Contacts of the strand formed by residues 487 - 493 (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 ARG 487 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382P ASP 3.5 11.8 + - - -
383P PHE* 4.4 2.3 + - - +
385P GLU* 2.5 36.8 + - - +
386P ARG 3.4 17.2 + - - -
387P MET* 3.1 47.4 - - + +
388P PRO* 4.7 2.8 - - - +
391P GLU* 3.1 26.0 + - - +
395P ILE* 4.0 13.5 - - + -
426P GLY 4.8 6.2 + - - -
476P VAL* 3.2 5.2 - - - +
477P CYS* 2.8 43.2 + - - +
478P ARG* 5.7 0.7 - - - -
485P ARG* 3.1 40.1 + - - +
486P HIS* 1.3 77.0 + - - +
488P ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 488 (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* 3.4 37.3 - - - +
383P PHE* 3.7 51.3 + - + +
387P MET* 4.2 3.3 - - - +
395P ILE* 5.7 0.2 - - - +
426P GLY* 3.0 29.3 + - - -
427P ASP* 3.2 23.6 - - + +
428P VAL* 3.2 23.4 + - - +
461P LEU* 4.5 11.4 - - + +
474P LEU* 6.5 0.2 - - + -
475P GLY 3.7 10.5 - - - +
477P CYS* 5.2 0.8 - - - -
487P ARG* 1.3 74.8 - - - +
489P LEU* 1.3 66.8 + - - +
490P ASP* 4.5 5.2 - - - +
704P D3T 5.5 0.2 + - - -
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Residues in contact with LEU 489 (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* 3.8 13.0 - - + -
399P VAL* 3.9 15.3 - - + -
427P ASP* 5.5 0.2 - - - -
428P VAL* 3.4 35.4 - - + +
430P VAL* 4.1 12.6 - - + -
456P PHE* 3.9 18.4 - - + -
457P LEU* 4.4 11.2 - - + -
473P TYR* 3.9 4.8 - - + +
474P LEU* 3.9 0.3 - - - -
475P GLY 2.8 36.0 + - - +
476P VAL 5.2 0.2 - - - -
477P CYS* 4.1 13.9 - - + -
487P ARG 3.8 0.6 + - - -
488P ARG* 1.3 74.6 - - - +
490P ASP* 1.3 71.8 + - - +
491P ILE* 3.7 28.3 - - + -
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Residues in contact with ASP 490 (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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427P ASP* 4.0 5.0 - - - +
428P VAL 2.8 10.5 + - - +
429P ASP* 3.2 19.4 - - + +
430P VAL* 2.7 33.1 + - - +
473P TYR 3.5 3.6 - - - +
474P LEU* 3.2 29.5 - - - +
488P ARG* 4.5 8.1 - - - +
489P LEU* 1.3 92.3 - - - +
491P ILE* 1.3 64.0 + - - +
492P ILE* 5.2 5.4 - - + +
506P PHE* 6.2 0.3 - - - -
704P D3T 6.1 0.7 - - - -
810P NA 2.7 25.8 - - - -
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Residues in contact with ILE 491 (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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399P VAL* 3.9 20.4 - - + -
430P VAL* 3.3 9.0 - - + +
432P ILE* 3.9 27.6 - - + -
444P PHE* 4.1 10.9 - - + -
447P LEU* 4.5 7.2 - - + -
448P LEU* 4.2 8.5 - - + -
451P LEU* 4.1 13.2 - - + -
457P LEU* 5.4 0.2 - - + -
471P GLN 3.7 1.0 - - - +
472P LYS* 3.4 0.9 - - - -
473P TYR* 2.8 59.6 + - + +
489P LEU* 3.7 28.5 - - + -
490P ASP* 1.3 80.5 - - - +
492P ILE* 1.3 67.5 + - - +
493P VAL* 5.3 1.1 - - + -
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Residues in contact with ILE 492 (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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430P VAL 3.1 11.8 + - - +
431P LEU* 3.3 28.0 - - + -
432P ILE* 2.9 22.0 + - - +
470P GLN* 5.2 2.5 - - + +
471P GLN 3.0 7.4 - - - +
472P LYS* 3.4 25.1 - - + -
473P TYR 4.4 1.1 - - - +
474P LEU* 6.3 1.1 - - + -
490P ASP* 5.2 5.2 - - + +
491P ILE* 1.3 85.1 - - - +
493P VAL* 1.3 62.9 + - - +
494P VAL* 3.4 22.9 - - + -
506P PHE* 3.5 39.7 - - + -
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Residues in contact with VAL 493 (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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432P ILE* 3.3 20.0 - - + +
440P HIS* 3.8 42.2 - - + +
443P ILE* 3.5 25.8 - - + -
444P PHE* 3.8 22.2 - - + -
447P LEU* 6.0 0.4 - - + -
469P GLN 4.7 0.3 - - - +
470P GLN* 3.5 4.0 - - - +
471P GLN* 2.9 43.6 + - - +
491P ILE* 5.3 1.6 - - + -
492P ILE* 1.3 73.0 - - - +
494P VAL* 1.3 73.8 + - - +
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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