Contacts of the helix formed by residues 600 - 617 (chain A) in PDB entry 1MP8
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 THR 600 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A VAL* 3.6 19.7 - - - +
592A GLU* 4.7 2.8 + - + -
598A ARG* 4.2 25.5 - - + -
599A PHE* 1.3 81.0 - - - +
601A SER* 1.3 64.7 + - - +
602A ALA* 3.0 21.7 + - - +
603A SER* 2.9 25.0 + - - -
604A ASP 3.0 7.4 + - - -
663A PRO* 5.3 1.0 - - - +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A GLU* 3.3 51.7 + - - +
541A ARG* 5.7 2.1 - - - -
542A PHE 4.8 4.2 + - - -
543A VAL* 3.8 11.7 - - - +
600A THR* 1.3 75.8 - - - +
602A ALA* 1.3 57.4 + - - +
604A ASP* 3.2 14.7 + - - +
605A VAL* 2.9 31.0 + - - +
669A PHE* 3.7 2.4 - - - -
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Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A THR* 3.0 11.6 + - - +
601A SER* 1.3 77.8 - - - +
603A SER* 1.3 64.4 + - - +
605A VAL* 3.2 18.8 + - - +
606A TRP 3.2 6.6 + - - -
663A PRO* 3.8 37.7 - - + +
666A ARG* 3.0 17.8 + - + +
667A PRO 5.8 0.4 - - - -
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Residues in contact with SER 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ALA* 3.7 5.2 - - - +
592A GLU* 3.4 18.4 - - - -
593A SER* 3.2 24.3 + - - -
598A ARG 4.1 2.0 - - - -
599A PHE* 3.2 12.7 - - - +
600A THR* 2.9 35.8 + - - -
602A ALA* 1.3 77.7 - - - +
604A ASP* 1.3 65.8 + - - +
606A TRP* 3.2 5.2 + - - +
607A MET* 3.2 27.9 + - - +
666A ARG* 3.7 3.3 - - - +
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Residues in contact with ASP 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 5.4 0.9 - - - +
542A PHE 4.3 2.6 - - - +
543A VAL* 3.4 12.5 - - - +
544A HIS* 2.7 26.8 + - - +
545A ARG* 2.9 27.7 + - - -
547A ILE* 3.5 22.6 - - + +
600A THR 3.0 11.9 + - - +
601A SER* 3.3 12.9 - - - +
603A SER* 1.3 79.0 + - - +
605A VAL* 1.3 57.4 + - - +
607A MET* 3.1 7.9 + - - +
608A PHE* 2.8 29.5 + - - +
669A PHE* 3.6 13.1 - - + -
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Residues in contact with VAL 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A GLU* 5.2 0.4 - - - +
601A SER 2.9 20.0 + - - +
602A ALA* 3.2 13.2 + - - +
604A ASP* 1.3 76.2 - - - +
606A TRP* 1.3 57.9 + - - +
608A PHE* 3.2 2.4 + - - +
609A GLY 2.9 24.3 + - - -
658A CYS* 3.5 32.9 - - + +
666A ARG* 4.0 9.2 - - + -
667A PRO* 3.4 28.7 - - + +
668A ARG* 4.6 1.3 - - - -
669A PHE* 3.6 34.1 - - + +
672A LEU* 4.0 5.8 - - + -
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Residues in contact with TRP 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LYS 5.4 1.0 + - - -
588A TRP 3.3 19.5 + - - -
589A MET 3.2 13.2 + - - -
590A ALA* 3.6 20.6 - - + -
591A PRO* 3.5 18.4 - - + -
602A ALA 3.2 3.2 + - - -
603A SER 3.4 9.4 - - - +
605A VAL* 1.3 80.5 - - - +
607A MET* 1.3 61.7 + - - +
609A GLY 3.0 9.9 + - - -
610A VAL* 3.1 17.8 + - + +
635A ILE* 3.6 41.2 - - + +
640A ARG* 4.1 9.0 - - - -
658A CYS 3.3 13.9 + - - +
659A TRP* 3.2 60.9 + + + -
660A ALA 3.5 7.4 - - - -
661A TYR* 4.4 0.2 - - - -
666A ARG* 3.5 22.9 - - - +
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Residues in contact with MET 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ARG* 3.5 38.6 - - - +
546A ASP* 3.8 4.0 - - - +
547A ILE* 3.6 34.4 - - + +
585A PRO* 4.4 6.7 - - + -
588A TRP* 3.3 43.7 - - + +
589A MET* 4.4 16.8 - - + -
590A ALA 4.8 1.1 - - - +
599A PHE* 5.8 4.7 - - - -
603A SER* 3.3 17.0 - - - +
604A ASP* 3.1 12.0 + - - +
606A TRP* 1.3 75.7 - - - +
608A PHE* 1.3 58.6 + - - +
610A VAL* 3.0 6.7 + - - +
611A CYS* 2.8 26.5 + - - +
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Residues in contact with PHE 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ALA* 3.4 20.9 - - - -
530A LEU* 3.8 28.0 - - + -
531A SER* 3.8 13.2 - - - -
534A LEU* 3.4 18.8 - - + -
547A ILE* 3.8 12.7 - - + +
604A ASP 2.8 14.0 + - - +
605A VAL 3.5 6.5 - - - +
607A MET* 1.3 74.8 - - - +
609A GLY* 1.3 67.3 + - - +
611A CYS* 3.1 6.4 + - + +
612A MET* 2.8 62.2 + - + +
615A ILE* 6.0 0.4 - - + -
669A PHE* 3.7 16.2 - + + -
672A LEU* 3.7 25.8 - - + -
676A LEU* 4.0 8.7 - - + -
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Residues in contact with GLY 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL 2.9 11.9 + - - -
606A TRP 3.0 6.0 + - - -
608A PHE* 1.3 78.8 - - - +
610A VAL* 1.3 59.8 + - - +
612A MET* 3.3 10.6 + - - +
613A TRP* 3.0 17.5 + - - +
655A MET* 4.1 3.9 - - - +
658A CYS* 3.8 20.0 - - - -
659A TRP* 3.4 22.6 - - - -
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LYS 4.2 4.9 - - - +
588A TRP* 3.5 42.2 - - + +
606A TRP* 3.1 21.5 + - - +
607A MET 3.0 7.2 + - - +
609A GLY* 1.3 75.2 - - - +
611A CYS* 1.3 58.7 + - - +
613A TRP* 3.1 5.2 + - + +
614A GLU* 2.9 27.0 + - + +
622A PRO* 3.6 31.0 - - + -
623A PHE* 5.9 1.1 - - + -
641A LEU* 4.2 7.9 - - + -
659A TRP* 3.5 19.5 - - + +
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Residues in contact with CYS 611 (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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530A LEU* 4.3 15.5 - - - -
547A ILE* 4.0 12.1 - - + -
548A ALA* 3.7 30.7 - - - -
549A ALA* 3.7 8.3 - - - -
552A VAL* 4.4 2.7 - - - -
588A TRP* 4.6 0.4 - - - -
607A MET 2.8 12.9 + - - +
608A PHE* 3.1 17.7 + - + +
610A VAL* 1.3 76.5 - - - +
612A MET* 1.3 62.2 + - - +
614A GLU* 3.1 13.5 + - - +
615A ILE* 2.9 40.1 + - - +
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Residues in contact with MET 612 (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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527A ALA* 4.0 12.6 - - + -
608A PHE* 2.8 60.0 + - + +
609A GLY* 3.6 10.5 - - - +
611A CYS* 1.3 71.5 - - - +
613A TRP* 1.3 64.1 + - - +
615A ILE* 3.0 9.7 + - - +
616A LEU* 2.9 31.0 + - + +
651A LEU* 4.3 7.4 - - + -
654A LEU* 4.5 2.9 - - + -
655A MET* 3.8 28.5 - - + +
658A CYS* 4.0 12.6 - - - -
672A LEU* 3.9 18.2 - - + -
676A LEU* 4.1 24.5 - - - -
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Residues in contact with TRP 613 (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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609A GLY 3.0 12.8 + - - +
610A VAL* 3.3 12.1 - - - +
612A MET* 1.3 76.6 - - - +
614A GLU* 1.3 64.2 + - + +
616A LEU* 3.2 2.6 + - - +
617A MET* 2.8 67.6 + - + +
620A VAL* 3.6 17.9 - - + -
621A LYS 3.8 0.7 - - - -
622A PRO* 3.6 25.1 - - + -
624A GLN* 3.5 21.3 - - - -
641A LEU* 3.5 38.2 - - + +
642A PRO* 2.7 38.9 + - + -
644A PRO* 3.7 15.2 - - + +
652A TYR* 4.9 0.2 - + - -
655A MET* 3.8 15.6 - - - +
659A TRP* 4.1 10.8 - + + -
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Residues in contact with GLU 614 (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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508A ARG* 4.2 11.8 + - - -
511A LEU* 4.8 0.4 - - - -
549A ALA* 2.9 39.4 + - + +
550A ARG 4.8 0.2 + - - -
588A TRP* 2.9 42.6 + - - +
610A VAL 2.9 14.4 + - - +
611A CYS* 3.1 14.4 + - - +
613A TRP* 1.3 83.4 - - + +
615A ILE* 1.3 61.7 + - - +
617A MET* 3.2 2.6 + - - +
618A HIS 3.2 4.2 + - - -
619A GLY* 2.9 28.9 + - - -
620A VAL 3.8 16.4 - - - +
621A LYS* 4.3 4.7 - - - -
622A PRO* 4.0 12.0 - - + +
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Residues in contact with ILE 615 (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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507A LEU* 4.0 23.6 - - + -
511A LEU* 3.7 14.0 - - + +
523A LEU* 3.7 48.1 - - + +
526A TYR* 4.4 9.0 - - + -
527A ALA* 4.3 15.9 - - + +
530A LEU* 4.0 27.6 - - + -
608A PHE* 6.0 0.4 - - + -
611A CYS* 2.9 21.5 + - - +
612A MET* 3.0 11.4 + - + +
614A GLU* 1.3 77.2 - - + +
616A LEU* 1.3 63.1 + - + +
618A HIS* 3.0 19.4 + - - -
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Residues in contact with LEU 616 (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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520A LEU* 3.6 31.6 - - + -
523A LEU* 4.3 20.5 - - + +
524A ILE* 4.9 1.1 - - + -
527A ALA* 5.4 4.0 - - + -
612A MET* 2.9 22.8 + - + +
615A ILE* 1.3 90.2 - - + +
617A MET* 1.3 56.0 + - - +
618A HIS* 3.3 18.0 + - - -
644A PRO* 3.9 30.5 - - + +
645A PRO* 4.4 6.5 - - - +
646A ASN 5.5 0.2 - - - -
647A CYS* 4.0 13.9 - - + +
651A LEU* 3.8 29.8 - - + -
655A MET* 3.9 8.3 - - + -
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Residues in contact with MET 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LYS* 5.7 0.5 - - - -
613A TRP* 2.8 65.9 + - + +
614A GLU 3.7 4.9 - - - +
615A ILE 3.1 0.6 - - - -
616A LEU* 1.3 75.2 - - - +
618A HIS* 1.3 77.6 + - - +
619A GLY 3.3 1.0 + - - -
620A VAL* 3.4 41.6 - - + +
624A GLN* 5.6 0.4 - - - +
642A PRO* 5.5 1.6 - - + +
644A PRO* 3.5 28.9 - - + -
645A PRO* 3.8 13.5 - - + -
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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