Contacts of the helix formed by residues 686 - 705 (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 ALA 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A SER* 4.8 1.8 - - - +
542A HIS* 4.0 31.4 - - + +
543A THR* 3.4 18.4 - - - +
655A TYR* 4.6 2.7 - - - +
680A PHE* 4.8 1.3 - - + -
684A SER* 2.9 11.7 + - - +
685A THR* 1.3 82.1 + - - +
687A THR* 1.3 70.2 + - - +
688A SER 3.5 0.4 - - - -
689A THR* 3.1 7.7 - - - +
690A GLU* 2.7 27.6 + - + +
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Residues in contact with THR 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ASP* 3.8 16.4 - - - +
680A PHE* 3.9 10.9 - - - -
681A PRO 2.8 27.8 + - - +
682A SER* 3.2 21.0 + - - +
684A SER* 3.1 27.8 + - - -
686A ALA* 1.3 78.5 - - - +
688A SER* 1.3 65.8 + - - +
690A GLU* 3.3 0.6 - - - +
691A HIS* 2.9 34.7 + - + +
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A SER 4.9 0.4 + - - -
685A THR 5.3 0.8 + - - -
686A ALA 3.2 1.2 + - - -
687A THR* 1.3 81.6 - - - +
689A THR* 1.3 58.4 + - - +
691A HIS* 3.3 6.6 + - - +
692A THR* 2.7 36.3 + - - -
732A GLN* 4.8 9.9 + - - +
733A GLY* 4.2 10.1 + - - -
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Residues in contact with THR 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A THR* 4.0 7.9 - - + -
546A ALA* 3.3 18.4 - - + +
547A ASP* 2.8 27.8 + - - +
550A ASN* 2.8 41.3 + - - +
685A THR 3.7 16.4 + - - +
686A ALA* 3.1 14.8 - - - +
688A SER* 1.3 77.9 + - - +
690A GLU* 1.3 60.2 + - - +
692A THR* 3.3 3.4 + - - -
693A ALA* 3.0 18.2 + - - +
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Residues in contact with GLU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TRP* 4.1 4.2 - - + -
542A HIS* 2.7 39.4 + - + +
546A ALA* 3.9 10.3 - - + -
593A ILE* 3.7 14.4 - - - +
599A LEU* 4.3 0.3 - - - +
602A ILE* 3.4 17.5 - - - +
680A PHE* 4.9 2.9 - - + -
686A ALA* 2.7 28.8 + - + +
687A THR* 3.3 3.1 - - - +
689A THR* 1.3 70.6 - - - +
691A HIS* 1.3 97.8 + - - +
693A ALA* 3.1 4.9 + - - +
694A ASN* 2.6 55.7 + - - -
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Residues in contact with HIS 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ILE* 5.6 0.7 - - - +
589A CYS* 3.4 31.6 - - + -
590A ASP* 2.8 30.7 + - - -
593A ILE* 3.7 21.0 - - + +
680A PHE* 3.9 19.1 - + + -
687A THR* 2.9 28.5 + - + +
688A SER* 3.7 4.9 - - - +
690A GLU* 1.3 105.1 + - - +
692A THR* 1.3 62.8 + - - +
694A ASN* 4.0 5.2 - - - +
695A ASN* 3.0 25.3 + - - +
733A GLY* 3.5 17.4 - - - +
734A ASP* 5.7 0.9 - - + -
769A TRP* 5.1 2.0 - - - -
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Residues in contact with THR 692 (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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550A ASN* 3.1 20.9 - - - +
556A SER* 3.5 26.2 - - - -
557A PRO 5.4 1.5 + - - +
688A SER* 2.7 23.2 + - - -
689A THR* 3.4 9.6 - - - -
690A GLU 3.1 0.2 - - - -
691A HIS* 1.3 78.7 - - - +
693A ALA* 1.3 60.7 + - - +
695A ASN* 3.4 4.1 - - - +
696A SER* 3.2 22.3 + - - -
731A CYS* 3.7 15.7 - - - +
732A GLN* 3.8 6.5 - - - +
733A GLY 3.0 20.6 + - - +
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Residues in contact with ALA 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TRP* 3.6 21.5 - - + -
546A ALA* 4.3 3.8 - - - +
549A ILE* 3.9 25.8 - - + -
550A ASN* 3.5 8.9 + - - +
689A THR 3.0 13.9 + - - +
690A GLU 3.1 7.8 + - - +
692A THR* 1.3 75.2 - - - +
694A ASN* 1.3 56.7 + - - +
696A SER* 3.1 6.6 + - - -
697A THR* 2.6 37.8 + - - -
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Residues in contact with ASN 694 (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* 3.6 6.4 - - - +
429A TRP* 3.1 24.6 + - - -
593A ILE* 3.9 11.3 - - + +
598A PHE* 3.7 14.8 - - + -
602A ILE* 3.2 10.9 - - - +
690A GLU* 2.6 50.3 + - - +
691A HIS* 4.2 2.6 - - - +
693A ALA* 1.3 72.2 - - - +
695A ASN* 1.3 66.7 + - - +
697A THR* 4.2 5.2 - - - -
698A MET* 2.9 29.9 + - - +
769A TRP* 3.6 17.7 - - + -
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Residues in contact with ASN 695 (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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584A ILE 5.7 0.2 + - - -
586A ILE* 3.5 22.5 - - + +
691A HIS 3.0 18.9 + - - +
692A THR 3.4 6.7 - - - +
694A ASN* 1.3 80.8 - - - +
696A SER* 1.3 62.9 + - - +
698A MET* 3.9 2.1 - - - +
699A MET* 3.0 19.2 + - - +
729A TYR* 2.6 31.5 + - - -
731A CYS* 3.8 16.2 - - - +
733A GLY 3.2 20.0 + - - +
734A ASP 3.9 10.9 + - - -
735A ASP 4.0 1.6 + - - -
769A TRP* 3.7 12.4 - - - -
771A TYR* 5.1 3.6 + - - -
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Residues in contact with SER 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ILE* 4.5 2.9 - - - +
554A ASN* 2.9 45.1 + - - +
692A THR 3.2 2.4 + - - -
693A ALA* 3.1 9.7 + - - -
695A ASN* 1.3 77.1 + - - +
697A THR* 1.3 64.6 + - - +
699A MET* 3.4 0.4 + - - -
700A GLU* 2.8 31.7 + - - +
725A ILE* 3.7 14.2 - - - +
729A TYR* 4.4 9.4 - - - -
731A CYS* 3.8 14.8 - - - -
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Residues in contact with THR 697 (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 4.5 0.2 - - - +
425A LEU* 4.0 15.5 - - + -
428A THR* 3.5 42.6 - - + +
429A TRP* 4.5 3.3 + - - -
549A ILE* 4.6 4.2 - - - +
693A ALA 2.6 22.6 + - - -
694A ASN* 3.3 6.5 + - - -
696A SER* 1.3 78.2 + - - +
698A MET* 1.3 76.4 + - + +
700A GLU* 3.3 6.4 + - - +
701A THR* 2.9 36.0 + - - +
725A ILE* 5.3 1.1 - - - -
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Residues in contact with MET 698 (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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421A ILE* 5.4 5.8 - - - +
425A LEU* 3.3 41.7 - - + +
597A PHE* 4.8 7.2 - - - -
598A PHE* 3.9 31.2 - - + -
694A ASN 2.9 19.7 + - - +
695A ASN 3.9 2.5 - - - +
697A THR* 1.3 89.4 - - + +
699A MET* 1.3 62.7 + - - +
701A THR* 3.3 8.1 + - + +
702A PHE 2.9 10.4 + - - -
763A TYR* 2.7 33.8 + - - +
767A PHE* 4.2 14.6 - - + -
769A TRP* 3.9 14.4 - - + -
771A TYR* 4.2 7.2 - - - +
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Residues in contact with MET 699 (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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584A ILE* 3.6 41.1 - - + -
695A ASN* 3.0 18.0 + - - +
696A SER 3.8 3.6 - - - +
698A MET* 1.3 76.5 - - - +
700A GLU* 1.3 63.8 + - - +
702A PHE* 3.2 24.5 + - - +
703A LEU* 3.0 29.6 + - + +
725A ILE* 4.0 2.7 - - + -
729A TYR* 3.9 37.2 - - + -
738A MET* 4.4 11.2 - - + -
760A ILE* 4.0 21.8 - - + -
763A TYR* 5.9 0.2 - - - -
771A TYR* 4.3 16.1 + - + +
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Residues in contact with GLU 700 (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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428A THR* 6.2 0.2 - - - -
696A SER 2.8 18.7 + - - +
697A THR* 3.5 7.4 - - - +
699A MET* 1.3 76.9 - - - +
701A THR* 1.3 66.9 + - - +
703A LEU* 3.1 5.2 + - - +
704A THR* 2.9 45.2 + - - +
725A ILE* 3.3 39.9 - - + +
726A GLN* 4.6 7.7 - - - +
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Residues in contact with THR 701 (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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421A ILE* 3.3 40.2 - - + +
424A TYR* 3.5 31.3 - - + +
697A THR* 2.9 19.7 + - - +
698A MET* 4.1 8.2 - - + +
700A GLU* 1.3 81.4 + - - +
702A PHE* 1.3 54.9 + - - +
704A THR* 4.6 1.6 - - - +
705A VAL* 2.7 34.0 + - + +
706A TRP 3.3 4.7 + - - -
763A TYR* 3.5 11.0 - - - +
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Residues in contact with PHE 702 (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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698A MET 2.9 6.0 + - - +
699A MET* 3.5 14.6 - - - +
700A GLU 3.1 0.2 - - - -
701A THR* 1.3 77.9 - - - +
703A LEU* 1.3 84.7 + - + +
706A TRP* 4.0 6.3 - + - -
707A GLY* 2.9 48.5 + - - -
708A PRO* 3.3 5.0 - - - +
720A MET* 4.2 11.2 - - - -
756A ASP* 3.6 15.0 - - - -
759A LEU* 3.7 14.8 - - + -
760A ILE* 3.3 48.7 - - + -
763A TYR* 3.5 44.3 + + + -
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Residues in contact with LEU 703 (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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699A MET* 3.0 28.6 + - + +
700A GLU* 3.1 4.2 + - - +
702A PHE* 1.3 98.7 - - + +
704A THR* 1.3 60.5 + - - +
708A PRO* 3.4 16.9 - - - +
720A MET* 4.0 37.4 - - + +
721A LYS* 5.2 1.2 + - - -
723A LEU* 4.0 43.1 - - + +
724A THR* 4.3 3.1 - - - +
725A ILE* 4.3 19.5 - - + +
729A TYR* 5.7 1.3 - - + -
738A MET* 4.6 11.2 - - + -
756A ASP* 4.9 1.3 - - - +
760A ILE* 6.0 0.2 - - + -
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Residues in contact with THR 704 (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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700A GLU* 2.9 34.1 + - - +
701A THR* 4.2 0.9 - - - -
703A LEU* 1.3 82.3 - - - +
705A VAL* 1.3 71.9 + - + +
708A PRO* 3.7 14.1 - - - +
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Residues in contact with VAL 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ILE* 5.3 2.9 - - + -
424A TYR* 3.7 52.0 - - + +
701A THR* 2.7 22.3 + - + +
703A LEU 3.8 0.2 - - - -
704A THR* 1.3 91.9 - - + +
706A TRP* 1.3 67.4 + - + +
707A GLY 3.5 1.1 - - - -
708A PRO* 3.4 4.0 - - - +
709A GLU* 3.1 52.1 + - - +
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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
------------------------------------------------------------
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