Contacts of the helix formed by residues 406 - 425 (chain D) in PDB entry 2QLR
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 SER 406 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLN* 5.2 1.8 - - - -
404D SER 3.5 3.0 + - - -
405D ALA* 1.3 76.2 - - - +
407D PRO* 1.4 76.5 - - - +
408D GLU* 3.2 17.8 - - - +
409D GLN* 3.0 30.1 + - - +
410D MET* 3.0 20.5 + - - +
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Residues in contact with PRO 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D GLN* 5.2 7.2 - - - +
332D ALA* 4.5 17.3 - - + +
405D ALA 4.9 0.2 - - - +
406D SER* 1.4 84.4 - - - +
408D GLU* 1.3 68.9 + - - +
410D MET* 3.2 14.5 + - - +
411D ASP* 2.9 27.7 + - - +
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Residues in contact with GLU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D SER* 3.2 23.7 - - - +
407D PRO* 1.3 88.0 - - - +
409D GLN* 1.3 64.3 + - + +
411D ASP* 3.2 9.4 + - - +
412D VAL* 3.1 28.6 + - + +
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Residues in contact with GLN 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET 5.1 4.8 + - - -
34C ILE* 2.7 51.6 - - + +
404D SER 4.7 0.9 - - - +
405D ALA* 3.5 10.2 - - + -
406D SER* 3.0 36.8 + - - +
408D GLU* 1.3 80.3 - - + +
410D MET* 1.3 62.1 + - - +
412D VAL* 3.5 3.9 + - - +
413D ALA 3.2 12.6 + - - -
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Residues in contact with MET 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 4.0 1.1 - - - +
36C LEU* 4.5 7.0 - - + -
329D GLN* 4.0 16.6 - - - +
332D ALA* 3.8 26.2 - - + -
333D ILE* 3.8 20.0 - - + -
336D ALA* 3.8 15.5 - - + -
401D SER 5.1 0.2 - - - +
402D PHE* 3.9 31.0 - - + -
405D ALA* 3.4 31.2 - - + +
406D SER 3.0 13.4 + - - +
407D PRO* 3.7 5.2 - - - +
409D GLN* 1.3 72.2 - - - +
411D ASP* 1.3 67.8 + - - +
413D ALA* 3.4 3.3 + - - -
414D PHE* 3.0 41.5 + - + +
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Residues in contact with ASP 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ALA* 4.3 9.1 - - + +
339D LYS* 2.9 36.4 + - - +
340D TRP* 2.9 28.7 + - - +
407D PRO 2.9 17.9 + - - +
408D GLU* 3.2 13.6 + - - +
410D MET* 1.3 72.4 - - - +
412D VAL* 1.3 59.7 + - + +
415D GLN* 2.9 33.3 + - - +
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Residues in contact with VAL 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 4.8 13.7 - - + -
379D VAL* 6.0 1.6 - - + -
408D GLU* 3.1 16.8 + - + +
409D GLN* 4.2 4.3 - - - +
411D ASP* 1.3 73.7 - - + +
413D ALA* 1.3 61.5 + - - +
415D GLN* 3.2 21.2 + - - +
416D VAL* 2.8 40.9 + - + +
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Residues in contact with ALA 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 3.8 22.8 - - + +
36C LEU* 4.3 20.0 - - + -
379D VAL* 3.8 29.4 - - + +
381D MET* 5.3 2.2 - - - -
409D GLN 3.2 16.0 + - - +
410D MET 3.8 2.9 - - - +
412D VAL* 1.3 79.0 - - - +
414D PHE* 1.3 53.2 + - - +
416D VAL* 3.5 0.7 + - - -
417D LEU* 2.7 34.9 + - - +
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Residues in contact with PHE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.5 29.6 - - + -
333D ILE* 3.7 32.1 - - + -
336D ALA* 3.8 28.5 - - + +
337D ALA* 3.8 13.5 - - + -
340D TRP* 3.4 9.6 - - + +
341D LEU* 3.3 36.5 - - + +
356D LEU* 4.3 11.4 - - + -
358D ILE* 5.2 2.5 - - + -
381D MET* 4.9 4.5 - - + -
400D ALA* 4.4 8.1 - - + -
410D MET* 3.0 29.1 + - + +
413D ALA* 1.3 73.9 - - - +
415D GLN* 1.3 65.8 + - - +
417D LEU* 3.8 12.9 - - + +
418D ALA* 3.0 26.0 + - - +
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Residues in contact with GLN 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D TRP* 3.3 47.5 - - + -
411D ASP* 2.9 21.6 + - - +
412D VAL* 3.2 28.4 + - - +
414D PHE* 1.3 77.1 - - - +
416D VAL* 1.3 78.5 + - - +
419D GLN* 2.6 39.7 + - - +
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Residues in contact with VAL 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D MET* 3.9 30.7 - - + +
379D VAL* 3.3 31.4 - - + -
412D VAL* 2.8 35.5 + - + +
413D ALA 3.9 0.2 - - - +
415D GLN* 1.3 84.1 - - - +
417D LEU* 1.3 67.3 + - - +
419D GLN* 3.4 7.1 + - - +
420D LEU* 3.3 37.0 + - + +
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU* 3.9 32.5 - - + -
358D ILE* 4.8 2.7 - - + -
369D LEU* 3.9 19.1 - - + -
370D ILE* 4.7 5.8 - - + -
374D ALA* 5.9 2.2 - - + -
379D VAL* 5.0 4.0 - - + +
381D MET* 4.2 30.5 - - + -
398D LEU* 4.1 15.9 - - + -
413D ALA 2.7 23.6 + - - +
414D PHE* 3.8 10.5 - - + +
415D GLN 3.4 0.2 - - - -
416D VAL* 1.3 72.1 - - - +
418D ALA* 1.3 59.1 + - - +
420D LEU* 3.0 12.1 + - + +
421D ILE* 2.8 45.2 + - + +
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Residues in contact with ALA 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D TRP* 3.4 30.3 - - + +
341D LEU* 3.7 13.9 - - + +
344D LEU* 3.9 9.3 - - + +
414D PHE 3.0 15.7 + - - +
415D GLN 3.8 4.3 - - - +
416D VAL 3.3 0.2 - - - -
417D LEU* 1.3 79.3 - - - +
419D GLN* 1.3 72.0 + - - +
421D ILE* 3.0 14.6 + - - +
422D LYS* 3.0 17.6 + - - +
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Residues in contact with GLN 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D TRP* 3.7 26.7 - - - -
415D GLN* 2.6 36.2 + - + +
416D VAL* 3.9 7.0 - - - +
417D LEU 3.3 0.4 - - - -
418D ALA* 1.3 79.0 - - - +
420D LEU* 1.3 53.0 + - + +
422D LYS* 3.2 25.0 + - - +
423D GLU* 2.7 49.3 + - - +
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Residues in contact with LEU 420 (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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369D LEU* 3.5 16.3 - - + +
373D LYS* 3.8 26.2 - - + +
374D ALA* 3.8 32.3 - - + +
377D MET* 4.5 15.3 - - + -
416D VAL* 3.3 33.6 + - + +
417D LEU* 3.0 10.6 + - + +
419D GLN* 1.3 72.7 - - + +
421D ILE* 1.3 62.0 + - - +
423D GLU* 3.8 19.6 - - + +
424D SER* 2.6 32.9 + - - -
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Residues in contact with ILE 421 (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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341D LEU* 4.6 12.1 - - + -
344D LEU* 4.2 30.7 - - + +
358D ILE* 5.4 1.3 - - + -
360D VAL* 4.1 24.7 - - + -
361D LYS 4.7 1.8 - - - +
363D ILE* 4.2 14.5 - - + +
369D LEU* 3.7 18.6 - - + -
417D LEU* 2.8 40.7 + - + +
418D ALA* 3.0 7.2 + - - +
420D LEU* 1.3 75.2 - - - +
422D LYS* 1.3 61.5 + - - +
424D SER* 3.0 12.3 + - - -
425D LEU* 3.1 33.0 + - + +
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Residues in contact with LYS 422 (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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340D TRP 4.7 5.9 + - - -
342D THR 5.6 2.0 + - - -
344D LEU* 3.8 38.4 - - + +
418D ALA* 3.0 14.2 + - - +
419D GLN* 3.6 27.8 - - - +
421D ILE* 1.3 72.0 - - - +
423D GLU* 1.3 63.0 + - - +
424D SER 2.9 5.4 + - - -
425D LEU* 3.2 25.4 + - + +
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Residues in contact with GLU 423 (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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373D LYS* 4.0 12.7 + - - +
377D MET* 5.6 2.3 - - - +
419D GLN* 2.7 29.4 + - - +
420D LEU* 3.8 26.9 - - + +
422D LYS* 1.3 71.0 - - - +
424D SER* 1.3 58.3 + - - +
425D LEU* 3.6 0.6 + - - -
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Residues in contact with SER 424 (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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362D GLY 5.2 0.5 - - - +
363D ILE* 3.9 22.5 - - - +
369D LEU* 3.7 4.6 - - - +
373D LYS* 2.9 35.2 + - - +
420D LEU 2.6 22.1 + - - -
421D ILE 3.0 5.7 + - - -
422D LYS 3.0 0.6 - - - -
423D GLU* 1.3 77.3 - - - +
425D LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 425 (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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344D LEU* 4.3 24.0 - - + -
361D LYS* 3.3 26.9 - - + +
362D GLY* 3.5 24.1 - - - +
363D ILE* 4.1 8.5 - - + -
421D ILE* 3.1 20.7 + - + +
422D LYS* 3.2 17.1 + - + +
423D GLU 3.6 0.4 - - - +
424D SER* 1.3 82.1 - - - +
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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