Contacts of the helix formed by residues 642 - 658 (chain A) in PDB entry 1MWH
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 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A SER* 2.7 53.4 + - - -
615A ILE 3.9 8.9 + - - -
617A LYS 3.7 4.3 - - - -
624A ALA* 3.7 7.0 - - - -
641A ILE* 1.3 77.5 - - - +
643A GLY* 1.3 54.6 + - - +
644A MET 3.6 1.2 + - - -
645A GLN* 2.8 30.4 + - - +
646A ASN* 2.8 33.1 + - - +
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Residues in contact with GLY 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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617A LYS 2.8 18.3 + - - -
618A PRO* 4.0 1.1 - - - -
619A PHE* 4.2 3.4 - - - -
622A VAL* 3.3 27.2 - - - +
623A PRO 3.4 13.2 - - - -
624A ALA* 3.7 2.6 - - - +
642A SER* 1.3 69.0 - - - +
644A MET* 1.3 65.6 + - - +
646A ASN* 2.9 3.6 + - - +
647A MET* 2.9 26.4 + - - +
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Residues in contact with MET 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A MET* 4.4 10.1 - - + +
437A ALA* 4.3 8.5 - - - -
442A THR* 4.0 9.4 - - + -
443A TRP* 3.7 13.9 - - + -
541A PRO* 3.7 21.8 - - + +
544A LEU* 4.9 1.1 - - + -
610A VAL* 3.4 36.8 - - + -
614A SER* 4.1 7.9 - - - +
617A LYS 4.4 0.8 + - - -
619A PHE* 3.5 60.0 - - + +
642A SER* 3.3 8.6 + - - +
643A GLY* 1.3 76.1 - - - +
645A GLN* 1.3 61.2 + - - +
647A MET* 3.2 21.9 + - - +
648A ILE* 3.3 7.0 + - + +
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Residues in contact with GLN 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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607A HIS* 2.9 47.2 + - - +
608A GLU* 4.9 1.4 + - - -
610A VAL* 3.7 16.6 - - + -
611A ALA* 3.4 29.0 - - - +
615A ILE 5.3 0.3 - - - +
640A PRO 4.5 1.0 - - - +
641A ILE* 3.1 23.3 - - + +
642A SER* 2.8 41.6 + - - +
643A GLY 3.1 0.4 - - - -
644A MET* 1.3 74.1 - - - +
646A ASN* 1.3 60.6 - - - +
648A ILE* 3.1 7.2 + - - +
649A GLN* 2.8 31.3 + - - +
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Residues in contact with ASN 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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502A PHE* 3.8 11.1 - - - -
622A VAL* 3.8 12.5 - - + +
623A PRO* 2.9 27.6 + - - +
625A SER* 3.6 27.8 + - - +
641A ILE* 4.2 4.7 - - + +
642A SER 2.8 15.3 + - - +
643A GLY 2.9 8.9 + - - +
645A GLN* 1.3 77.0 - - - +
647A MET* 1.3 62.5 + - - +
649A GLN* 3.2 10.6 - - - +
650A HIS* 3.0 41.6 + - - -
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Residues in contact with MET 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLN* 3.0 28.5 - - + +
538A VAL* 3.4 29.9 - - + +
540A ALA* 4.0 6.3 - - + -
541A PRO* 3.4 25.4 - - + -
619A PHE* 3.7 34.1 - - + +
620A MET* 3.8 17.5 - - + -
622A VAL* 3.7 22.9 - - + +
643A GLY 2.9 16.0 + - - +
644A MET* 3.3 8.1 - - - +
645A GLN 3.1 0.2 - - - -
646A ASN* 1.3 75.1 - - - +
648A ILE* 1.3 60.3 + - - +
650A HIS 3.0 2.9 + - - -
651A LEU* 2.8 28.9 + - - +
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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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411A ILE* 5.0 1.6 - - + -
541A PRO* 3.5 32.5 - - + -
542A HIS 4.3 7.6 - - - +
603A MET* 3.1 51.3 - - + +
606A ILE* 3.7 24.2 - - + -
607A HIS* 3.8 17.9 - - + +
610A VAL* 6.2 0.7 - - + -
644A MET* 3.3 6.5 + - + +
645A GLN* 3.1 10.3 + - - +
647A MET* 1.3 77.9 - - - +
649A GLN* 1.3 55.4 + - - +
651A LEU* 4.1 6.5 - - + -
652A SER* 2.8 42.6 + - - +
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Residues in contact with GLN 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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408A ILE 3.5 12.4 + - - -
409A GLY* 3.1 2.9 - - - -
410A GLU* 2.4 68.9 + - + +
411A ILE* 4.6 3.8 - - - +
607A HIS* 3.2 31.3 + - - -
627A VAL* 3.8 28.0 - - + +
641A ILE* 4.1 3.4 - - + +
645A GLN 2.8 10.4 + - - +
646A ASN* 3.2 20.9 - - - +
648A ILE* 1.3 79.9 - - - +
650A HIS* 1.3 61.6 + - + +
652A SER* 3.8 5.1 + - - -
653A LYS* 3.8 1.6 + - - +
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Residues in contact with HIS 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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502A PHE* 3.8 20.4 - + - -
506A SER* 4.0 23.6 + - - -
509A ILE* 3.8 29.3 - - + +
510A LEU* 4.9 0.7 - - - +
538A VAL* 3.8 13.7 - - + -
646A ASN* 3.0 38.8 + - - +
647A MET 3.0 8.2 + - - +
649A GLN* 1.3 78.0 - - + +
651A LEU* 1.3 66.2 + - - +
653A LYS* 3.4 23.6 + - + +
654A LEU 3.7 3.8 + - - -
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Residues in contact with LEU 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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531A LEU* 6.4 0.2 - - + -
535A GLN 4.8 0.7 - - - +
538A VAL* 3.5 29.8 - - + +
539A SER* 3.4 28.9 - - - +
542A HIS* 3.9 14.1 - - + -
603A MET* 3.3 23.3 - - + -
647A MET 2.8 14.7 + - - +
648A ILE* 4.1 5.4 - - + -
650A HIS* 1.3 75.2 - - - +
652A SER* 1.3 60.4 + - - +
654A LEU* 3.1 17.7 + - + +
655A TYR* 2.9 64.0 + - + +
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Residues in contact with SER 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU* 4.1 8.5 - - - -
411A ILE* 3.3 30.0 - - - +
595A TRP* 3.9 16.3 - - - -
603A MET* 3.0 19.0 - - - +
648A ILE* 2.8 22.1 + - - +
649A GLN 3.9 6.1 - - - -
650A HIS 3.3 0.2 - - - -
651A LEU* 1.3 73.3 - - - +
653A LYS* 1.3 57.0 + - - +
655A TYR* 3.8 1.5 - - - +
656A LYS* 2.7 39.4 + - - +
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Residues in contact with LYS 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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410A GLU* 3.5 38.9 + - + +
510A LEU* 3.9 33.0 - - + -
649A GLN 3.8 4.2 + - - +
650A HIS* 3.4 19.9 + - + +
651A LEU 3.2 0.6 - - - -
652A SER* 1.3 78.7 - - - +
654A LEU* 1.3 57.1 + - - +
656A LYS* 3.8 3.8 - - - +
657A ARG* 2.9 33.5 + - + +
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Residues in contact with LEU 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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509A ILE* 3.6 33.9 - - + +
510A LEU* 3.9 20.8 - - + +
511A ALA 5.5 1.3 - - - +
531A LEU* 5.4 5.8 - - + -
535A GLN* 3.9 20.9 - - + +
650A HIS 3.7 4.1 + - - +
651A LEU* 3.1 17.5 + - + +
653A LYS* 1.3 76.8 - - - +
655A TYR* 1.3 72.2 - - + +
657A ARG* 3.2 5.1 + - - +
658A GLY* 2.9 37.3 + - - +
659A PHE* 3.3 40.1 - - + -
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Residues in contact with TYR 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 6.2 2.9 - - + -
539A SER* 4.4 5.1 + - - -
542A HIS* 2.7 41.0 + + - +
595A TRP* 3.9 23.5 + - + +
599A LEU* 3.8 25.8 - - + +
603A MET* 3.8 22.9 - - + -
651A LEU* 2.9 47.9 + - + +
652A SER 3.8 3.1 - - - +
654A LEU* 1.3 80.4 - - + +
656A LYS* 1.3 62.7 + - - +
658A GLY* 3.6 8.1 + - - -
659A PHE* 3.6 28.7 - + - -
678A THR* 6.1 1.7 - - - +
680A PHE* 3.4 24.6 - + - -
681A PRO* 5.1 1.3 - - + -
684A SER* 4.7 1.9 + - - -
686A ALA* 4.6 3.1 - - - +
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Residues in contact with LYS 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU* 2.8 53.7 + - - +
595A TRP* 3.7 47.5 - - + +
652A SER 2.7 25.1 + - - +
653A LYS* 3.8 3.6 - - - +
655A TYR* 1.3 73.9 - - - +
657A ARG* 1.3 63.4 - - - +
658A GLY* 3.5 0.3 + - - -
678A THR* 6.0 1.6 - - - +
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Residues in contact with ARG 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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510A LEU* 2.9 53.9 + - + +
653A LYS* 2.9 20.8 + - + +
654A LEU* 3.8 4.6 - - - +
656A LYS* 1.3 77.7 - - - +
658A GLY* 1.3 70.9 + - - +
660A SER* 5.1 7.9 + - - -
676A MET* 4.3 27.3 - - + +
678A THR* 5.7 1.3 - - - +
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Residues in contact with GLY 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LEU* 2.9 25.1 + - - +
655A TYR 3.6 6.9 + - - -
656A LYS 3.3 2.4 - - - -
657A ARG* 1.3 91.9 + - - +
659A PHE* 1.3 68.2 + - - -
660A SER 4.3 0.2 + - - -
676A MET* 4.1 6.0 - - - +
677A THR 3.7 10.3 - - - -
678A THR* 4.6 10.5 - - - -
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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