Contacts of the strand formed by residues 458 - 464 (chain A) in PDB entry 6N8Q
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 ARG 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LEU 4.7 8.1 - - - +
377A PRO* 3.8 27.8 - - - +
401A TRP* 5.8 0.2 - - - -
405A ILE* 4.4 19.8 - - - +
450A TRP* 3.4 2.8 - - - -
451A ASP* 2.8 54.9 + - + +
456A CYS* 3.2 9.1 + - + +
457A LEU* 1.3 74.6 - - - +
459A LEU* 1.3 71.8 + - - +
460A LEU* 3.5 29.9 + - - +
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Residues in contact with LEU 459 (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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375A GLN* 5.2 7.4 + - - -
376A LEU 5.1 4.9 + - - +
412A ASN* 5.8 3.0 + - - +
448A ARG* 3.8 32.1 - - + +
449A PHE 3.3 17.5 - - - +
450A TRP* 3.6 26.0 - - + -
458A ARG* 1.3 85.6 + - - +
460A LEU* 1.3 61.2 + - - +
461A TYR 3.4 22.0 - - - +
462A LYS* 4.9 13.0 - - + -
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TRP* 3.7 34.8 - - + -
404A ILE* 3.9 8.2 - - + +
405A ILE* 3.7 30.7 - - + +
408A GLY* 3.2 23.0 - - - -
412A ASN* 5.1 3.9 + - - -
437A LEU* 3.9 13.7 - - + -
449A PHE* 2.8 16.1 + - + +
450A TRP 4.2 0.2 - - - -
451A ASP* 3.7 22.7 - - + +
458A ARG* 3.5 42.4 - - - +
459A LEU* 1.3 76.2 - - - +
461A TYR* 1.3 59.5 + - + +
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Residues in contact with TYR 461 (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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404A ILE* 3.7 24.5 - - + +
407A ALA* 4.2 5.2 - - + -
408A GLY* 4.1 11.4 - - - -
411A GLN* 3.1 26.9 - - - -
449A PHE* 2.8 54.0 + + + +
459A LEU* 3.4 10.0 - - - +
460A LEU* 1.3 81.0 - - - +
462A LYS* 1.3 71.2 + - - +
463A LEU* 3.6 32.6 - - + +
574A GLU* 6.2 0.2 - - + -
575A PRO 4.1 7.5 + - - -
576A GLY* 3.6 17.8 - - - -
577A PHE* 3.1 43.0 + + - -
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Residues in contact with LYS 462 (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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411A GLN* 3.0 36.8 + - - +
446A THR* 3.9 25.0 - - + +
447A VAL 3.6 3.1 - - - +
448A ARG* 3.7 47.7 - - + +
459A LEU* 4.9 11.0 - - + +
461A TYR* 1.3 84.8 + - - +
463A LEU* 1.3 65.2 - - - +
464A SER* 4.3 3.7 + - - +
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Residues in contact with LEU 463 (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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446A THR* 3.1 10.3 - - - -
447A VAL* 2.8 45.2 + - + +
449A PHE* 4.8 3.1 - - + -
461A TYR* 3.6 22.8 - - + +
462A LYS* 1.3 74.6 - - - +
464A SER* 1.3 91.7 + - - +
465A THR* 3.7 17.7 - - + -
519A LEU* 3.5 23.3 - - + -
521A VAL* 5.6 1.3 - - + -
531A LEU* 3.6 16.8 - - + -
577A PHE* 3.5 34.1 - - + +
579A PRO* 5.9 0.9 - - + -
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Residues in contact with SER 464 (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 ASP 5.3 0.3 + - - -
445A GLY 4.1 2.8 - - - -
446A THR* 3.9 16.2 - - - +
462A LYS* 4.3 5.5 + - - -
463A LEU* 1.3 85.5 - - - +
465A THR* 1.3 60.2 + - - +
466A VAL* 3.4 24.3 - - - +
467A ARG* 4.5 16.1 - - - +
468A VAL* 5.7 0.9 - - - +
573A PHE* 5.8 2.6 - - - -
579A PRO* 6.1 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