Contacts of the helix formed by residues 609 - 619 (chain B) in PDB entry 4MVY
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 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604B GLY 3.3 11.3 + - - -
605B GLU* 3.3 17.5 + - - +
608B ASP* 1.3 78.6 - - - +
610B LEU* 1.3 65.3 + - - +
613B LEU* 3.4 13.4 + - - +
669B PHE* 4.3 9.9 - - + -
672B LEU* 3.8 23.1 - - + -
673B ARG* 4.1 26.4 + - + +
676B ASN* 3.0 34.6 + - - +
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Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B GLU 3.1 9.2 + - - +
606B LEU* 3.4 13.2 - - + +
609B THR* 1.3 78.6 - - - +
611B GLY* 1.3 68.3 + - - +
613B LEU* 3.3 4.8 + - + +
614B VAL* 3.1 39.5 + - + +
669B PHE* 4.5 9.2 - - + -
672B LEU* 4.0 25.6 - - + -
706B VAL* 5.3 1.8 - - + -
709B THR* 5.3 0.4 - - - +
710B THR* 4.6 8.3 - - - +
713B LEU* 4.3 13.0 - - + -
717B LEU* 4.0 27.4 - - + -
724B ILE* 4.1 20.9 - - + -
761B LEU* 4.4 2.7 - - + -
762B PHE* 4.1 14.8 - - + -
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Residues in contact with GLY 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B LEU 2.8 17.8 + - - -
607B ALA* 3.3 8.4 + - - -
610B LEU* 1.3 73.6 - - - +
612B ASN* 1.3 62.2 + - - +
614B VAL* 3.2 4.3 + - - +
615B MET* 3.0 30.5 + - - +
761B LEU* 3.9 26.0 - - - +
762B PHE* 4.7 1.1 - - - -
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Residues in contact with ASN 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ALA 2.8 12.4 + - - +
608B ASP* 3.1 25.6 + - - +
611B GLY* 1.3 73.0 - - - +
613B LEU* 1.3 55.9 + - - +
615B MET* 3.4 7.2 + - - +
616B ARG* 3.0 46.9 + - - +
676B ASN* 3.4 20.4 + - - -
804B GOL 3.7 33.2 + - - -
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Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B THR 3.4 15.7 + - - +
610B LEU* 3.3 4.0 + - + +
611B GLY 3.3 0.2 - - - -
612B ASN* 1.3 77.1 - - - +
614B VAL* 1.3 64.6 + - - +
616B ARG* 3.2 7.7 + - + +
617B CYS* 3.1 24.0 + - - -
672B LEU* 3.9 21.8 - - + +
675B ILE* 3.6 32.1 - - + -
676B ASN* 3.9 25.4 - - - +
679B VAL* 4.0 13.5 - - + -
702B THR* 3.7 24.0 - - + -
706B VAL* 3.7 20.6 - - + -
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Residues in contact with VAL 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B LEU* 3.1 33.4 + - + +
611B GLY* 3.2 8.9 + - - +
613B LEU* 1.3 75.1 - - - +
615B MET* 1.3 57.7 + - - +
617B CYS* 3.5 7.4 - - - -
618B THR* 2.7 35.0 + - - +
706B VAL* 4.0 18.6 - - + -
724B ILE* 4.1 26.2 - - + -
727B MET* 3.7 30.3 - - + -
728B LEU* 4.6 9.0 - - + -
761B LEU* 4.5 4.9 - - + -
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Residues in contact with MET 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611B GLY 3.0 20.3 + - - +
612B ASN* 3.7 9.4 - - - +
614B VAL* 1.3 77.8 - - - +
616B ARG* 1.3 60.7 + - + +
618B THR* 3.2 7.6 + - - -
619B SER* 2.8 33.9 + - - -
727B MET* 4.7 20.4 - - + +
759B GLU* 3.0 35.4 - - + +
760B VAL* 3.9 11.2 - - + -
761B LEU* 4.3 9.2 - - + +
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Residues in contact with ARG 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B ASN* 3.0 39.4 + - - +
613B LEU* 3.2 10.9 + - + +
615B MET* 1.3 78.9 - - + +
617B CYS* 1.3 60.2 + - - +
618B THR 3.4 0.3 + - - -
619B SER* 3.5 10.1 + - - -
622B ILE* 3.6 36.3 - - + +
676B ASN* 3.4 23.8 + - - +
679B VAL* 3.5 33.7 - - + +
680B THR* 3.6 23.8 + - - +
685B TRP* 3.6 24.0 - - + -
804B GOL 2.9 39.8 + - - +
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Residues in contact with CYS 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B LEU 3.1 19.1 + - - +
614B VAL* 3.5 15.3 - - - -
616B ARG* 1.3 76.5 - - - +
618B THR* 1.3 61.3 + - - +
619B SER 3.6 0.2 - - - -
622B ILE* 5.5 0.2 - - - -
623B ASN* 3.4 27.1 + - - +
699B LEU* 3.9 11.4 - - + +
702B THR* 3.8 24.2 - - + -
703B LEU* 3.7 32.0 - - + +
706B VAL* 4.1 17.7 - - - -
728B LEU* 4.3 4.9 - - - -
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Residues in contact with THR 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B VAL* 2.7 24.3 + - + +
615B MET* 3.2 13.5 + - - -
616B ARG 3.2 0.2 - - - -
617B CYS* 1.3 81.2 - - - +
619B SER* 1.3 65.0 + - - +
620B ALA* 3.4 2.6 + - - -
623B ASN* 4.6 1.2 - - - +
727B MET* 4.2 24.6 - - + +
728B LEU* 3.5 29.8 - - + -
752B LEU* 3.9 25.5 - - + +
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Residues in contact with SER 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B MET 2.8 17.9 + - - -
616B ARG* 3.5 12.4 + - - -
618B THR* 1.3 78.5 - - - +
620B ALA* 1.3 56.4 + - - +
621B LYS* 3.2 27.4 + - - +
622B ILE* 3.1 11.8 + - - +
623B ASN* 2.7 34.1 + - - +
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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
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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