Contacts of the helix formed by residues 610 - 618 (chain A) in PDB entry 3M6L
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 LYS 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A GLU* 3.6 24.1 + - + +
609A GLY* 1.3 71.5 - - - +
611A ASP* 1.3 69.3 + - - +
612A LYS* 4.5 3.6 - - + +
613A ASP* 2.9 39.8 + - - +
614A VAL* 2.9 11.3 + - - +
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Residues in contact with ASP 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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444A ILE 5.0 0.4 - - - +
445A GLY* 3.4 31.3 - - - +
446A VAL 5.3 0.2 - - - +
447A GLY* 4.0 11.4 - - - +
448A GLU* 4.5 3.2 + - - +
499A ARG* 5.6 4.9 + - - +
500A GLN* 4.3 16.3 - - + +
609A GLY 3.3 3.2 + - - -
610A LYS* 1.3 72.0 - - - +
612A LYS* 1.3 94.7 + - - +
614A VAL* 3.2 4.3 + - - +
615A PHE* 3.0 34.6 + - + -
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Residues in contact with LYS 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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610A LYS* 3.2 2.8 - - + -
611A ASP* 1.3 96.2 + - - +
613A ASP* 1.3 64.4 + - - +
615A PHE* 3.6 6.5 + - + +
616A GLU* 3.1 24.8 + - - +
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Residues in contact with ASP 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* 5.3 2.0 - - - -
610A LYS* 2.9 40.7 + - + +
612A LYS* 1.3 76.3 - - - +
614A VAL* 1.4 58.5 + - + +
616A GLU* 3.5 6.8 + - - +
617A ARG* 3.0 28.1 + - - +
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Residues in contact with VAL 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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444A ILE* 3.7 32.1 - - + +
447A GLY* 4.7 3.6 - - - -
607A GLU* 3.6 30.7 - - + +
608A SER 4.6 0.2 - - - -
609A GLY* 3.6 21.1 - - - +
610A LYS 2.9 19.0 + - - +
611A ASP 3.8 3.6 - - - +
613A ASP* 1.4 73.8 - - + +
615A PHE* 1.3 66.8 + - - +
617A ARG* 3.2 6.6 + - - +
618A PHE* 3.1 46.5 + - + -
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Residues in contact with PHE 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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443A SER* 3.8 3.8 - - - -
444A ILE* 3.8 27.8 - - + -
445A GLY* 3.4 33.4 - - - -
500A GLN* 3.8 21.5 - - + -
535A SER* 4.7 1.3 - - - -
536A GLU* 4.0 20.6 - - - -
586A ALA* 4.2 8.1 - - + -
611A ASP* 3.0 31.9 + - + +
612A LYS* 4.0 5.6 - - - +
614A VAL* 1.3 76.9 - - - +
616A GLU* 1.3 61.6 + - - +
618A PHE 3.3 2.4 + - - -
619A GLY 3.1 4.7 + - - -
620A PHE* 2.9 52.6 + + + +
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Residues in contact with GLU 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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612A LYS 3.1 19.1 + - - +
613A ASP* 3.7 6.7 - - - +
615A PHE* 1.3 71.4 - - - +
617A ARG* 1.3 66.8 + - - +
619A GLY* 3.0 8.0 + - - -
620A PHE 4.8 4.1 + - - +
621A SER* 3.5 23.7 + - - -
624A LYS* 3.0 53.3 + - - +
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Residues in contact with ARG 617 (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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604A SER* 4.5 6.5 + - - -
607A GLU* 4.6 21.3 + - + +
613A ASP 3.0 17.1 + - - +
614A VAL* 3.2 6.9 + - - +
616A GLU* 1.3 78.1 - - - +
618A PHE* 1.3 103.5 + - + +
619A GLY* 3.4 2.3 + - - -
624A LYS* 4.9 3.5 + - - +
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Residues in contact with PHE 618 (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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444A ILE* 3.8 21.3 - - + -
600A TYR* 4.7 3.6 + - - -
601A GLY 4.6 5.9 - - - +
602A ILE* 3.8 20.2 - - + -
604A SER* 3.3 21.5 - - - -
605A PHE 3.4 19.5 - - - -
606A GLY* 3.8 10.5 - - - -
607A GLU* 4.0 17.7 - - + -
614A VAL* 3.1 45.8 + - + +
617A ARG* 1.3 107.7 - - + +
619A GLY* 1.3 61.1 + - - +
620A PHE* 3.5 20.9 - - + -
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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