Contacts of the helix formed by residues 642 - 657 (chain A) 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 ALA 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A TYR* 6.5 0.2 - - + -
583A HIS* 4.0 8.5 - - + +
598A SER* 3.3 26.6 + - - +
599A GLY* 3.4 16.6 - - - +
600A THR* 3.0 19.9 + - - +
615A GLY* 5.0 5.4 - - - -
616A TRP 4.9 0.8 - - - +
617A PHE* 4.3 0.2 - - - -
641A MSE 1.3 77.0 - - + +
643A SER* 1.3 65.6 + - - +
644A TYR 3.0 3.1 + - - -
645A ASN* 3.3 14.8 + - - +
646A ALA* 3.5 8.1 + - - +
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Residues in contact with SER 643 (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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583A HIS* 3.7 20.2 - - - -
586A ASP* 3.1 28.4 + - - -
639A LYS 4.6 0.2 + - - -
640A GLY* 2.5 31.4 + - - -
642A ALA* 1.3 78.6 - - - +
644A TYR* 1.3 61.1 + - - +
646A ALA* 3.3 3.1 + - - +
647A LYS* 3.0 26.5 + - - +
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Residues in contact with TYR 644 (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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339A ASN 5.0 1.7 + - - -
343A ASP* 3.0 43.4 + - - -
633A VAL* 4.3 6.1 - - + -
636A VAL* 4.0 14.8 - - + -
639A LYS* 3.5 44.4 - - + +
640A GLY 3.9 0.4 + - - -
641A MSE 3.2 14.4 + - - +
642A ALA 3.0 0.8 - - - -
643A SER* 1.3 82.3 + - - +
645A ASN* 1.3 66.2 + - - +
647A LYS* 3.3 21.2 + - + +
648A ILE* 3.1 45.0 + - + +
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Residues in contact with ASN 645 (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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615A GLY* 2.9 33.7 + - - -
616A TRP* 3.0 3.1 - - - +
617A PHE* 3.4 17.9 - - + +
631A ILE* 2.8 37.0 + - + +
633A VAL* 3.6 23.5 - - - +
636A VAL* 4.0 8.9 - - - +
642A ALA 3.3 8.1 + - - +
644A TYR* 1.3 75.7 - - - +
646A ALA* 1.3 57.5 + - - +
648A ILE* 3.3 7.7 + - - +
649A SER* 2.6 39.9 + - - -
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Residues in contact with ALA 646 (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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583A HIS* 4.0 15.3 - - + +
586A ASP* 3.4 14.9 - - + +
587A ILE* 3.3 21.0 - - + +
617A PHE* 3.4 36.6 - - + -
642A ALA 3.5 2.4 + - - +
643A SER 3.3 10.2 + - - +
645A ASN* 1.3 78.6 - - - +
647A LYS* 1.3 56.7 + - - +
649A SER* 4.3 1.3 - - - -
650A GLY 2.9 21.1 + - - -
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Residues in contact with LYS 647 (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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585A GLU 5.2 1.2 + - - -
586A ASP* 3.1 39.2 + - + +
589A ARG* 4.9 0.7 + - - +
639A LYS 5.6 2.9 - - - -
643A SER* 3.0 13.9 + - - +
644A TYR* 3.5 26.7 - - + +
645A ASN 3.1 0.2 - - - -
646A ALA* 1.3 74.9 - - - +
648A ILE* 1.3 69.5 + - + +
650A GLY* 2.8 11.8 + - - -
651A LYS* 2.9 40.7 + - + +
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Residues in contact with ILE 648 (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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336A ILE* 5.3 1.1 - - - +
339A ASN* 3.6 33.8 - - + +
340A MSE 3.8 20.9 - - + -
343A ASP* 4.1 3.8 - - - +
631A ILE* 4.0 22.0 - - + -
633A VAL* 4.2 10.5 - - + -
644A TYR* 3.1 46.5 + - + +
645A ASN* 3.6 8.1 - - - +
647A LYS* 1.3 79.8 - - + +
649A SER* 1.3 65.9 + - - +
651A LYS* 3.2 9.2 + - - +
652A VAL* 3.0 29.5 + - + +
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Residues in contact with SER 649 (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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587A ILE* 3.5 22.0 - - - -
617A PHE* 4.2 8.1 + - - +
619A SER* 4.2 3.3 + - - -
629A MSE 3.7 20.9 - - - +
631A ILE* 3.3 20.0 - - - +
645A ASN 2.6 22.4 + - - -
646A ALA* 3.7 0.4 - - - -
648A ILE* 1.3 78.3 - - - +
650A GLY* 1.3 58.1 + - - +
652A VAL* 3.5 2.7 + - - +
653A TYR* 2.8 36.8 + - - -
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Residues in contact with GLY 650 (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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586A ASP 4.0 1.1 - - - -
587A ILE* 3.9 11.4 - - - +
589A ARG* 3.3 24.6 + - - -
646A ALA 2.9 12.7 + - - -
647A LYS 2.8 8.9 + - - -
649A SER* 1.3 76.0 - - - +
651A LYS* 1.3 61.7 + - - -
653A TYR* 3.3 5.5 + - - +
654A ASP* 3.0 27.5 + - - +
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Residues in contact with LYS 651 (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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339A ASN* 3.4 29.9 + - + +
589A ARG* 3.8 3.8 - - - +
647A LYS* 2.9 38.5 + - + +
648A ILE* 3.6 9.4 - - - +
650A GLY* 1.3 76.4 - - - +
652A VAL* 1.3 63.0 + - - +
654A ASP* 3.2 11.4 + - - +
655A GLU* 3.1 25.3 + - + +
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Residues in contact with VAL 652 (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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332A VAL* 5.5 0.7 - - + +
335A SER* 3.4 39.0 - - - +
336A ILE* 4.0 17.7 - - + -
339A ASN* 3.9 9.6 - - + +
627A MSE 4.9 0.2 - - + -
629A MSE 3.7 26.7 - - + -
631A ILE* 5.8 0.2 - - + -
648A ILE* 3.0 26.0 + - + +
649A SER 3.7 4.5 - - - +
650A GLY 3.3 0.2 - - - -
651A LYS* 1.3 75.3 - - - +
653A TYR* 1.3 64.1 + - - +
655A GLU* 3.0 14.0 + - - +
656A LEU* 3.0 29.6 + - + +
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Residues in contact with TYR 653 (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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587A ILE* 4.4 2.7 - - + -
589A ARG* 5.3 0.7 - - + -
591A TYR* 3.4 11.0 - + + +
594A LEU* 3.9 38.6 - - + -
619A SER* 2.8 35.9 + - - -
620A TYR* 2.9 28.7 + - - -
621A ASP* 4.6 3.8 - - + -
627A MSE 3.8 23.5 - - + +
629A MSE 3.3 18.5 - - + +
649A SER* 2.8 30.8 + - - +
650A GLY 3.3 5.1 + - - +
652A VAL* 1.3 75.8 - - - +
654A ASP* 1.3 57.9 + - - +
656A LEU* 3.4 4.7 + - + +
657A TYR* 2.8 56.3 + + + +
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Residues in contact with ASP 654 (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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589A ARG* 2.7 44.2 + - - -
591A TYR* 2.4 33.6 + - - -
650A GLY 3.0 8.6 + - - +
651A LYS* 3.5 11.7 - - - +
652A VAL 3.2 0.2 - - - -
653A TYR* 1.3 76.0 - - - +
655A GLU* 1.3 54.1 + - + +
658A GLU* 2.6 13.3 + - - -
659A ASN* 2.6 52.6 + - - +
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Residues in contact with GLU 655 (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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335A SER* 3.3 31.4 + - - +
338A ASN* 5.0 8.9 + - - +
339A ASN* 2.9 24.9 + - - +
651A LYS* 3.1 12.3 + - - +
652A VAL 3.0 7.5 + - - +
654A ASP* 1.3 77.9 - - + +
656A LEU* 1.3 65.7 + - + +
658A GLU* 3.1 20.3 + - - +
659A ASN* 5.4 0.4 - - - -
662A LYS* 5.7 0.5 + - - -
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Residues in contact with LEU 656 (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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331A LYS* 3.8 44.1 - - + +
332A VAL* 4.3 7.6 - - + -
335A SER* 4.4 7.2 - - - -
627A MSE 3.9 33.9 - - + -
652A VAL* 3.0 26.1 + - + +
653A TYR* 3.9 7.0 - - + +
655A GLU* 1.3 77.4 - - + +
657A TYR* 1.3 65.3 + - + +
658A GLU 3.4 0.2 - - - -
662A LYS* 3.5 19.8 + - - +
664A TYR* 3.8 40.2 - - + -
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Residues in contact with TYR 657 (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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591A TYR* 3.5 42.2 - + + -
592A ALA* 4.5 3.1 - - + -
621A ASP* 2.6 37.1 + - + +
624A ASN* 2.8 25.5 + - - -
626A ASN* 5.2 0.2 + - - -
653A TYR* 2.8 41.6 + + - +
656A LEU* 1.3 85.5 - - + +
658A GLU* 1.3 67.6 + - - +
660A GLY 2.9 11.4 + - - +
661A ASN 3.0 10.4 + - - -
662A LYS* 3.1 30.0 + - - +
663A LYS* 4.1 9.0 - - + -
664A TYR* 3.5 23.7 - - + +
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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
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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