Contacts of the helix formed by residues 645 - 659 (chain A) in PDB entry 2MPF
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 TYR 645 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A ASP* 4.8 11.7 - - + -
551A ASN* 3.6 26.9 + - + +
552A PHE* 3.6 45.8 - + + -
555A ALA* 3.5 25.9 - - + +
641A VAL* 3.4 16.2 - - + -
642A LEU 3.1 9.9 + - - +
644A GLU* 1.3 103.1 + - + +
646A PRO* 1.4 60.5 - - - +
647A MET* 3.2 4.5 - - + -
648A MET* 2.9 26.6 + - + +
649A ARG 3.2 7.3 + - - -
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Residues in contact with PRO 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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642A LEU 4.3 0.9 - - - +
643A GLU 4.0 10.3 - - - +
644A GLU 3.6 8.1 - - - +
645A TYR* 1.4 87.6 - - - +
647A MET* 1.3 60.8 + - - +
649A ARG* 3.6 22.7 + - + +
650A ARG* 3.3 24.1 + - - +
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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
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547A ASN 5.5 2.2 - - - +
549A ASP* 4.1 23.6 - - + +
645A TYR* 3.0 2.9 + - + +
646A PRO* 1.3 77.3 - - - +
648A MET* 1.3 95.8 + - + +
650A ARG* 3.1 48.7 + - - +
651A ALA* 3.4 8.4 + - - +
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Residues in contact with MET 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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544A LEU* 5.0 11.4 - - + +
547A ASN 4.8 3.6 - - - +
548A ALA* 4.2 13.7 - - + +
549A ASP* 4.1 15.0 - - + -
552A PHE* 3.8 38.4 - - + -
642A LEU* 3.8 15.7 - - + -
645A TYR* 2.9 17.7 + - + +
647A MET* 1.3 98.0 - - + +
649A ARG* 1.3 65.2 + - - +
651A ALA* 3.3 16.9 + - + +
652A PHE* 3.3 35.6 + - + -
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Residues in contact with ARG 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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642A LEU* 3.7 42.0 - - + +
643A GLU* 4.0 29.9 + - + +
645A TYR 3.2 4.9 + - - -
646A PRO* 3.3 21.6 + - + +
648A MET* 1.3 74.2 - - - +
650A ARG* 1.3 60.7 + - - +
652A PHE* 3.2 14.2 + - - +
653A GLU* 3.2 43.0 + - - +
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Residues in contact with ARG 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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646A PRO 3.3 9.2 + - - +
647A MET* 3.1 44.2 + - - +
649A ARG* 1.3 73.3 - - - +
651A ALA* 1.3 62.7 + - - +
652A PHE 3.1 4.5 - - - -
653A GLU* 3.0 28.4 + - + +
654A THR* 3.3 14.7 + - - +
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Residues in contact with ALA 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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647A MET 3.7 9.9 - - - +
648A MET* 3.3 28.0 + - + +
650A ARG* 1.3 85.4 - - + +
652A PHE* 1.3 57.0 + - + +
654A THR* 3.3 21.6 - - - +
655A VAL* 3.4 11.6 - - - +
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Residues in contact with PHE 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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542A MET* 6.2 0.2 - - + -
544A LEU* 3.6 44.6 - - + -
552A PHE* 4.8 4.0 - + - -
611A CYS* 5.5 4.5 - - - -
612A LEU* 3.5 21.8 - - + -
613A LEU* 3.9 23.5 - - + +
638A PHE* 3.7 29.6 - + - -
642A LEU* 3.7 21.5 - - + -
648A MET* 3.3 24.6 + - + -
649A ARG 3.2 10.4 + - - +
650A ARG 3.1 0.8 - - - -
651A ALA* 1.3 76.9 - - + +
653A GLU* 1.3 59.6 + - - +
654A THR 3.2 4.9 + - - -
655A VAL* 3.2 14.4 - - + +
656A ALA* 3.1 25.6 + - - +
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Residues in contact with GLU 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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613A LEU* 3.5 23.9 - - - +
649A ARG* 3.2 34.9 + - - +
650A ARG* 3.0 16.6 + - + +
652A PHE* 1.3 73.0 - - - +
654A THR* 1.3 58.1 + - - +
656A ALA* 3.9 13.3 - - - +
657A ILE* 4.8 4.3 + - - +
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Residues in contact with THR 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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650A ARG 3.3 11.0 + - - +
651A ALA* 3.3 22.7 - - - +
653A GLU* 1.3 75.4 - - - +
655A VAL* 1.3 56.1 + - + +
656A ALA 3.2 1.3 - - - -
657A ILE* 3.0 13.1 + - - +
658A ASP* 2.8 43.7 + - - +
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Residues in contact with VAL 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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544A LEU* 5.6 9.6 - - + -
611A CYS* 5.6 3.8 - - - -
651A ALA 3.4 17.0 - - - +
652A PHE* 3.2 33.4 - - + +
654A THR* 1.3 71.9 - - + +
656A ALA* 1.3 55.0 + - - +
657A ILE 3.0 7.6 + - - -
658A ASP* 4.1 9.4 - - - +
659A ARG* 2.9 49.5 + - + +
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Residues in contact with ALA 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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611A CYS* 4.7 6.5 - - - -
613A LEU* 4.1 30.1 - - + -
652A PHE 3.1 18.9 + - - +
653A GLU 3.9 12.8 - - - +
655A VAL* 1.3 74.2 - - - +
657A ILE* 1.3 58.8 + - - +
659A ARG* 2.9 17.2 + - - +
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Residues in contact with ILE 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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653A GLU 4.8 4.7 + - - +
654A THR* 3.0 11.1 + - - +
655A VAL 3.8 0.7 - - - -
656A ALA* 1.3 78.8 - - - +
658A ASP* 1.3 66.1 + - + +
659A ARG* 3.2 9.0 + - - +
660A LEU* 3.9 13.5 + - - +
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Residues in contact with ASP 658 (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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654A THR* 2.8 34.8 + - - +
655A VAL* 4.2 3.6 - - - -
657A ILE* 1.3 76.3 - - + +
659A ARG* 1.3 58.4 + - - +
660A LEU* 3.3 2.6 + - - +
661A ASP 4.7 1.0 + - - -
662A ARG* 2.8 52.5 + - - +
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Residues in contact with ARG 659 (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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611A CYS* 4.5 24.9 - - - +
614A THR* 5.4 4.9 + - - +
655A VAL* 2.9 39.9 + - + +
656A ALA* 2.9 33.7 + - - +
657A ILE* 3.2 3.6 + - - +
658A ASP* 1.3 75.4 - - - +
660A LEU* 1.3 69.4 + - - +
661A ASP 3.4 1.3 - - - -
662A ARG* 3.1 27.5 + - + +
663A ILE* 4.4 1.2 + - - -
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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