Contacts of the helix formed by residues 402 - 424 (chain A) in PDB entry 2WMN
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 LEU 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ILE* 3.7 25.0 - - + +
399A GLU* 2.9 32.2 - - + +
401A GLN* 1.3 69.9 - - - +
403A GLU* 1.3 63.2 - - - +
404A TYR 3.3 0.6 - - - +
405A GLN* 3.3 8.0 + - - +
406A GLU* 3.1 21.7 + - - +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLN 2.3 20.9 + - - +
402A LEU* 1.3 68.1 - - - +
404A TYR* 1.3 60.6 + - - +
406A GLU* 2.8 26.1 + - + +
407A GLU* 3.1 12.5 + - + +
70B LEU* 3.8 29.7 - - + +
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Residues in contact with TYR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN* 3.9 18.4 - - - +
340A GLN* 2.7 40.3 + - + +
344A SER* 5.8 0.7 - - - -
397A ILE* 5.8 0.9 - - + -
401A GLN* 3.2 50.9 + - + -
403A GLU* 1.3 80.4 - - - +
405A GLN* 1.3 61.6 + - - +
406A GLU 3.1 1.2 + - - -
407A GLU* 3.4 3.1 + - + +
408A MET* 3.2 54.7 + - + +
5B LYS* 4.6 6.5 - - - -
56B PHE* 4.2 2.8 - - - -
70B LEU* 3.3 49.0 - - + +
71B SER* 4.6 2.9 - - - -
73B PRO* 5.3 0.7 - - + -
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 5.0 1.0 - - - +
390A LEU* 3.1 39.3 - - - +
393A ASN* 2.8 33.7 - - - +
394A GLU* 3.5 30.2 + - - +
397A ILE* 3.6 25.4 - - + -
402A LEU 3.3 11.3 + - - +
403A GLU 3.2 0.6 - - - -
404A TYR* 1.3 79.3 - - - +
406A GLU* 1.3 58.8 + - - +
408A MET* 4.1 15.4 - - - +
409A LYS* 2.8 29.5 + - + +
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU* 5.0 7.4 - - - +
402A LEU 3.1 11.9 + - - +
403A GLU* 2.8 17.1 + - + +
405A GLN* 1.3 76.3 - - - +
407A GLU* 1.3 54.4 + - - +
409A LYS* 3.2 5.2 + - - +
410A ALA* 2.5 39.7 + - + +
413A ARG* 3.6 29.9 + - - +
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 5.2 2.7 - - - +
403A GLU 3.1 6.0 + - - +
404A TYR* 3.8 3.1 - - + +
406A GLU* 1.3 75.2 - - - +
408A MET* 1.3 52.6 + - + +
410A ALA* 2.9 11.7 + - - +
411A ASN* 2.6 63.2 + - - +
67B LEU* 3.1 36.8 - - + +
70B LEU* 3.6 29.4 - - + -
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Residues in contact with MET 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN* 4.5 8.3 - - + -
339A LEU* 4.3 13.7 - - + -
340A GLN* 3.7 31.9 - - - -
343A VAL* 4.0 7.5 - - + +
344A SER* 3.1 23.1 - - - +
390A LEU* 4.1 9.6 - - + -
393A ASN* 4.0 22.7 - - - +
404A TYR* 3.2 53.4 + - + +
405A GLN* 3.7 12.3 - - - +
407A GLU* 1.3 77.6 - - + +
409A LYS* 1.3 53.8 + - - +
411A ASN* 2.9 3.3 + - - +
412A TYR* 2.8 34.7 + - - +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.8 21.7 - - + +
394A GLU* 5.8 3.6 - - - +
405A GLN* 2.8 28.5 + - + +
406A GLU* 3.4 12.3 - - - +
408A MET* 1.3 73.2 - - - +
410A ALA* 1.3 60.8 + - - +
412A TYR* 3.6 2.6 - - - +
413A ARG* 3.2 50.5 + - - +
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Residues in contact with ALA 410 (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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406A GLU* 2.5 23.1 + - + +
407A GLU* 3.2 19.1 - - - +
409A LYS* 1.3 75.2 - - - +
411A ASN* 1.3 56.9 + - - +
413A ARG* 3.6 17.2 + - - +
414A GLU* 2.9 29.9 + - - +
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Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A VAL* 3.4 22.5 - - - +
344A SER* 3.4 30.9 + - - +
407A GLU* 2.6 44.7 + - - +
408A MET 3.5 4.0 - - - +
410A ALA* 1.3 70.6 - - - +
412A TYR* 1.3 66.7 + - - +
414A GLU* 3.4 7.2 - - - +
415A MET* 2.9 28.4 + - - +
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Residues in contact with TYR 412 (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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343A VAL* 4.1 16.4 - - + +
383A VAL* 3.2 42.4 + - + +
384A GLU* 5.0 1.0 - - - -
386A CYS* 3.4 18.2 - - + -
387A GLY* 3.2 29.7 - - - -
390A LEU* 3.2 29.8 - - + -
408A MET 2.8 17.7 + - - +
409A LYS 3.6 5.4 - - - +
411A ASN* 1.3 73.5 - - - +
413A ARG* 1.3 81.3 + - + +
415A MET* 3.3 7.6 - - + +
416A ALA* 2.8 39.4 + - + +
427A LEU 4.2 7.3 + - - -
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Residues in contact with ARG 413 (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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406A GLU* 3.6 19.8 + - - -
409A LYS* 3.2 38.7 + - - +
410A ALA* 3.8 19.1 - - - +
412A TYR* 1.3 95.3 - - + +
414A GLU* 1.3 67.5 + - - +
416A ALA* 3.1 8.2 - - + +
417A LYS* 3.0 19.2 + - - +
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Residues in contact with GLU 414 (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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410A ALA 2.9 20.4 + - - +
411A ASN* 3.2 10.3 + - - +
413A ARG* 1.3 74.7 - - - +
415A MET* 1.3 62.8 + - - +
417A LYS* 3.0 23.7 + - - +
418A GLU* 3.3 4.4 + - - +
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Residues in contact with MET 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER 4.5 6.3 - - - +
343A VAL* 3.6 33.0 - - + +
351A PRO* 4.7 8.5 - - - -
352A LEU* 4.0 23.6 - - + -
382A PHE* 3.5 35.9 - - + -
383A VAL* 5.0 6.3 - - + -
386A CYS* 4.3 5.6 - - + -
411A ASN 2.9 16.2 + - - +
412A TYR* 3.3 18.2 - - + +
414A GLU* 1.3 70.1 - - - +
416A ALA* 1.3 61.8 + - - +
418A GLU* 2.7 29.1 + - - +
419A LEU* 2.9 29.6 + - + +
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Residues in contact with ALA 416 (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 VAL* 4.4 14.1 - - + -
412A TYR* 2.8 23.5 + - + +
413A ARG* 3.1 15.5 - - + +
414A GLU 3.1 0.2 - - - -
415A MET* 1.3 78.1 - - - +
417A LYS* 1.3 54.6 + - - +
419A LEU* 4.0 7.5 - - - +
420A SER* 3.1 33.5 + - - -
427A LEU* 3.4 24.9 - - + +
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Residues in contact with LYS 417 (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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413A ARG 3.0 9.3 + - - +
414A GLU* 3.0 16.6 + - - +
416A ALA* 1.3 75.0 - - - +
418A GLU* 1.3 52.8 + - - +
420A SER* 3.5 6.7 + - - -
421A GLU* 2.7 38.2 + - - +
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Residues in contact with GLU 418 (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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352A LEU* 3.2 30.3 - - + -
356A ARG* 3.2 29.0 + - - +
414A GLU 3.3 3.1 + - - +
415A MET* 2.7 20.8 + - - +
417A LYS* 1.3 74.7 - - - +
419A LEU* 1.3 57.1 + - - +
421A GLU* 3.1 26.4 - - - +
422A ILE* 2.9 49.9 + - + +
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Residues in contact with LEU 419 (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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352A LEU* 3.7 22.9 - - + -
355A ALA* 3.8 14.8 - - + -
379A PHE* 3.6 38.4 - - + -
382A PHE* 4.9 2.0 - - + -
383A VAL* 3.8 28.9 - - + -
415A MET* 2.9 35.7 + - + +
416A ALA* 4.0 4.0 - - - +
418A GLU* 1.3 74.2 - - - +
420A SER* 1.3 67.5 + - - +
422A ILE* 3.1 6.2 + - - +
423A MET* 2.8 45.0 + - + +
427A LEU* 5.4 1.6 - - + -
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Residues in contact with SER 420 (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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416A ALA 3.1 10.4 + - - -
417A LYS* 3.5 7.2 - - - -
419A LEU* 1.3 77.6 - - - +
421A GLU* 1.3 55.2 + - - +
423A MET* 4.8 3.3 - - - +
424A HIS* 2.8 31.0 + - - -
425A GLU* 2.9 23.9 + - - +
426A GLN* 2.9 3.7 - - - -
427A LEU* 2.8 43.1 + - - +
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Residues in contact with GLU 421 (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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417A LYS* 2.7 21.4 + - - +
418A GLU* 3.1 30.5 - - - +
420A SER* 1.3 77.3 - - - +
422A ILE* 1.3 68.0 + - + +
424A HIS* 3.3 17.3 + - - -
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Residues in contact with ILE 422 (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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355A ALA* 4.4 20.2 - - + +
356A ARG* 4.3 17.3 - - + -
359A LEU* 3.1 36.3 - - + +
360A ASP* 4.1 20.4 - - + +
418A GLU* 2.9 47.2 + - + +
419A LEU* 4.0 3.4 - - - +
421A GLU* 1.3 82.9 - - + +
423A MET* 1.3 58.9 + - + +
424A HIS* 3.2 22.2 + - - -
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Residues in contact with MET 423 (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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355A ALA* 6.3 0.7 - - + -
359A LEU* 4.0 19.1 - - + -
376A LYS* 3.4 63.9 + - - +
379A PHE* 3.9 26.2 - - + +
380A ARG* 5.1 4.9 - - + +
419A LEU* 2.8 40.8 + - + +
420A SER* 4.3 1.1 - - - +
422A ILE* 1.3 75.5 - - + +
424A HIS* 1.3 76.4 + - - +
425A GLU* 3.3 25.5 - - + +
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Residues in contact with HIS 424 (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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360A ASP* 5.9 3.6 + - - -
361A ASP* 5.3 11.0 - - + +
376A LYS* 5.0 5.6 - - - -
420A SER 2.8 12.0 + - - -
421A GLU 3.3 11.7 + - - -
422A ILE* 3.2 18.9 + - - -
423A MET* 1.3 89.3 - - - +
425A GLU* 1.3 56.8 + - - +
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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