Contacts of the strand formed by residues 427 - 433 (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 ASP 427 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387P MET* 3.8 6.1 - - - -
417P SER* 4.2 2.3 + - - -
418P TYR* 5.7 1.7 + - - +
425P CYS* 3.2 16.0 - - - +
426P GLY* 1.3 78.6 - - - +
428P VAL* 1.3 67.4 + - - +
429P ASP* 3.3 3.8 + - - +
488P ARG* 3.2 39.8 + - + +
490P ASP* 4.0 5.2 - - - +
704P D3T 2.7 11.0 + - - -
804P MG 2.1 33.7 - - - -
810P NA 2.4 28.3 - - - -
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Residues in contact with VAL 428 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387P MET* 3.5 25.4 - - + -
392P ALA* 3.6 39.5 - - + +
395P ILE* 3.8 14.4 - - + -
396P GLU* 4.7 3.4 - - - +
414P ALA* 4.8 11.0 - - + -
418P TYR* 6.0 4.3 - - + -
427P ASP* 1.3 74.9 - - - +
429P ASP* 1.3 64.4 + - - +
430P VAL* 3.8 21.1 - - + -
488P ARG 3.2 4.8 + - - +
489P LEU* 3.4 15.1 - - + +
490P ASP* 2.8 27.8 + - - +
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Residues in contact with ASP 429 (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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413P VAL 3.5 1.2 - - - +
414P ALA* 3.2 4.5 - - - +
415P CYS* 2.7 50.2 + - + +
416P GLY* 3.5 10.4 - - - +
418P TYR* 6.0 0.2 - - - +
427P ASP* 3.5 1.9 - - - +
428P VAL* 1.3 71.6 - - - +
430P VAL* 1.3 62.9 + - - +
490P ASP* 3.2 18.3 - - + +
506P PHE* 4.8 8.5 - - + +
704P D3T 3.2 13.1 + - - +
804P MG 2.0 30.0 - - - -
810P NA 2.5 25.6 - - - -
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Residues in contact with VAL 430 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396P GLU* 4.5 24.5 - - + +
399P VAL* 4.6 16.4 - - + -
412P CYS* 4.5 12.8 - - + -
413P VAL 3.7 5.8 - - - +
414P ALA* 5.2 0.9 - - - -
428P VAL* 3.8 21.1 - - + -
429P ASP* 1.3 74.1 - - - +
431P LEU* 1.3 62.5 + - - +
432P ILE* 4.1 23.5 + - + -
489P LEU* 4.1 10.5 - - + -
490P ASP 2.7 20.3 + - - +
491P ILE* 3.3 7.0 - - + +
492P ILE* 3.1 26.7 + - - +
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Residues in contact with LEU 431 (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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411P LEU 3.5 1.7 - - - +
412P CYS* 3.3 5.5 - - - -
413P VAL* 2.8 43.5 + - + +
415P CYS* 3.9 16.2 - - - -
429P ASP 3.8 0.2 + - - -
430P VAL* 1.3 73.4 - - - +
432P ILE* 1.3 78.9 + - - +
492P ILE* 3.3 22.4 - - + -
494P VAL* 3.6 19.5 - - + -
499P PHE* 4.0 16.6 - - + -
502P ALA* 4.0 5.6 - - + +
503P LEU* 3.4 45.3 - - + +
506P PHE* 4.5 2.0 - - + -
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Residues in contact with ILE 432 (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* 4.3 7.4 - - + -
403P ALA* 4.3 4.7 - - + -
410P LEU* 4.5 15.0 - - + -
411P LEU 3.4 6.3 - - - +
412P CYS* 3.8 23.8 - - - -
430P VAL* 4.1 6.7 - - + -
431P LEU* 1.3 82.8 - - - +
433P THR* 1.3 73.8 + - - +
443P ILE* 4.2 18.4 - - + -
447P LEU* 3.5 32.1 - - + -
491P ILE* 3.9 18.2 - - + -
492P ILE 2.9 10.6 + - - +
493P VAL* 3.3 13.1 - - + -
494P VAL 3.0 24.4 + - - -
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Residues in contact with THR 433 (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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410P LEU* 3.6 8.8 - - - +
411P LEU* 3.0 38.8 + - + +
432P ILE* 1.3 80.2 - - - +
434P HIS* 1.3 71.9 + - - +
440P HIS* 4.3 8.5 - - - -
494P VAL* 2.7 29.0 + - - +
495P PRO 3.7 0.3 + - - -
496P TYR* 3.4 21.7 + - + -
499P PHE* 3.3 39.3 - - + -
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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