Contacts of the helix formed by residues 663 - 675 (chain C) in PDB entry 5MYV
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 PRO 663 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661C GLY 4.0 4.0 - - - +
662C TRP* 1.4 89.1 - - + +
664C HIS* 1.3 64.9 + - + +
665C GLU* 3.2 4.6 + - + +
666C ASP* 3.3 30.2 + - + +
667C ALA* 3.1 21.3 + - - +
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Residues in contact with HIS 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C PHE* 3.5 32.5 - + + -
657C VAL* 3.8 28.3 - - + +
662C TRP 4.4 2.2 - - - -
663C PRO* 1.3 71.8 - - + +
665C GLU* 1.3 61.5 + - + +
667C ALA* 4.5 0.9 - - - -
668C ALA* 3.1 26.0 + - - +
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Residues in contact with GLU 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C PRO* 3.2 4.6 - - + +
664C HIS* 1.3 78.5 - - + +
666C ASP* 1.3 72.3 + - - +
668C ALA* 3.3 7.0 + - - +
669C GLN* 3.1 38.5 + - - +
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Residues in contact with ASP 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C VAL* 6.5 0.4 - - + -
662C TRP* 3.8 19.1 - - + -
663C PRO* 3.3 30.1 + - + +
665C GLU* 1.3 83.0 - - - +
667C ALA* 1.3 61.4 + - - +
669C GLN* 3.6 13.2 + - - +
670C PHE* 3.2 24.8 + - - +
696C TRP* 5.1 1.4 + - - -
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Residues in contact with ALA 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C PHE* 3.7 16.4 - - + -
656C LEU* 3.9 18.5 - - + +
657C VAL* 3.7 16.8 - - + -
662C TRP* 3.9 12.3 - - + -
663C PRO 3.1 16.2 + - - +
664C HIS 3.7 4.3 - - - +
666C ASP* 1.3 75.6 - - - +
668C ALA* 1.3 56.4 + - - +
670C PHE* 3.5 1.6 + - - +
671C THR* 2.8 37.9 + - - -
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Residues in contact with ALA 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C PHE* 3.8 15.7 - - + -
664C HIS 3.1 18.3 + - - +
665C GLU* 3.8 8.3 - - - +
667C ALA* 1.3 77.4 - - - +
669C GLN* 1.3 57.4 + - + +
671C THR* 3.3 3.8 + - - -
672C ASP* 2.8 41.8 + - - +
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Residues in contact with GLN 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LYS* 5.8 1.6 + - - -
665C GLU* 3.1 28.9 + - - +
666C ASP* 4.1 14.7 - - - +
668C ALA* 1.3 77.6 - - + +
670C PHE* 1.3 60.9 + - - +
672C ASP* 3.6 9.7 + - - +
673C PHE* 3.3 16.1 + - - +
694C HIS* 4.5 1.9 - - - -
696C TRP* 3.6 26.6 - - + +
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Residues in contact with PHE 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C ALA* 3.8 28.3 - - + -
586C PHE* 4.3 8.1 - + - -
589C ALA* 4.0 20.2 - - + -
656C LEU* 3.8 20.9 - - + -
662C TRP* 3.7 23.3 - + + -
666C ASP 3.2 16.5 + - - +
667C ALA 3.8 3.1 - - - +
669C GLN* 1.3 74.8 - - - +
671C THR* 1.3 65.3 + - - +
673C PHE* 3.2 5.1 + + - +
674C LEU* 3.0 59.0 + - + +
696C TRP* 3.2 50.6 - + - +
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Residues in contact with THR 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C LEU* 4.1 14.5 - - + +
653C PHE* 3.6 37.4 + - + +
656C LEU* 3.6 9.3 - - - +
667C ALA 2.8 22.1 + - - -
668C ALA* 3.7 6.7 - - - -
670C PHE* 1.3 77.2 - - - +
672C ASP* 1.3 64.5 + - - +
673C PHE 3.3 0.2 + - - -
674C LEU 3.3 0.3 + - - -
675C ILE* 3.1 42.2 + - + +
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Residues in contact with ASP 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C ALA* 2.8 32.3 + - - +
669C GLN* 3.7 9.9 - - - +
670C PHE 3.3 0.2 - - - -
671C THR* 1.3 75.4 - - - +
673C PHE* 1.3 58.2 + - - +
675C ILE* 5.3 1.3 - - - -
676C PRO* 3.1 22.6 - - - +
694C HIS* 3.1 21.2 + - + +
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Residues in contact with PHE 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ILE* 4.0 24.9 - - + -
209C LEU* 4.1 4.5 - - + -
585C ALA* 4.9 3.4 - - + -
669C GLN 3.3 10.8 + - - +
670C PHE* 3.2 9.3 + + - +
671C THR 3.2 0.4 - - - -
672C ASP* 1.3 79.4 - - - +
674C LEU* 1.3 81.0 + - + +
676C PRO* 3.5 9.5 - - - +
677C MET* 3.5 40.1 - - + +
691C CYS* 3.9 15.2 - - + -
694C HIS* 3.6 21.0 + + + -
696C TRP* 3.6 51.1 - + + -
697C LEU* 3.8 24.0 - - + -
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Residues in contact with LEU 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C ALA* 3.8 32.8 - - + +
585C ALA* 4.2 5.2 - - + -
586C PHE* 4.6 10.3 - - + -
594C LEU* 6.0 1.3 - - + -
652C LEU* 3.7 33.0 - - + -
670C PHE* 3.0 55.1 + - + +
671C THR 4.2 0.2 - - - +
673C PHE* 1.3 92.4 - - + +
675C ILE* 1.3 61.2 + - - +
677C MET* 2.8 24.5 + - - +
678C LEU* 3.0 20.5 + - + +
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Residues in contact with ILE 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU 5.7 0.9 - - - +
617C LEU* 3.9 28.3 - - + -
652C LEU* 4.3 17.7 - - + -
671C THR* 3.1 34.4 + - + +
672C ASP* 5.0 1.8 - - - +
674C LEU* 1.3 74.8 - - - +
676C PRO* 1.3 70.5 - - + +
678C LEU* 3.1 15.4 + - + +
679C GLU* 3.3 23.6 + - - +
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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