Contacts of the helix formed by residues 421 - 439 (chain A) in PDB entry 1MUK
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 ILE 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A VAL* 5.8 8.1 - - + +
419A SER 5.5 0.4 - - - +
420A SER* 1.3 73.6 + - - +
422A ALA* 1.3 66.1 + - - +
423A ARG 3.0 1.8 + - - -
424A TYR* 3.0 25.5 + - + +
425A LEU* 3.7 3.6 + - - +
597A PHE* 4.6 11.2 - - + -
698A MET* 5.6 6.0 - - + +
701A THR* 3.8 25.8 - - + -
706A TRP* 4.0 18.6 - - + -
763A TYR* 4.2 13.0 - - + +
766A GLU* 3.9 38.1 - - + +
767A PHE* 4.2 14.6 - - + -
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 3.4 34.8 - - + -
414A LEU* 4.5 8.7 - - + -
420A SER* 3.0 10.7 + - - +
421A ILE* 1.3 78.3 - - - +
423A ARG* 1.3 63.5 + - - +
425A LEU* 2.9 8.3 + - - +
426A TYR* 2.8 25.3 + - - +
597A PHE* 4.0 13.2 - - + -
601A VAL* 3.8 12.9 - - + +
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Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 4.1 8.7 - - - +
416A ASP* 4.2 11.2 + - - +
418A THR* 3.7 37.1 + - + -
419A SER* 5.2 6.4 + - - +
420A SER 3.2 15.9 + - - +
421A ILE 3.0 0.4 - - - -
422A ALA* 1.3 77.8 - - - +
424A TYR* 1.3 83.8 + - + +
426A TYR* 3.3 4.3 - - - +
427A ARG* 2.7 74.8 + - - +
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Residues in contact with TYR 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER 6.0 0.4 - - - -
420A SER 4.8 1.3 - - - -
421A ILE* 3.0 23.8 + - + +
423A ARG* 1.3 102.0 + - + +
425A LEU* 1.3 65.3 + - - +
426A TYR 3.0 1.9 + - - -
427A ARG* 3.8 32.2 + - + +
428A THR* 3.2 28.3 + - - +
697A THR* 4.3 0.4 - - - +
698A MET* 5.6 0.4 - - + -
701A THR* 3.4 36.1 - - + +
705A VAL* 3.8 40.6 - - + +
709A GLU* 5.4 0.5 + - - -
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ILE 3.7 1.9 + - - +
422A ALA* 2.9 13.6 + - - +
424A TYR* 1.3 77.8 - - - +
426A TYR* 1.3 60.1 + - - +
428A THR* 4.2 0.3 - - - -
429A TRP* 3.1 46.4 + - + +
597A PHE* 4.2 11.0 - - + -
598A PHE* 3.4 36.1 - - + +
601A VAL* 3.5 28.3 - - + +
602A ILE* 4.4 1.3 - - + -
694A ASN* 3.4 24.0 - - - +
697A THR* 4.1 7.6 - - + -
698A MET* 3.4 33.3 - - + +
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Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 3.7 17.8 - - + +
414A LEU* 4.0 39.9 - - + -
422A ALA 2.8 10.5 + - - +
423A ARG* 3.3 13.5 - - - +
425A LEU* 1.3 75.7 - - - +
427A ARG* 1.3 74.1 + - + +
429A TRP 3.1 3.5 + - - -
430A TYR* 2.8 42.8 + + + +
601A VAL* 3.8 19.3 - - + +
604A ALA* 3.8 21.9 + - + -
605A ALA* 3.4 33.7 - - + +
608A GLU* 3.9 13.0 - - - +
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASP* 3.1 27.1 + - - +
423A ARG* 2.7 65.8 + - + +
424A TYR* 3.5 28.7 + - - +
426A TYR* 1.3 83.9 - - + +
428A THR* 1.3 56.5 + - - +
430A TYR* 3.6 6.6 - - - +
431A LEU* 2.8 39.7 + - + +
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Residues in contact with THR 428 (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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424A TYR 3.2 15.0 + - - -
425A LEU 4.2 0.9 - - - -
426A TYR 3.2 0.8 - - - -
427A ARG* 1.3 79.6 - - - +
429A TRP* 1.3 59.5 + - + +
431A LEU* 3.5 5.0 + - - +
432A ALA* 3.0 27.2 + - - +
549A ILE* 4.3 14.8 - - + -
553A MET* 4.4 14.9 - - + +
697A THR* 3.6 36.0 - - + +
700A GLU* 5.8 0.2 + - - -
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Residues in contact with TRP 429 (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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425A LEU* 3.1 36.8 + - + +
426A TYR 3.1 2.0 + - - -
428A THR* 1.3 80.1 - - + +
430A TYR* 1.3 60.4 + - - +
433A ALA* 2.9 31.5 + - - +
542A HIS* 3.8 22.0 - + - -
545A THR* 3.6 23.7 - - + +
546A ALA* 3.8 40.4 - - + -
549A ILE* 3.9 14.2 - - + +
602A ILE* 3.5 38.9 - - + +
605A ALA* 3.8 17.4 - - + -
606A ILE* 3.9 5.1 - - + +
690A GLU* 4.2 4.3 - - + -
693A ALA* 3.8 17.3 - - + -
694A ASN* 3.0 33.1 + - - -
697A THR* 4.6 5.6 + - - -
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Residues in contact with TYR 430 (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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426A TYR* 2.8 38.0 + + + +
427A ARG* 3.6 7.4 - - - +
429A TRP* 1.3 74.2 - - - +
431A LEU* 1.3 76.7 + - + +
433A ALA* 3.2 3.5 + - - +
434A ALA* 3.0 26.6 + - + +
605A ALA* 3.5 29.7 - - + +
608A GLU* 3.6 19.9 + - + +
609A GLY* 3.4 22.1 - - - -
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 2.8 23.9 + - + +
428A THR* 3.6 6.1 - - - +
430A TYR* 1.3 89.3 - - + +
432A ALA* 1.3 64.1 + - - +
434A ALA* 3.1 7.5 + - + +
435A ARG* 3.0 65.9 + - + +
553A MET* 4.4 7.2 - - + -
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR 3.0 11.3 + - - +
429A TRP 3.8 0.4 - - - +
431A LEU* 1.3 79.9 - - - +
433A ALA* 1.3 57.6 + - - +
435A ARG* 3.1 2.1 + - - +
436A MET* 2.8 31.9 + - - +
545A THR* 3.7 12.8 - - + -
548A TYR* 3.9 10.9 - - + -
549A ILE* 3.3 34.1 - - + -
553A MET* 3.6 17.6 - - + +
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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
----------------------------------------------------------
429A TRP 2.9 19.3 + - - +
430A TYR 3.2 4.9 + - - +
432A ALA* 1.3 75.3 - - - +
434A ALA* 1.3 54.3 + - - +
436A MET* 3.4 2.8 - - - +
437A ALA* 2.7 36.9 + - - +
545A THR* 3.4 18.7 - - + +
606A ILE* 3.8 27.1 - - - +
609A GLY* 4.0 5.6 - - - -
610A VAL* 3.9 15.1 - - + +
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Residues in contact with ALA 434 (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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430A TYR* 3.0 17.9 + - + +
431A LEU* 3.1 12.8 + - + +
433A ALA* 1.3 76.5 - - - +
435A ARG* 1.3 59.8 + - + +
437A ALA* 3.9 2.3 - - - +
438A ALA* 3.0 28.9 + - - +
609A GLY* 3.0 24.8 + - - +
612A SER* 6.2 0.2 - - - +
613A SER* 4.3 3.6 + - - -
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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
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431A LEU* 3.0 41.8 + - + +
432A ALA 3.8 1.6 - - - +
434A ALA* 1.3 74.0 - - + +
436A MET* 1.3 68.9 + - - +
438A ALA* 3.3 12.3 + - - +
439A GLN* 3.2 18.5 + - - +
548A TYR* 3.2 39.9 + - + +
552A HIS* 6.3 0.4 - - - +
553A MET* 4.3 13.7 - - - +
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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
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432A ALA 2.8 17.9 + - - +
433A ALA* 3.4 7.4 - - - +
435A ARG* 1.3 77.4 - - - +
437A ALA* 1.3 68.9 + - - +
439A GLN* 3.1 17.2 + - - +
442A THR* 2.9 63.3 + - + +
447A PHE* 4.7 2.0 - - + -
541A PRO* 6.2 0.7 - - - -
544A LEU* 3.5 58.8 - - + +
545A THR* 4.3 6.7 - - - +
548A TYR* 3.7 23.9 - - + -
610A VAL* 5.2 1.8 - - - -
644A MET* 4.5 9.9 - - + +
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Residues in contact with ALA 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 2.7 20.8 + - - +
434A ALA 4.1 2.2 - - - +
436A MET* 1.3 82.1 - - - +
438A ALA* 1.3 57.8 + - - +
439A GLN 3.4 0.7 + - - +
442A THR* 4.4 2.5 - - - -
443A TRP* 2.8 35.5 + - + -
610A VAL* 3.7 28.5 - - + +
613A SER* 3.4 20.4 - - - -
644A MET* 4.4 7.6 - - - -
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Residues in contact with ALA 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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434A ALA 3.0 19.6 + - - +
435A ARG* 3.8 8.3 - - - +
436A MET 3.2 1.0 - - - -
437A ALA* 1.3 75.8 - - - +
439A GLN* 1.3 62.9 + - - +
440A PRO* 3.3 9.7 - - - +
443A TRP* 5.1 0.8 - - - -
613A SER* 3.5 17.0 + - - +
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Residues in contact with GLN 439 (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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435A ARG 3.2 13.9 - - - +
436A MET* 3.1 21.6 + - - +
438A ALA* 1.3 77.5 - - - +
440A PRO* 1.3 73.0 - - + +
441A ARG* 4.0 37.3 + - + +
442A THR* 3.1 26.5 + - - +
443A TRP* 3.6 6.2 - - - -
548A TYR* 3.6 27.2 - - + -
552A HIS* 4.1 11.9 + - - -
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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