 + - - +
382D GLN* 2.8 29.7 + - - +
395D ILE* 3.7 29.7 - - - +
399D ASN* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D TRP* 4.1 11.4 - - + -
363D LYS* 6.0 1.7 - - - -
375D THR* 2.8 33.4 + - - +
376D TYR* 3.4 12.1 - - + +
378D GLY* 1.3 76.4 - - - +
380D TYR* 1.3 64.6 + - - +
382D GLN* 3.5 7.6 + - - +
383D ASN* 3.0 23.6 + - - +
395D ILE* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU 5.9 0.9 - - - -
299D TRP* 3.7 21.8 - + + -
305D LYS* 2.5 38.6 + - + -
306D GLY* 3.4 8.6 - - - -
321D GLN* 4.6 9.2 - - + -
329D MET* 4.0 24.0 - - + -
333D GLN* 3.1 31.5 + - - +
360D TRP* 3.7 24.0 - + + -
376D TYR* 2.9 15.3 + - + +
377D GLN* 3.0 15.9 + - + +
379D ASP* 1.3 76.1 - - - +
381D ILE* 1.3 66.5 + - + +
383D ASN* 3.2 6.3 + - + +
384D LEU* 3.1 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.4 49.8 - - + -
328D ASN 4.5 4.7 - - - +
329D MET* 3.8 30.3 - - + +
332D ALA* 4.0 11.2 - - + -
377D GLN* 2.9 23.3 + - + +
378D GLY* 3.6 3.8 - - - +
380D TYR* 1.3 76.5 - - + +
382D GLN* 1.3 65.1 + - - +
384D LEU* 3.0 9.1 + - - +
385D ILE* 2.9 35.6 + - + +
393D PHE* 4.4 11.2 - - + -
395D ILE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D GLY 2.8 17.1 + - - +
379D ASP* 3.6 10.3 - - - +
380D TYR 3.3 0.2 - - - -
381D ILE* 1.3 76.8 - - - +
383D ASN* 1.3 63.2 + - - +
385D ILE* 3.4 24.5 + - - +
386D ASP* 3.0 56.1 + - - +
392D SER* 3.7 9.3 + - - -
393D PHE 4.7 4.9 - - - +
395D ILE* 3.7 23.6 - - + +
396D PRO* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 383 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LYS* 2.9 33.4 + - - +
360D TRP* 4.5 20.5 - - + +
379D ASP 3.0 15.1 + - - +
380D TYR* 3.2 10.2 + - + +
382D GLN* 1.3 77.9 - - - +
384D LEU* 1.3 62.7 + - + +
386D ASP* 3.8 11.2 + - - +
387D MET* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LYS* 3.9 22.9 - - + +
307D VAL* 5.2 0.2 - - + -
329D MET* 5.0 0.4 - - + +
332D ALA* 3.8 24.6 - - + +
333D GLN* 3.8 22.0 - - + +
336D TYR* 4.0 29.3 - - + +
380D TYR* 3.1 47.2 + - + +
381D ILE* 3.0 9.7 + - + +
383D ASN* 1.3 74.3 - - - +
385D ILE* 1.3 65.3 + - - +
387D MET* 3.1 31.3 + - + +
388D THR* 3.8 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 385 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ASN 5.6 0.2 - - - +
332D ALA* 3.8 18.6 - - + +
381D ILE* 2.9 23.9 + - + +
382D GLN* 3.5 35.9 - - - +
384D LEU* 1.3 75.0 - - - +
386D ASP* 1.3 61.5 + - - +
388D THR* 2.9 31.5 + - - +
390D TYR* 3.5 33.5 - - + +
391D PRO 4.4 1.1 - - - +
392D SER* 3.6 32.5 + - - +
393D PHE* 4.3 15.7 - - + +
395D ILE* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D GLN* 3.0 49.8 + - - +
383D ASN* 4.1 9.1 - - - +
384D LEU 3.2 0.2 - - - -
385D ILE* 1.3 76.0 - - - +
387D MET* 1.3 61.5 + - + +
388D THR 3.4 2.0 - - - +
392D SER* 4.2 4.9 + - - -
----------------------------------------------------------
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