Contacts of the helix formed by residues 549 - 563 (chain A) in PDB entry 4MS0
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A PHE* 1.3 76.0 - - - +
550A ASP* 1.3 64.2 + - - +
551A LEU* 3.5 9.6 + - - +
552A GLU* 3.0 39.9 + - - +
553A ARG* 3.0 23.1 + - - +
662A ARG* 4.5 6.7 - - - +
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Residues in contact with ASP 550 (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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498A CYS* 4.9 4.3 - - + +
502A CYS* 5.5 1.4 - - - -
545A HIS* 5.2 0.3 + - - -
549A THR* 1.3 73.2 - - - +
551A LEU* 1.3 60.5 + - - +
553A ARG* 2.5 39.5 + - - +
554A LYS* 3.2 25.5 + - - +
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Residues in contact with LEU 551 (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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549A THR* 3.1 9.1 + - - +
550A ASP* 1.3 79.0 - - - +
552A GLU* 1.3 65.1 + - - +
554A LYS* 4.1 4.1 - - + +
555A GLY* 3.0 22.2 + - - -
611A PHE* 5.8 0.2 - - + -
614A LEU* 3.9 35.4 - - + -
618A GLU* 3.7 37.2 - - + +
621A GLN* 3.8 29.2 - - + +
622A VAL* 4.0 19.2 - - + +
625A ILE* 4.1 10.1 - - + +
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Residues in contact with GLU 552 (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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548A PHE* 3.4 14.3 - - + -
549A THR* 3.0 36.2 + - - +
551A LEU* 1.3 76.1 - - - +
553A ARG* 1.3 57.5 + - - +
555A GLY 3.8 0.2 - - - -
556A LEU* 2.9 42.6 + - + +
625A ILE* 4.0 23.6 - - + +
659A GLN* 5.0 4.9 + - - +
662A ARG* 2.5 48.0 + - - +
666A ILE* 3.8 23.2 - - + +
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Residues in contact with ARG 553 (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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497A SER* 3.3 37.8 + - - +
498A CYS* 4.0 14.8 + - - +
541A LEU* 3.8 33.0 - - + -
545A HIS* 3.1 45.9 + - - +
546A THR* 5.7 0.2 - - - +
548A PHE* 3.0 28.5 + - + -
549A THR 3.0 14.0 + - - +
550A ASP* 2.5 38.7 + - - +
552A GLU* 1.3 72.4 - - - +
554A LYS* 1.3 68.6 + - - +
556A LEU* 3.4 1.0 + - - +
557A LEU* 3.1 29.1 + - - +
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Residues in contact with LYS 554 (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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498A CYS* 3.7 11.0 - - - -
502A CYS* 4.0 13.9 - - - -
503A PHE* 3.6 28.0 - - + -
550A ASP 3.2 15.0 + - - +
551A LEU* 4.2 5.2 - - + +
553A ARG* 1.3 79.5 - - - +
555A GLY* 1.3 63.6 + - - +
557A LEU* 3.4 2.5 + - - +
558A ILE* 3.2 27.9 + - - +
611A PHE* 4.5 7.6 - - + -
622A VAL* 5.5 0.4 - - + -
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Residues in contact with GLY 555 (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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551A LEU 3.0 13.9 + - - -
552A GLU 3.8 0.9 - - - -
554A LYS* 1.3 75.5 - - - +
556A LEU* 1.3 58.5 + - - +
558A ILE* 3.4 1.0 + - - +
559A ALA* 2.9 28.9 + - - +
611A PHE* 4.5 1.3 - - - -
622A VAL* 3.7 25.4 - - - +
625A ILE* 4.4 4.7 - - - -
626A ILE* 3.5 16.7 - - - +
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Residues in contact with LEU 556 (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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537A MET* 4.1 21.3 - - + -
541A LEU* 4.6 8.3 - - + -
548A PHE* 5.0 1.3 - - + -
552A GLU* 2.9 30.4 + - + +
553A ARG 4.1 2.7 - - - +
554A LYS 3.3 0.2 - - - -
555A GLY* 1.3 71.3 - - - +
557A LEU* 1.3 60.3 + - - +
559A ALA* 3.7 1.6 - - + +
560A CYS* 2.9 34.0 + - - -
625A ILE* 4.0 14.1 - - + -
629A ALA* 3.6 31.0 - - + -
666A ILE* 3.8 28.9 - - + -
669A MET* 4.0 26.7 - - + -
670A MET* 4.4 7.0 - - - -
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Residues in contact with LEU 557 (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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490A PHE* 3.4 28.9 - - + -
493A MET* 4.3 5.6 - - + +
494A VAL* 4.2 19.1 - - + -
497A SER* 3.9 28.7 - - - +
498A CYS* 4.1 11.4 - - - -
534A ALA* 3.7 24.2 - - - +
537A MET* 4.1 7.0 - - + -
538A TYR* 3.8 24.7 - - + +
541A LEU* 4.1 6.3 - - + -
553A ARG 3.1 17.7 + - - +
554A LYS* 4.1 2.5 - - - +
556A LEU* 1.3 75.1 - - - +
558A ILE* 1.3 63.3 + - + +
560A CYS* 3.8 3.9 - - - +
561A LEU 3.1 17.5 + - - -
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Residues in contact with ILE 558 (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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490A PHE* 3.9 25.8 - - + -
494A VAL* 5.2 1.8 - - + -
503A PHE* 4.7 8.3 - - + -
508A LEU* 4.7 6.7 - - + -
511A PHE* 3.7 34.1 - - + -
554A LYS 3.2 18.2 + - - +
555A GLY 3.8 2.9 - - - +
557A LEU* 1.3 76.6 - - + +
559A ALA* 1.3 64.1 + - - +
561A LEU* 3.3 2.5 + - + +
562A CYS* 3.0 27.4 + - - -
599A THR* 4.9 3.4 - - + -
610A ILE* 3.6 25.6 - - + -
611A PHE* 4.2 14.4 - - + -
626A ILE* 4.2 17.3 - - + -
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Residues in contact with ALA 559 (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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555A GLY 2.9 19.3 + - - +
556A LEU* 3.7 6.3 - - - +
558A ILE* 1.3 76.7 - - - +
560A CYS* 1.3 58.9 + - - +
562A CYS 3.1 1.7 + - - -
563A HIS* 2.8 34.1 + - - +
626A ILE* 4.2 14.6 - - - +
629A ALA* 4.0 27.4 - - + -
630A ILE* 3.8 18.1 - - + +
670A MET* 4.2 2.9 - - + -
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Residues in contact with CYS 560 (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 ALA* 3.7 8.9 - - - +
533A VAL* 3.9 15.0 - - + +
534A ALA* 3.6 23.8 - - - +
537A MET* 3.6 25.1 - - + -
556A LEU 2.9 21.4 + - - +
557A LEU 3.8 2.5 - - - +
559A ALA* 1.3 77.2 - - - +
561A LEU* 1.3 63.4 + - - +
563A HIS* 2.9 25.9 + - - -
670A MET* 3.6 29.8 - - - -
673A CYS* 4.4 2.0 - - - -
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Residues in contact with LEU 561 (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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490A PHE* 3.8 45.3 - - + -
511A PHE* 4.9 5.8 - - + -
512A ILE* 4.4 13.5 - - + -
515A VAL* 3.9 28.5 - - + +
519A TYR* 2.8 25.1 + - - -
527A TRP* 3.7 28.3 - - + -
530A ALA* 3.4 15.0 - - - +
531A VAL* 4.0 15.7 - - + +
534A ALA* 4.3 0.8 - - + +
557A LEU 3.1 17.8 + - - +
558A ILE 3.8 4.7 - - - +
559A ALA 3.3 0.2 - - - -
560A CYS* 1.3 77.1 - - - +
562A CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 562 (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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511A PHE* 3.6 32.8 - - - -
515A VAL* 4.1 13.0 - - - -
519A TYR* 3.4 5.6 - - - -
558A ILE* 3.0 24.3 + - - +
559A ALA 3.9 1.8 - - - +
561A LEU* 1.3 79.7 - - - +
563A HIS* 1.3 63.5 + - - +
564A ASP 3.2 3.9 + - - -
565A LEU* 3.2 25.3 + - + +
595A HIS* 4.0 4.0 - - - +
599A THR* 3.2 34.2 + - + +
630A ILE* 4.2 3.7 - - + +
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Residues in contact with HIS 563 (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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519A TYR* 4.5 0.6 + - - -
529A HIS* 3.3 13.0 - + - -
530A ALA* 4.7 3.4 - - - -
533A VAL* 3.5 24.9 - - + +
559A ALA 2.8 16.6 + - - +
560A CYS* 2.9 24.8 + - - +
561A LEU 3.5 0.4 - - - -
562A CYS* 1.3 76.9 - - - +
564A ASP* 1.3 65.0 + - + +
565A LEU 3.6 0.2 - - - -
595A HIS* 3.0 23.9 - - - +
630A ILE* 3.9 21.5 - - + +
633A THR* 3.8 26.4 + - + +
670A MET* 4.4 7.9 - - + -
674A ASP* 2.9 4.1 + - + -
901A NI 2.0 45.4 - - + +
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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