Contacts of the strand formed by residues 471 - 477 (chain P) in PDB entry 3HX0
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 GLN 471 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440P HIS* 4.9 0.9 - - - +
441P ARG* 5.4 1.6 - - - -
442P GLY* 4.8 11.6 + - - +
444P PHE* 3.0 59.6 + - + +
445P SER* 5.4 0.8 - - - +
464P GLN* 5.1 2.2 + - - -
465P GLU 3.4 5.2 - - - -
466P GLU* 3.7 20.4 + - - +
469P GLN 5.0 3.4 - - - +
470P GLN* 1.3 80.4 - - - +
472P LYS* 1.3 60.7 + - - +
491P ILE 3.7 1.4 - - - +
492P ILE* 3.0 6.0 - - - -
493P VAL* 2.9 42.2 + - + +
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Residues in contact with LYS 472 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444P PHE* 3.9 2.9 - - - -
462P VAL* 4.2 1.4 - - - +
464P GLN* 3.7 6.1 - - - -
465P GLU* 3.1 53.7 + - + +
467P ASN* 5.8 3.4 - - + -
470P GLN* 4.2 1.3 - - + -
471P GLN* 1.3 74.6 - - - +
473P TYR* 1.3 61.5 + - - +
474P LEU* 5.4 6.3 - - + -
491P ILE 3.4 3.6 - - - -
492P ILE* 3.4 19.5 - - + -
506P PHE* 5.9 2.0 - - + -
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Residues in contact with TYR 473 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444P PHE* 4.0 15.7 - - + -
448P LEU* 3.7 25.4 - - + -
457P LEU* 3.8 31.1 - - + +
459P ASP 3.1 23.7 + - - -
460P ASP* 3.1 29.3 + - - -
462P VAL 3.5 3.8 - - - -
463P SER* 3.4 21.8 - - - -
472P LYS* 1.3 75.1 - - - +
474P LEU* 1.3 82.3 + - - +
475P GLY* 3.4 19.3 - - - -
489P LEU* 4.8 5.6 - - + -
490P ASP* 3.5 3.5 - - - -
491P ILE* 2.8 51.0 + - + +
492P ILE* 5.3 0.5 - - - +
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Residues in contact with LEU 474 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342P TRP* 4.4 15.7 - - + -
460P ASP 3.8 0.2 - - - -
461P LEU* 2.7 25.2 + - + +
462P VAL* 2.7 67.2 + - + -
465P GLU* 5.0 9.4 - - - +
472P LYS* 5.4 4.9 - - + -
473P TYR* 1.3 86.7 - - - +
475P GLY* 1.3 52.4 + - - +
488P ARG* 6.4 0.4 - - + -
489P LEU 3.9 2.0 - - - -
490P ASP* 3.2 35.2 - - - +
6R T 4.8 12.8 - - + +
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Residues in contact with GLY 475 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459P ASP 3.5 4.9 - - - -
461P LEU* 3.8 9.1 - - - +
473P TYR* 3.4 25.2 - - - -
474P LEU* 1.3 75.8 - - - +
476P VAL* 1.3 65.9 + - - +
488P ARG* 3.7 6.8 - - - +
489P LEU* 2.8 33.5 + - - +
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Residues in contact with VAL 476 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375P ILE* 4.1 20.6 - - + -
379P HIS* 3.6 20.0 - - + +
383P PHE* 3.4 26.5 - - + -
457P LEU* 3.7 6.8 - - - +
458P THR* 2.9 38.3 + - - +
459P ASP* 3.0 13.9 + - + +
461P LEU* 4.5 9.0 - - + -
475P GLY* 1.3 78.2 - - - +
477P CYS* 1.3 71.8 + - - +
486P HIS* 4.1 6.1 - - + -
487P ARG 3.2 16.6 - - - +
488P ARG* 4.9 0.4 - - - -
489P LEU* 5.1 0.7 - - - -
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Residues in contact with CYS 477 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395P ILE* 4.0 26.2 - - - -
456P PHE* 3.3 51.1 - - + +
457P LEU* 4.4 5.2 - - + -
458P THR* 4.0 4.9 - - - -
476P VAL* 1.3 77.0 - - - +
478P ARG* 1.3 70.3 + - - +
486P HIS* 3.5 5.4 - - - -
487P ARG* 2.8 35.6 + - - -
488P ARG 5.2 0.2 - - - -
489P LEU* 4.1 13.0 - - + -
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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