Contacts of the helix formed by residues 374 - 391 (chain D) in PDB entry 2QMR
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 ASN 374 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274D LEU* 3.6 16.3 - - - +
314D ASP* 4.3 16.1 + - - +
370D ILE* 3.8 27.3 - - - +
371D SER* 4.6 10.0 + - - -
373D TRP* 1.3 77.0 - - - +
375D LEU* 1.3 59.0 + - - +
376D ARG* 3.1 11.0 + - - +
377D LYS* 2.8 45.9 + - - +
378D CYS* 2.8 30.7 + - - +
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D THR* 4.6 11.9 - - + +
270D GLU* 3.9 26.7 - - - +
273D ALA* 4.1 24.2 - - + +
274D LEU* 3.9 13.8 - - + +
277D CYS* 3.8 24.7 - - + -
307D GLY* 4.0 21.3 - - - +
374D ASN* 1.3 75.2 - - - +
376D ARG* 1.3 51.9 + - - +
378D CYS* 3.7 0.7 - - - +
379D SER* 2.7 51.6 + - - +
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Residues in contact with ARG 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLY 3.5 15.3 + - - +
308D MET* 2.9 27.3 + - - +
309D LYS 4.5 3.8 - - - +
310D TYR* 3.3 48.0 + - - +
314D ASP* 5.1 5.2 - - - +
370D ILE* 6.2 1.1 - - - -
374D ASN* 3.1 13.7 + - - +
375D LEU* 1.3 75.0 - - - +
377D LYS* 1.3 70.4 + - + +
379D SER* 3.4 0.9 + - - -
380D ALA* 2.9 28.1 + - - +
415D GLU* 2.4 39.7 + - - -
419D LEU* 3.2 35.5 - - + +
457D ILE* 4.5 6.3 - - - +
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Residues in contact with LYS 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE* 4.2 11.7 - - - +
371D SER 2.7 29.7 + - - -
372D ASP* 3.4 19.8 + - - +
373D TRP* 3.8 21.0 - - + -
374D ASN* 2.8 33.0 + - - +
376D ARG* 1.3 77.8 - - + +
378D CYS* 1.3 57.8 + - - +
380D ALA* 3.9 5.3 - - - +
381D ALA* 3.0 29.3 + - - +
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Residues in contact with CYS 378 (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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274D LEU* 3.8 14.6 - - + -
277D CYS* 3.6 20.9 - - - -
278D GLU* 3.8 26.0 - - - -
281D LEU* 4.0 8.0 - - - +
373D TRP* 3.7 30.4 - - + -
374D ASN 2.8 17.9 + - - +
375D LEU 3.7 3.4 - - - +
377D LYS* 1.3 74.9 - - - +
379D SER* 1.3 66.5 + - - +
381D ALA* 3.0 4.3 + - - +
382D ALA* 2.9 22.4 + - - +
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Residues in contact with SER 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D THR* 5.5 1.2 - - - +
277D CYS* 3.5 18.6 - - - -
304D LEU* 3.4 39.6 + - - +
307D GLY* 4.0 5.3 - - - -
308D MET* 3.6 10.1 - - - -
375D LEU* 2.7 36.7 + - - +
378D CYS* 1.3 72.5 - - - +
380D ALA* 1.3 52.0 + - - +
382D ALA* 3.0 5.0 + - - +
383D LEU* 2.8 35.2 + - - +
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Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D MET* 3.6 30.6 - - + +
376D ARG* 2.9 18.9 + - + +
377D LYS* 3.9 6.1 - - - +
379D SER* 1.3 75.9 - - - +
381D ALA* 1.3 57.2 + - - +
383D LEU* 3.9 1.3 - - - +
384D ASP* 3.0 29.1 + - - +
419D LEU* 4.3 16.8 - - + -
423D ALA* 4.3 6.7 - - + +
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D LEU* 4.2 13.7 - - + -
373D TRP* 3.9 18.4 - - + -
377D LYS 3.0 20.8 + - - +
378D CYS 3.0 5.1 + - - +
380D ALA* 1.3 73.2 - - - +
382D ALA* 1.3 64.0 + - - +
384D ASP* 3.4 6.5 + - - +
385D VAL* 3.0 29.9 + - + +
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Residues in contact with ALA 382 (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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277D CYS* 5.1 3.1 - - - -
280D TRP* 4.2 20.4 - - + -
281D LEU* 4.1 18.7 - - + +
284D ALA* 5.6 0.2 - - - -
304D LEU* 4.0 20.2 - - + -
378D CYS 2.9 11.6 + - - +
379D SER* 3.3 9.2 - - - +
381D ALA* 1.3 75.7 - - - +
383D LEU* 1.3 51.8 + - - +
385D VAL* 3.0 5.3 + - - +
386D LEU* 2.7 41.9 + - + +
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Residues in contact with LEU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ILE* 4.4 13.7 - - + -
304D LEU* 4.4 13.2 - - + +
305D VAL* 4.1 10.8 - - + +
308D MET* 3.6 29.4 - - + -
379D SER 2.8 19.3 + - - +
380D ALA 3.9 3.6 - - - +
382D ALA* 1.3 70.1 - - - +
384D ASP* 1.3 65.3 + - - +
386D LEU* 4.4 5.6 - - + -
387D ALA* 3.0 24.3 + - - +
394D LEU* 4.2 10.5 - - + -
398D ILE* 4.0 17.9 - - + -
420D VAL* 3.8 27.8 - - + -
423D ALA* 4.6 3.8 - - + -
424D ILE* 3.9 15.3 - - + -
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Residues in contact with ASP 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D ALA 3.0 19.2 + - - +
381D ALA* 3.5 8.1 - - - +
383D LEU* 1.3 76.8 - - - +
385D VAL* 1.3 61.6 + - + +
387D ALA* 3.4 4.3 + - - +
388D ASN* 2.8 35.5 + - - -
423D ALA* 3.4 30.5 + - + +
426D GLU* 3.7 7.8 - - - +
460D TRP* 5.5 2.8 - - - -
464D ARG* 3.5 15.9 + - - -
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D LEU* 4.1 15.3 - - + -
284D ALA* 3.6 28.9 - - + +
285D GLU* 3.6 35.2 - - + +
381D ALA* 3.0 17.0 + - + +
382D ALA* 3.6 6.1 - - - +
384D ASP* 1.3 75.7 - - + +
386D LEU* 1.3 65.6 + - - +
388D ASN* 3.1 18.7 + - + +
389D VAL* 3.1 15.6 + - + +
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Residues in contact with LEU 386 (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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280D TRP* 5.1 4.7 - - + +
284D ALA* 4.1 17.9 - - + -
289D CYS* 4.3 4.5 - - - -
293D LEU* 3.9 24.7 - - + -
297D LEU* 5.0 0.4 - - + -
300D LEU* 3.7 17.7 - - + -
301D ILE* 4.8 7.2 - - + -
304D LEU* 3.5 32.1 - - + -
382D ALA* 2.7 24.8 + - + +
383D LEU* 4.0 6.7 - - + +
385D VAL* 1.3 72.3 - - - +
387D ALA* 1.3 56.4 + - - +
389D VAL* 3.2 4.6 + - + +
390D TYR* 3.0 53.5 + - + +
394D LEU* 4.3 11.3 - - + +
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Residues in contact with ALA 387 (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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383D LEU 3.0 18.3 + - - +
384D ASP 3.5 6.3 - - - +
385D VAL 3.1 0.2 - - - -
386D LEU* 1.3 77.7 - - - +
388D ASN* 1.3 57.1 + - - +
391D ARG* 2.9 31.6 + - - +
394D LEU* 3.6 15.6 - - + +
424D ILE* 4.0 17.5 - - - -
427D GLY* 3.6 12.4 - - - +
428D CYS* 3.7 21.5 - - - -
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Residues in contact with ASN 388 (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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384D ASP* 2.8 32.1 + - - -
385D VAL* 3.1 12.8 + - + +
387D ALA* 1.3 77.7 - - - +
389D VAL* 1.3 62.8 + - + +
391D ARG* 3.8 22.6 + - - +
426D GLU* 3.0 41.7 + - - +
427D GLY* 3.8 12.9 - - - +
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Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ALA* 3.6 24.2 - - - +
285D GLU* 5.8 0.7 - - - +
289D CYS* 4.7 6.1 - - + -
290D LYS* 3.9 48.1 + - + +
385D VAL* 3.1 17.7 + - + +
386D LEU* 3.7 8.5 - - - +
387D ALA 3.2 0.4 - - - -
388D ASN* 1.3 81.6 - - + +
390D TYR* 1.3 74.6 + - + +
391D ARG* 3.5 5.7 + - - +
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Residues in contact with TYR 390 (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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289D CYS* 4.9 1.3 - - - -
290D LYS* 2.7 53.9 + - + +
293D LEU* 3.2 12.7 - - + +
294D VAL* 3.1 30.4 + - + -
297D LEU* 3.6 37.9 - - + -
386D LEU* 3.0 36.2 + - + +
389D VAL* 1.3 82.8 - - + +
391D ARG* 1.3 69.3 + - - +
392D ASP 3.3 0.2 + - - -
393D GLU* 3.1 34.7 + - + +
394D LEU* 4.0 23.1 - - + +
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Residues in contact with ARG 391 (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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387D ALA 2.9 16.9 + - - -
388D ASN* 3.8 26.2 + - - +
389D VAL 3.9 4.9 - - - +
390D TYR* 1.3 77.6 - - - +
392D ASP* 1.3 69.7 + - + +
394D LEU* 3.1 19.8 + - - +
426D GLU* 3.5 24.9 + - - +
427D GLY* 3.4 23.2 + - - +
428D CYS* 3.5 9.4 - - - -
429D MET* 6.2 0.2 - - - +
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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