Contacts of the helix formed by residues 382 - 400 (chain A) in PDB entry 2QFZ
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 GLN 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.5 21.8 - - + +
376A ASP 3.6 1.3 - - - -
377A ASN 2.6 29.1 + - - +
378A TYR* 3.6 9.8 - - - +
379A THR 2.8 19.0 + - - +
381A ALA* 1.3 77.9 - - - +
383A PRO* 1.4 64.3 - - - +
384A GLY 3.2 3.1 - - - -
385A ILE* 3.0 25.5 + - + +
386A GLN* 2.9 15.8 - - - +
419A PHE* 3.5 22.1 - - + -
423A ASN* 2.9 24.9 + - - +
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Residues in contact with PRO 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP* 3.3 18.4 - - + +
379A THR* 3.5 17.3 - - - +
380A PHE 3.6 10.3 - - - +
381A ALA* 3.3 5.6 - - + +
382A GLN* 1.4 86.9 - - - +
384A GLY* 1.3 62.7 + - - +
386A GLN* 4.1 7.8 - - + +
387A MET* 3.3 25.3 + - - +
386B GLN* 6.1 0.7 - - + -
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Residues in contact with GLY 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP* 2.8 49.0 + - - +
377A ASN* 3.5 11.2 - - - -
383A PRO* 1.3 71.1 - - - +
385A ILE* 1.3 63.0 + - - +
387A MET* 3.8 3.1 - - - +
388A LYS* 3.1 30.5 + - - +
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 3.4 46.9 - - + +
378A TYR* 5.1 0.2 - - + -
382A GLN* 3.0 21.6 + - + +
384A GLY* 1.3 76.4 - - - +
386A GLN* 1.3 58.8 + - - +
388A LYS* 3.1 5.9 + - - +
389A VAL* 2.9 33.5 + - + +
419A PHE* 3.5 37.7 - - + +
422A MET* 3.8 16.2 - - + -
423A ASN* 3.7 28.9 - - - +
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.3 11.8 - - - +
382A GLN* 2.9 24.7 + - - +
383A PRO* 4.3 7.6 - - + +
384A GLY 3.5 0.4 - - - -
385A ILE* 1.3 78.2 - - - +
387A MET* 1.3 64.2 + - - +
389A VAL* 3.5 6.5 + - - +
390A LYS* 3.0 24.9 + - - +
415A LEU* 3.5 34.0 - - + +
419A PHE* 3.9 18.0 - - - -
381B ALA* 3.9 24.0 - - + +
382B GLN 5.6 0.2 - - - +
383B PRO* 6.2 1.6 - - + -
386B GLN* 3.8 24.5 - - + +
415B LEU* 3.9 12.1 - - - +
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Residues in contact with MET 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP* 5.7 1.8 - - - +
383A PRO 3.3 17.2 + - - +
384A GLY* 3.8 6.3 - - - +
385A ILE 3.3 0.6 - - - -
386A GLN* 1.3 79.3 - - - +
388A LYS* 1.3 56.6 + - + +
390A LYS* 3.2 3.1 + - - +
391A MET* 2.9 51.1 + - + +
380B PHE* 3.4 37.2 - - + +
381B ALA* 4.1 15.6 - - + +
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 3.7 22.0 - - - +
376A ASP* 4.5 9.7 + - - -
377A ASN* 3.1 37.6 + - - +
384A GLY* 3.1 17.5 + - - +
385A ILE 3.1 3.3 + - - +
387A MET* 1.3 73.3 - - + +
389A VAL* 1.3 59.4 + - - +
391A MET* 3.8 18.5 - - + +
392A LEU* 2.9 28.6 + - - +
422A MET* 3.7 22.8 - - + +
425A LEU* 6.4 0.4 - - - +
449A PHE 4.6 1.6 + - - +
450A SER* 3.8 22.9 + - - +
453A HIS* 5.9 2.0 - - + -
454A LEU* 3.7 28.0 - - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 2.9 23.0 + - + +
386A GLN 3.8 5.2 - - - +
388A LYS* 1.3 75.9 - - - +
390A LYS* 1.3 57.5 + - - +
392A LEU* 3.4 8.4 + - - +
393A GLU* 3.0 25.8 + - + +
414A TYR* 3.8 14.7 - - + +
415A LEU* 3.7 47.3 - - + +
418A ALA* 3.8 31.6 - - + +
419A PHE 4.1 0.7 - - - +
422A MET* 3.9 9.6 - - + -
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLN 3.0 18.0 + - - +
387A MET 3.6 4.3 - - - +
389A VAL* 1.3 75.8 - - - +
391A MET* 1.3 59.1 + - - +
393A GLU* 3.1 27.0 + - - +
394A GLU* 2.9 51.0 + - - +
380B PHE* 3.3 45.8 - - + +
381B ALA* 3.9 25.1 - - + +
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Residues in contact with MET 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 2.9 42.7 + - + +
388A LYS* 3.8 20.6 - - + +
390A LYS* 1.3 72.2 - - - +
392A LEU* 1.3 60.4 + - - +
394A GLU* 3.3 8.6 + - - +
395A LEU* 2.9 29.7 + - - +
454A LEU* 3.9 28.5 - - + -
380B PHE* 4.7 12.3 - - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS 2.9 18.8 + - - +
389A VAL* 3.5 5.8 - - - +
390A LYS 3.2 0.2 - - - -
391A MET* 1.3 75.7 - - - +
393A GLU* 1.3 58.8 + - - +
395A LEU* 3.3 5.7 + - + +
396A VAL* 2.9 36.7 + - + +
414A TYR* 4.0 18.6 - - + -
417A PHE* 5.0 0.9 - - + -
418A ALA* 3.7 29.8 - - + -
421A TRP* 4.6 7.9 - - + -
422A MET* 4.2 13.5 - - + -
454A LEU* 4.1 8.4 - - + +
457A CYS* 4.0 13.2 - - + +
458A ALA* 3.6 38.4 - - + +
461A LEU* 5.3 2.0 - - + -
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A VAL* 3.0 15.0 + - - +
390A LYS* 3.1 30.4 + - + +
392A LEU* 1.3 77.4 - - - +
394A GLU* 1.3 65.1 + - - +
396A VAL* 3.9 0.9 - - - +
397A SER* 3.0 28.4 + - - -
404A HIS* 3.6 22.2 + - + -
414A TYR* 3.7 40.7 + - + +
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LYS* 2.9 45.3 + - - +
391A MET* 3.8 8.1 - - - +
393A GLU* 1.3 80.4 - - - +
395A LEU* 1.3 61.6 + - - +
397A SER* 2.7 23.0 + - - -
398A ARG* 3.3 18.3 - - - +
380B PHE* 4.2 22.8 - - + -
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A MET 2.9 17.8 + - - +
392A LEU* 3.6 7.0 - - - +
394A GLU* 1.3 76.5 - - - +
396A VAL* 1.3 58.5 + - - +
398A ARG* 3.0 12.7 + - + +
399A ILE* 3.0 37.3 + - + +
454A LEU* 4.1 17.5 - - + +
455A TYR* 3.8 29.8 - - + -
458A ALA* 3.7 29.2 - - + -
504A LEU* 4.8 2.5 - - + +
508A PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 2.9 37.1 + - + +
395A LEU* 1.3 71.6 - - - +
397A SER* 1.3 64.6 + - - +
399A ILE* 3.9 8.7 - - + -
400A ASP* 3.0 42.8 + - + +
403A VAL* 4.5 5.6 - - + -
404A HIS 4.3 5.4 - - - +
414A TYR* 3.3 23.8 - - + +
458A ALA* 4.1 18.8 - - + +
461A LEU* 4.1 23.3 - - + -
462A VAL* 4.7 2.0 - - + -
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLU 3.0 13.1 + - - -
394A GLU* 2.7 31.1 + - - -
396A VAL* 1.3 77.9 - - - +
398A ARG* 1.3 61.3 + - - +
401A GLU* 3.5 22.0 - - - +
404A HIS* 3.8 35.7 - - - -
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU* 3.3 18.2 - - - +
395A LEU* 3.0 11.9 + - + +
397A SER* 1.3 84.9 + - - +
399A ILE* 1.3 65.8 + - + +
401A GLU* 5.1 0.9 + - - +
508A PHE* 5.6 12.6 - - + +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LEU* 3.0 37.5 + - + +
396A VAL* 3.9 9.4 - - + -
398A ARG* 1.3 81.0 - - + +
400A ASP* 1.3 64.8 + - + +
401A GLU 4.1 0.4 - - - -
458A ALA* 4.3 9.9 - - + -
462A VAL* 4.1 26.0 - - + -
504A LEU* 3.5 50.5 - - + -
507A ALA* 4.8 14.4 - - + -
508A PHE* 5.0 4.5 - - + +
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A VAL* 3.0 15.2 + - + +
398A ARG 3.5 0.2 - - - -
399A ILE* 1.3 81.5 - - + +
401A GLU* 1.3 64.7 + - - +
402A GLN* 3.3 3.3 + - - +
403A VAL* 3.3 19.5 + - + +
404A HIS 3.1 17.8 + - - -
462A VAL* 3.2 37.3 - - + +
465A ARG* 3.1 40.7 + - - -
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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
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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