Contacts of the strand formed by residues 490 - 494 (chain B) in PDB entry 5NV6
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 490 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B LEU* 3.5 7.5 - - - +
410B LEU 3.1 6.8 + - - -
411B THR* 3.4 5.0 - - - +
412B LEU 3.0 24.3 + - - -
443B GLN* 3.2 25.9 + - - +
444B LEU 3.4 26.9 + - - +
445B ALA* 5.3 0.2 - - - -
483B ASP* 4.0 17.3 - - + +
484B LYS 3.4 13.5 - - - +
485B ARG* 3.5 15.4 + - + +
489B GLY* 1.4 71.4 - - - -
491B LEU* 1.4 61.3 + - - +
492B PHE* 3.9 16.4 - - + -
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Residues in contact with LEU 491 (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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379B LEU* 3.9 5.6 - - + +
382B LEU* 4.1 22.0 - - + +
383B ALA* 4.0 19.7 - - + -
386B SER* 4.2 4.7 - - - +
388B VAL* 3.9 23.3 - - + -
412B LEU* 3.9 19.5 - - + +
414B ALA* 3.8 28.9 - - + -
483B ASP* 3.7 9.4 - - - +
484B LYS* 3.0 44.1 + - + +
490B THR* 1.4 71.6 - - - +
492B PHE* 1.3 62.7 + - - +
493B THR* 3.9 16.2 + - - +
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Residues in contact with PHE 492 (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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411B THR* 3.7 21.1 - - + -
412B LEU 2.7 16.2 + - - +
413B LEU* 3.7 19.7 - - + -
414B ALA* 2.9 28.6 + - - +
444B LEU* 3.7 25.4 - - + -
445B ALA 4.0 3.8 - - - -
446B SER* 3.4 29.6 - - - -
449B LEU* 3.9 23.8 - - + -
455B LEU* 5.5 2.9 - - + -
474B ILE* 3.8 14.1 - - + -
479B ILE* 4.0 14.4 - - + -
483B ASP* 3.8 16.2 - - - +
490B THR* 3.9 4.5 + - + -
491B LEU* 1.3 79.3 - - - +
493B THR* 1.3 62.2 + - - +
494B MET* 3.4 11.6 + - - +
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Residues in contact with THR 493 (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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386B SER* 5.7 1.4 - - - -
387B ASP* 5.0 2.5 - - - +
388B VAL* 3.7 21.0 - - + +
414B ALA 3.5 4.3 - - - -
416B LEU* 3.7 33.4 - - + -
479B ILE* 3.4 8.9 - - - +
480B ALA* 2.8 28.4 + - + -
481B ALA* 3.7 37.7 + - + +
482B HIS 4.8 5.5 + - - -
491B LEU* 3.9 16.5 + - - +
492B PHE* 1.3 68.9 - - - +
494B MET* 1.3 55.5 + - - +
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Residues in contact with MET 494 (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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413B LEU* 3.9 28.7 - - + -
414B ALA 2.8 9.6 + - - +
415B PRO* 4.0 5.6 - - + -
416B LEU* 3.1 32.6 + - - +
438B HIS* 5.8 1.1 - - + -
474B ILE* 3.8 22.7 - - + -
477B SER* 3.1 47.8 - - - +
478B CYS 3.4 22.7 - - - -
479B ILE* 3.8 16.6 - - + +
480B ALA* 3.8 3.4 - - - -
492B PHE* 3.5 25.6 - - - +
493B THR* 1.3 77.5 - - - +
495B ASP* 1.4 56.0 + - - +
496B ARG 3.5 7.0 - - - +
498B LEU* 6.5 0.2 - - + -
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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