Contacts of the helix formed by residues 564 - 581 (chain B) in PDB entry 1MWR
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 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ILE* 1.3 77.3 - - - +
565B LYS* 1.3 66.3 + - - +
566B GLU* 3.6 20.4 - - - +
567B ASN* 2.6 48.7 + - - +
568B ILE* 2.9 15.6 + - - +
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Residues in contact with LYS 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B ASN 6.1 2.3 - - - -
563B ILE 4.2 0.6 + - - -
564B SER* 1.3 73.3 - - - +
566B GLU* 1.3 71.0 + - - +
568B ILE* 3.3 22.6 + - + +
569B ASN* 3.2 36.6 + - - +
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Residues in contact with GLU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B SER* 3.6 23.9 - - - +
565B LYS* 1.3 85.7 + - - +
567B ASN* 1.3 66.3 + - - +
569B ASN* 3.7 10.8 + - - +
570B LEU* 3.4 17.2 + - - +
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Residues in contact with ASN 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 3.1 47.0 + - + +
415B ASN* 5.9 0.4 - - - +
420B ASP* 5.4 2.8 - - - +
563B ILE* 3.6 19.7 - - + +
564B SER* 2.6 27.7 + - - +
566B GLU* 1.3 80.1 - - - +
568B ILE* 1.3 67.3 + - - +
569B ASN 3.2 0.2 - - - -
570B LEU* 3.0 14.0 + - - +
571B LEU* 3.0 25.3 + - - +
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Residues in contact with ILE 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B ALA 3.8 3.8 - - - +
538B LEU* 3.3 37.0 - - + +
539B GLU* 5.6 0.4 - - - +
541B ASN* 4.2 5.8 - - - -
542B GLY* 3.5 28.7 - - - +
563B ILE* 3.4 28.7 - - + -
564B SER 2.9 12.5 + - - +
565B LYS* 3.5 15.7 - - + +
567B ASN* 1.3 76.9 - - - +
569B ASN* 1.3 60.3 + - - +
571B LEU* 2.9 5.4 + - - +
572B THR* 2.7 46.0 + - + +
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Residues in contact with ASN 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B LYS* 3.2 37.1 + - - +
566B GLU* 3.9 10.1 - - - +
567B ASN 3.2 0.2 - - - -
568B ILE* 1.3 83.3 - - - +
570B LEU* 1.3 54.4 + - - +
572B THR* 2.9 11.0 + - - +
573B ASP* 2.7 48.4 + - - +
622B LYS* 5.2 4.0 + - - -
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 3.8 22.2 - - + -
420B ASP* 4.5 0.4 - - + -
421B ASP* 3.8 39.3 - - + +
455B LEU* 3.5 34.0 - - + +
456B LYS* 5.3 18.8 + - + +
459B ILE* 4.7 2.9 - - - +
566B GLU 3.4 9.5 + - - +
567B ASN* 3.0 19.7 + - - +
569B ASN* 1.3 81.5 - - - +
571B LEU* 1.3 58.2 + - + +
573B ASP* 3.8 6.8 - - - +
574B GLY* 3.5 13.3 + - - -
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Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ILE* 4.2 27.1 - - + +
410B ALA* 4.3 9.6 - - + -
411B MSE 4.3 7.9 - - + -
414B LEU* 4.0 15.5 - - + -
455B LEU* 4.0 18.8 - - + -
459B ILE* 3.7 25.0 - - + +
538B LEU* 4.2 14.4 - - + -
563B ILE* 3.8 22.4 - - + -
567B ASN 3.0 13.2 + - - +
568B ILE 2.9 6.7 + - - +
570B LEU* 1.3 75.7 - - - +
572B THR* 1.3 60.3 + - - +
574B GLY* 2.9 2.4 + - - -
575B MSE 2.9 40.0 + - - +
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Residues in contact with THR 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B LEU* 4.7 4.3 - - + -
539B GLU* 4.5 2.2 - - - +
568B ILE* 2.7 35.3 + - + +
569B ASN* 2.9 25.7 + - - +
571B LEU* 1.3 71.4 - - - +
573B ASP* 1.3 64.1 + - - +
574B GLY 3.1 0.7 + - - -
575B MSE 3.3 14.9 + - + +
576B GLN* 3.1 24.9 + - - +
595B ILE* 4.1 5.6 - - - +
620B TYR* 3.7 19.7 - - - +
622B LYS* 3.1 34.4 + - - +
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Residues in contact with ASP 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LYS* 3.6 27.9 + - - +
569B ASN* 2.7 37.1 + - - +
570B LEU* 3.8 7.5 + - + +
572B THR* 1.3 75.5 + - - +
574B GLY* 1.3 61.4 + - - +
576B GLN* 3.8 16.1 + - - +
577B GLN* 4.1 11.4 + - - +
622B LYS* 6.1 1.3 - - - +
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Residues in contact with GLY 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LYS* 4.1 22.4 - - - +
459B ILE* 3.8 19.0 - - - +
460B GLU* 4.8 0.9 - - - -
570B LEU 3.5 6.8 + - - -
571B LEU 2.9 7.1 + - - -
573B ASP* 1.3 77.2 - - - +
575B MSE 1.3 56.4 + - - +
576B GLN 3.0 4.3 - - - -
577B GLN* 3.0 27.1 + - - +
578B VAL* 3.6 6.1 + - - +
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Residues in contact with MSE 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ILE* 4.4 20.6 - - + -
459B ILE* 3.8 12.5 - - + +
535B TYR* 5.0 4.9 - - - -
538B LEU* 3.4 34.3 - - + -
571B LEU* 2.9 16.1 + - - +
572B THR* 3.6 16.2 - - + +
574B GLY* 1.3 70.5 - - - +
576B GLN* 1.3 59.8 + - - +
577B GLN 3.3 0.2 - - - -
578B VAL* 3.2 17.2 - - - +
579B VAL 3.7 1.4 + - - -
595B ILE* 3.4 29.3 - - + -
596B GLY* 2.8 51.0 + - - +
597B LYS* 4.9 3.4 - - + +
620B TYR* 3.9 7.6 - - + +
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Residues in contact with GLN 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B THR 3.1 12.9 + - - +
573B ASP* 4.0 10.4 + - - +
574B GLY 3.0 0.6 + - - -
575B MSE 1.3 75.7 - - - +
577B GLN* 1.3 66.4 + - - +
579B VAL* 3.3 4.9 + - - +
580B ASN* 3.0 43.4 + - - +
593B ASN* 3.0 36.2 + - - +
594B LEU 4.5 1.6 - - - +
595B ILE* 3.3 24.8 - - + +
622B LYS* 4.3 6.9 - - + +
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Residues in contact with GLN 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LYS* 5.3 11.9 - - + +
460B GLU* 3.8 27.9 + - + +
573B ASP 4.1 11.9 - - - +
574B GLY* 3.0 9.9 + - - +
576B GLN* 1.3 81.9 + - - +
578B VAL* 1.3 61.0 + - - +
579B VAL 3.0 2.5 - - - -
580B ASN* 3.3 22.3 + - - +
581B LYS* 2.6 71.0 + - + +
582B THR* 3.6 1.8 + - - -
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Residues in contact with VAL 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ILE* 3.4 28.3 - - + +
460B GLU* 4.3 3.3 - - - +
574B GLY 3.8 2.5 - - - +
575B MSE 3.2 18.4 - - - +
577B GLN* 1.3 78.7 - - - +
579B VAL* 1.3 56.9 + - - +
582B THR* 2.7 26.6 + - - +
583B HIS* 2.9 24.1 + - + +
596B GLY 3.1 27.8 - - - +
597B LYS* 4.6 2.0 - - - -
598B SER* 3.2 31.9 - - - +
617B PHE* 4.3 5.8 - - + -
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B MSE 3.7 0.2 + - - -
576B GLN 3.3 3.5 + - - +
577B GLN 3.0 0.6 - - - -
578B VAL* 1.3 77.3 - - - +
580B ASN* 1.3 64.2 + - - +
584B LYS* 3.0 31.7 + - - +
587B ILE* 3.9 21.5 - - + -
588B TYR* 3.7 27.5 - - + +
594B LEU* 3.0 48.0 - - + +
595B ILE* 3.4 17.7 - - - +
596B GLY* 3.8 2.7 - - - +
617B PHE* 4.7 7.6 - - + -
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Residues in contact with ASN 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B GLN* 3.0 33.7 + - - +
577B GLN* 3.1 26.6 + - - +
579B VAL* 1.3 82.7 - - - +
581B LYS* 1.3 63.0 + - + +
584B LYS* 3.1 34.9 + - - +
588B TYR* 3.6 26.9 - - - -
593B ASN* 5.5 2.9 + - - +
594B LEU 4.8 1.0 - - - +
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Residues in contact with LYS 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B GLU* 3.8 26.8 + - - +
577B GLN* 2.6 45.7 + - - +
580B ASN* 1.3 80.9 - - + +
582B THR* 1.3 66.8 + - + +
583B HIS 3.4 1.5 + - - -
584B LYS* 3.7 22.0 + - - +
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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
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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