Contacts of the helix formed by residues 287 - 302 (chain D) in PDB entry 1QMZ
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 287 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D VAL* 4.4 3.6 - - - -
286D TYR* 1.3 76.9 - - - +
288D LYS* 1.3 64.4 + - - +
289D LYS* 3.5 9.4 + - - +
290D GLN* 2.8 47.7 + - - +
291D VAL* 3.0 13.3 + - - +
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Residues in contact with LYS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR* 5.6 0.4 - - + -
40C GLU* 3.0 51.2 + - + +
41C THR* 3.3 28.5 + - - +
42C GLU* 4.4 6.3 + - - -
274D GLU* 5.5 1.0 + - - -
275D VAL* 4.1 20.9 - - + -
276D ALA* 4.2 24.2 - - + +
279D VAL* 3.7 22.3 - - + +
287D THR* 1.3 73.0 - - - +
289D LYS* 1.4 57.6 + - - +
291D VAL* 3.1 3.3 + - - +
292D LEU* 2.9 37.2 + - + +
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR* 2.8 47.5 + - + +
73C GLU* 6.0 5.6 - - - +
287D THR* 3.2 8.9 + - - +
288D LYS* 1.4 80.1 - - - +
290D GLN* 1.3 61.6 + - - +
292D LEU* 3.4 6.6 + - + -
293D ARG* 2.9 69.0 + - + +
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Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 4.9 4.6 + - - -
25A LEU* 4.2 13.6 - - + +
252D LYS* 4.5 18.2 - - - +
255D LEU* 3.9 16.5 - - + +
285D THR 4.5 0.9 - - - +
286D TYR* 3.1 25.7 - - + -
287D THR* 2.8 43.2 + - - +
289D LYS* 1.3 74.5 - - + +
291D VAL* 1.3 64.7 + - - +
293D ARG* 3.9 1.5 - - - +
294D MET* 2.8 27.2 + - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 3.9 19.5 - - + -
258D THR* 4.3 26.2 - - + -
259D ALA* 4.2 9.3 - - - +
262D LEU* 4.3 17.0 - - + -
275D VAL* 4.2 19.5 - - + -
278D PHE* 5.0 3.6 - - + -
279D VAL* 4.2 15.9 - - + -
282D THR* 5.7 0.7 - - + -
286D TYR* 4.5 8.7 - - + -
287D THR 3.0 13.7 + - - +
288D LYS 3.1 6.9 + - - +
290D GLN* 1.3 77.4 - - - +
292D LEU* 1.3 56.8 + - - +
294D MET* 3.3 1.8 + - - +
295D GLU* 2.8 27.5 + - - +
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR* 3.6 27.1 - - + -
40C GLU 3.9 12.3 - - - +
41C THR 4.2 9.9 - - - +
42C GLU 4.3 0.2 - - - -
43C GLY* 3.8 26.5 - - - +
262D LEU* 4.6 4.7 - - + -
275D VAL* 3.7 33.4 - - + -
288D LYS* 2.9 25.0 + - + +
289D LYS* 3.8 12.6 - - + +
291D VAL* 1.3 77.6 - - - +
293D ARG* 1.3 61.9 + - - +
295D GLU* 3.3 11.6 + - - +
296D HIS* 3.3 20.4 + - - +
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Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 2.5 50.3 + - - +
3A ASN* 4.1 8.7 + - - +
24A LYS* 5.9 4.9 - - - +
25A LEU* 3.6 30.4 - - + +
73C GLU* 5.7 2.7 - - - +
289D LYS* 2.9 63.9 + - - +
290D GLN* 5.4 0.4 - - - +
292D LEU* 1.3 74.2 - - - +
294D MET* 1.3 60.5 - - - +
296D HIS* 3.4 8.5 + - - +
297D LEU 3.0 22.3 + - - -
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Residues in contact with MET 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.4 43.6 - - + +
26A THR* 4.5 3.8 - - + -
242D PHE* 4.2 7.6 - - - -
252D LYS 4.9 0.2 - - - +
255D LEU* 3.6 33.4 - - + +
256D VAL* 4.0 20.6 - - + -
259D ALA* 3.5 17.3 - - + -
290D GLN 2.8 21.1 + - - +
291D VAL 3.8 3.4 - - - +
293D ARG* 1.3 72.4 - - - +
295D GLU* 1.3 58.0 + - - +
297D LEU* 3.0 17.0 + - - -
298D VAL* 2.8 41.9 + - + +
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY* 3.3 8.0 - - - -
44C VAL* 2.7 33.9 + - + +
259D ALA* 3.7 11.1 - - + +
262D LEU* 2.9 27.7 - - + +
263D LEU* 4.0 26.6 - - + +
266D LYS* 2.8 26.8 + - - +
291D VAL 2.8 14.8 + - - +
292D LEU* 3.3 13.2 - - - +
293D ARG 3.2 0.4 - - - -
294D MET* 1.3 74.2 - - - +
296D HIS* 1.3 56.8 + - - +
298D VAL* 3.4 2.8 + - - +
299D LEU* 3.0 33.0 + - + +
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Residues in contact with HIS 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 5.7 5.6 - - - -
37C LEU* 5.5 0.6 - - - +
44C VAL* 5.5 1.3 - - + +
71C HIS* 2.7 52.4 + + + -
72C THR 2.9 28.5 + - - -
73C GLU* 4.4 4.7 - - + -
292D LEU 3.3 9.7 + - - +
293D ARG* 3.7 9.9 - - - +
295D GLU* 1.3 74.2 - - - +
297D LEU* 1.4 67.3 + - + +
299D LEU* 3.4 3.4 + - - +
300D LYS* 2.3 67.4 + - - +
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASN* 4.9 11.4 - - + +
23A ASN* 4.6 8.5 - - - +
25A LEU* 3.9 32.3 - - + -
26A THR* 4.2 10.3 - - + -
242D PHE* 4.1 22.4 - - + -
246D MET* 4.1 10.8 - - + -
293D ARG 3.0 14.8 + - - +
294D MET* 3.0 9.8 + - - +
296D HIS* 1.4 77.5 - - - +
298D VAL* 1.4 64.0 + - - +
300D LYS* 3.2 17.7 + - + -
301D VAL* 2.9 36.7 + - + +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D TYR* 4.8 8.7 - - + -
242D PHE* 3.9 29.8 - - + -
256D VAL* 4.6 11.2 - - + +
259D ALA* 4.4 8.1 - - + -
260D ALA* 5.0 4.9 - - + +
263D LEU* 3.6 22.2 - - + -
294D MET* 2.8 38.3 + - + +
295D GLU 3.8 2.9 - - - +
297D LEU* 1.4 70.2 - - - +
299D LEU* 1.4 64.0 + - - +
301D VAL 3.2 0.5 + - - -
302D LEU* 2.8 50.5 + - + +
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.8 32.5 - - + -
49C ILE* 3.9 7.0 - - + -
71C HIS* 4.2 7.0 - - + +
263D LEU* 3.8 16.8 - - + -
295D GLU* 3.0 22.9 + - + +
296D HIS* 3.9 3.4 - - - +
298D VAL* 1.4 76.8 - - - +
300D LYS* 1.3 56.6 - - - +
302D LEU* 3.4 2.9 + - - -
303D THR 2.9 7.1 + - - -
304D PHE* 2.8 77.9 + - + +
306D LEU* 3.8 29.4 - - + -
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Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 5.9 3.1 - - - +
71C HIS* 3.5 16.5 + - - +
296D HIS* 2.3 57.3 + - + +
297D LEU* 3.9 17.3 - - + +
299D LEU* 1.3 73.2 - - - +
301D VAL* 1.3 70.0 + - + +
303D THR* 2.9 22.4 + - - +
304D PHE* 5.0 5.6 - - + -
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D ARG 4.7 0.9 - - - +
242D PHE* 3.6 45.1 - - + -
245D SER* 3.7 22.4 - - - +
246D MET* 3.7 26.2 - - + -
297D LEU* 2.9 25.8 + - + +
298D VAL 3.9 0.2 - - - +
300D LYS* 1.3 78.8 - - + +
302D LEU* 1.3 64.6 + - + +
303D THR* 3.3 5.9 + - - +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D TYR* 3.7 40.2 - - + +
241D ARG* 3.5 50.5 + - + +
242D PHE* 3.8 16.6 - - + +
298D VAL* 2.8 33.1 + - + +
299D LEU 4.1 2.7 - - - +
301D VAL* 1.3 80.5 - - + +
303D THR* 1.4 73.6 + - - +
304D PHE 4.3 2.2 - - - +
305D ASP* 2.9 19.8 + - - +
306D LEU* 4.1 14.4 - - + -
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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) + - + + + + + -
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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