Contacts of the helix formed by residues 428 - 452 (chain A) in PDB entry 5MQI
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 GLU 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.2 32.1 + - - +
425A ASP* 2.9 32.3 + - - +
427A LYS* 1.3 89.0 - - + +
429A ALA* 1.3 63.5 + - - +
430A ALA* 3.2 3.1 - - - -
431A SER* 3.0 35.5 + - - -
432A TRP* 3.1 18.9 + - + +
435A ARG* 5.8 0.4 - - - +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A MET* 3.6 33.4 - - + +
425A ASP 3.4 5.0 + - - -
426A ARG* 3.2 33.8 + - - +
427A LYS 3.6 0.4 + - - -
428A GLU* 1.3 76.5 - - - +
430A ALA* 1.3 57.1 + - - +
432A TRP 3.3 1.4 + - - -
433A ALA* 2.8 29.6 + - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU 3.2 0.8 - - - -
429A ALA* 1.3 79.0 - - - +
431A SER* 1.3 61.1 + - - +
433A ALA* 3.4 7.5 + - - +
434A ARG* 3.1 49.3 + - - +
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 3.0 29.5 + - - -
430A ALA* 1.3 75.5 - - - +
432A TRP* 1.3 65.7 + - - +
434A ARG* 3.2 26.6 + - - +
435A ARG* 3.1 49.8 + - - +
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Residues in contact with TRP 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 5.6 0.4 - - - -
417A ASN* 4.5 6.7 - - - -
418A TYR* 3.7 35.5 - + - +
421A MET* 3.3 57.2 - - + -
422A MET* 3.6 23.3 - - - +
425A ASP* 2.8 28.2 + - - +
428A GLU* 3.1 30.7 + - + +
429A ALA 3.8 2.0 - - - +
431A SER* 1.3 77.1 - - - +
433A ALA* 1.4 55.4 + - - +
435A ARG* 3.3 39.8 + - - +
436A MET* 2.9 30.0 + - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A MET* 3.6 25.5 - - - -
429A ALA 2.8 17.5 + - - +
430A ALA* 3.7 9.2 - - - +
431A SER 3.3 0.2 - - - -
432A TRP* 1.4 76.2 - - - +
434A ARG* 1.3 57.3 + - + +
436A MET* 3.3 4.7 + - - +
437A HIS* 2.9 28.9 + - - +
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Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 5.6 7.3 - - - +
173A LEU 5.9 4.5 - - - +
430A ALA* 3.1 35.1 + - - +
431A SER* 3.2 36.7 + - - +
432A TRP 3.3 0.2 - - - -
433A ALA* 1.3 77.7 - - + +
435A ARG* 1.3 62.3 + - + +
437A HIS* 3.2 9.7 + - - +
438A LEU* 3.2 26.8 + - + +
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Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 5.5 1.6 + - - -
375A GLU* 5.0 2.9 - - - -
376A THR* 3.9 26.0 - - + +
418A TYR* 3.3 35.1 - - + -
428A GLU* 5.8 0.6 - - - +
431A SER* 3.1 36.1 + - - +
432A TRP* 3.4 57.6 - - - +
434A ARG* 1.3 74.6 - - + +
436A MET* 1.3 62.7 + - - +
438A LEU* 3.2 9.2 + - - +
439A ALA 3.0 18.7 + - - -
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 3.7 24.1 - - + +
418A TYR* 3.7 19.0 - - + -
419A TYR* 3.8 49.8 - - + +
422A MET* 4.0 18.4 - - + +
432A TRP 2.9 17.5 + - - +
433A ALA* 3.5 6.5 - - - +
435A ARG* 1.3 76.6 - - - +
437A HIS* 1.3 58.6 + - - +
439A ALA 3.4 0.5 + - - -
440A LEU* 2.9 38.8 + - + +
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Residues in contact with HIS 437 (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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433A ALA 2.9 13.4 + - - +
434A ARG* 3.4 13.0 - - - +
436A MET* 1.3 78.5 - - - +
438A LEU* 1.3 64.4 + - + +
440A LEU* 3.4 10.3 + - - +
441A LYS* 3.0 72.2 + - + +
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Residues in contact with LEU 438 (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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173A LEU* 4.2 25.1 - - + +
376A THR* 3.7 35.4 - - + +
379A MET* 3.8 17.9 - - + +
380A TRP* 4.0 31.4 - - + -
434A ARG* 3.2 15.9 + - + +
435A ARG* 3.2 7.2 + - - +
437A HIS* 1.3 81.2 - - + +
439A ALA* 1.3 65.7 + - - +
441A LYS* 3.4 11.4 + - + +
442A ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 4.0 21.0 - - + +
411A ILE* 3.5 13.9 - - + +
415A LEU* 4.1 20.9 - - + +
418A TYR* 3.8 24.2 - - + -
435A ARG 3.0 16.1 + - - +
436A MET 3.8 3.1 - - - +
438A LEU* 1.3 76.5 - - - +
440A LEU* 1.3 63.6 + - - +
442A ALA* 3.3 1.4 + - - +
443A TYR* 2.9 19.3 + - - +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 4.1 23.9 - - + +
436A MET* 2.9 26.2 + - + +
437A HIS* 3.8 9.9 - - - +
439A ALA* 1.3 78.7 - - - +
441A LYS* 1.3 57.5 + - - +
443A TYR* 3.2 14.5 + - + +
444A GLN* 2.8 52.9 + - + +
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Residues in contact with LYS 441 (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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383A ALA* 4.0 12.6 - - + +
437A HIS* 3.0 56.0 + - + +
438A LEU* 3.8 14.4 - - + +
439A ALA 3.3 0.2 - - - -
440A LEU* 1.3 77.9 - - + +
442A ALA* 1.3 60.7 + - - +
444A GLN* 3.4 19.5 + - - +
445A GLU* 3.1 21.8 + - - +
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 3.6 36.6 - - - +
382A LEU* 3.6 20.3 - - + +
383A ALA* 4.1 7.3 - - - +
411A ILE* 4.4 8.3 - - + -
438A LEU 3.1 10.9 + - - +
439A ALA 3.3 8.7 + - - +
441A LYS* 1.3 75.8 - - - +
443A TYR* 1.3 61.1 + - - +
445A GLU* 3.2 4.5 + - - +
446A LEU* 3.0 26.1 + - - +
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Residues in contact with TYR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 3.8 27.4 - + - -
411A ILE* 3.7 22.6 - - + +
412A GLU* 2.6 46.3 + - + +
415A LEU* 5.2 10.8 - - + -
439A ALA 2.9 12.7 + - - +
440A LEU* 3.4 22.4 - - + +
442A ALA* 1.3 74.8 - - - +
444A GLN* 1.3 58.1 + - + +
446A LEU* 3.1 10.3 + - + +
447A LEU* 2.9 55.0 + - + +
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Residues in contact with GLN 444 (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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440A LEU* 2.8 41.7 + - + +
441A LYS* 3.6 24.1 - - - +
442A ALA 3.3 0.2 - - - -
443A TYR* 1.3 77.7 - - + +
445A GLU* 1.4 57.0 + - - +
447A LEU* 3.4 13.3 + - + +
448A ALA* 2.8 29.9 + - - +
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Residues in contact with GLU 445 (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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382A LEU* 4.2 2.5 - - + +
383A ALA* 3.8 22.6 - - + +
386A MET* 3.6 22.6 - - + -
387A ALA* 3.6 26.5 + - - +
390A ARG* 2.9 34.9 + - - -
441A LYS 3.1 13.8 + - - +
442A ALA 3.2 8.2 + - - +
444A GLN* 1.4 74.1 - - - +
446A LEU* 1.3 65.3 + - - +
448A ALA* 4.4 1.5 - - - +
449A THR* 2.8 51.3 + - - -
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Residues in contact with LEU 446 (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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382A LEU* 4.1 4.7 - - + -
386A MET* 3.9 18.4 - - + -
402A THR 3.3 27.1 - - - +
403A LEU* 5.0 3.6 - - + -
407A THR* 4.0 21.3 - - + -
408A PHE* 3.8 44.9 - - + -
411A ILE* 4.1 13.7 - - + -
442A ALA 3.0 16.8 + - - +
443A TYR* 3.1 16.4 + - + +
445A GLU* 1.3 76.2 - - - +
447A LEU* 1.3 57.8 + - - +
449A THR* 3.3 4.4 + - - -
450A VAL* 2.9 34.7 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 3.9 21.5 - - + -
443A TYR* 2.9 48.2 + - + +
444A GLN* 3.7 12.6 - - + +
446A LEU* 1.3 76.1 - - - +
448A ALA* 1.3 58.3 + - - +
450A VAL* 3.8 3.9 - - + +
451A ASN* 2.9 49.5 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 3.7 28.5 - - - +
444A GLN 2.8 18.0 + - - +
445A GLU* 3.9 4.3 - - - +
447A LEU* 1.3 77.2 - - - +
449A THR* 1.3 61.9 + - - +
451A ASN* 4.0 6.5 - - - +
452A GLU* 3.3 28.5 + - - +
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Residues in contact with THR 449 (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 MET* 4.1 16.6 + - + +
390A ARG* 3.6 17.7 + - + +
399A VAL* 5.7 2.0 - - + -
403A LEU* 3.8 34.1 - - + -
445A GLU* 2.8 39.6 + - - -
446A LEU 3.7 4.0 - - - -
448A ALA* 1.3 77.1 - - - +
450A VAL* 1.4 62.8 + - - +
452A GLU* 3.3 13.2 + - - +
453A MET* 3.5 14.8 + - + +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 4.0 21.5 - - + -
408A PHE* 3.9 24.9 - - + -
446A LEU 2.9 19.5 + - - +
447A LEU* 4.0 4.5 - - + +
449A THR* 1.4 74.5 - - - +
451A ASN* 1.3 63.9 + - - +
453A MET* 2.9 36.8 + - + +
454A ASP* 3.9 3.1 + - - +
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Residues in contact with ASN 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 2.9 38.2 + - - +
448A ALA* 4.0 6.5 - - - +
449A THR 3.3 0.4 - - - -
450A VAL* 1.3 83.3 - - - +
452A GLU* 1.3 61.2 + - + +
453A MET 3.5 0.3 + - - -
454A ASP* 3.8 15.5 + - - +
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 2.9 48.0 + - - +
448A ALA* 3.3 13.3 + - - +
449A THR* 3.3 7.9 + - - +
450A VAL 3.2 1.2 - - - -
451A ASN* 1.3 76.4 - - + +
453A MET* 1.3 60.4 + - - +
454A ASP 3.4 8.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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