Contacts of the strand formed by residues 427 - 433 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387F MET* 3.6 5.6 - - - -
417F SER* 4.4 2.1 + - - -
418F TYR* 5.7 1.2 - - - +
425F CYS* 3.5 19.4 - - - +
426F GLY* 1.3 76.3 + - - +
428F VAL* 1.3 66.2 + - - +
429F ASP* 2.8 17.9 + - - +
488F ARG* 2.9 43.9 + - - +
489F LEU 5.4 0.2 - - - -
490F ASP* 4.1 9.0 - - - +
702F D3T 2.7 15.9 + - - -
802F MG 1.9 32.3 - - - -
6H T 4.6 6.9 + - - +
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Residues in contact with VAL 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F MET* 3.8 12.3 - - + -
392F ALA* 3.9 24.7 - - + +
395F ILE* 3.5 48.0 - - + -
396F GLU* 4.3 8.5 - - + +
414F ALA* 4.7 7.2 - - + -
418F TYR* 5.9 4.7 - - + -
427F ASP* 1.3 79.8 - - - +
429F ASP* 1.3 63.0 + - - +
430F VAL* 4.1 17.9 - - + -
488F ARG 3.2 5.1 + - - +
489F LEU* 3.4 8.6 - - + +
490F ASP 3.1 23.9 + - - +
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Residues in contact with ASP 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414F ALA* 3.3 3.6 - - - +
415F CYS* 2.7 45.0 + - - +
416F GLY* 3.5 6.7 - - - +
417F SER 4.5 0.2 + - - -
418F TYR* 5.9 1.0 - - - +
427F ASP* 2.8 21.6 + - - +
428F VAL* 1.3 72.3 - - - +
430F VAL* 1.3 61.2 + - - +
490F ASP* 3.3 19.5 - - - +
506F PHE* 3.6 20.2 - - + -
702F D3T 3.0 24.7 + - - +
802F MG 1.9 28.0 - - - -
6H T 5.0 0.2 - - - +
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Residues in contact with VAL 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F GLU* 4.2 17.3 - - + -
399F VAL* 3.9 37.9 - - + -
412F CYS* 4.2 13.0 - - + -
413F VAL 3.6 8.1 - - - +
428F VAL* 4.1 20.0 - - + -
429F ASP* 1.3 76.1 - - - +
431F LEU* 1.3 63.1 + - - +
432F ILE* 3.9 15.2 + - + -
489F LEU* 4.4 6.5 - - + -
490F ASP 2.8 12.2 + - - +
491F ILE* 3.5 9.8 - - + +
492F ILE 3.1 26.0 + - - +
506F PHE* 3.5 5.4 - - - -
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Residues in contact with LEU 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411F LEU 3.5 1.6 - - - +
412F CYS* 3.5 3.8 - - - -
413F VAL* 2.9 39.2 + - + +
415F CYS* 3.8 12.1 - - - -
430F VAL* 1.3 71.4 - - - +
432F ILE* 1.3 69.1 + - - +
433F THR* 5.1 0.5 - - - +
492F ILE* 3.6 18.2 - - + -
494F VAL* 3.6 27.6 - - + -
499F PHE* 3.9 19.6 - - + -
502F ALA* 3.8 8.1 - - + +
503F LEU* 3.5 49.8 - - + +
506F PHE* 4.1 4.0 - - + -
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Residues in contact with ILE 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F VAL* 4.2 11.0 - - + -
403F ALA* 4.6 3.6 - - + -
410F LEU* 4.3 11.2 - - + -
411F LEU 3.3 6.1 - - - +
412F CYS* 3.8 20.9 - - - -
430F VAL* 4.0 8.7 - - + -
431F LEU* 1.3 77.5 - - - +
433F THR* 1.3 67.8 + - - +
443F ILE* 3.6 27.4 - - + -
447F LEU* 3.4 33.0 - - + -
491F ILE* 3.7 15.7 - - + -
492F ILE 2.9 8.3 + - - +
493F VAL* 3.0 16.5 - - + +
494F VAL 2.9 26.3 + - - -
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Residues in contact with THR 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F LEU* 4.5 4.0 - - - -
411F LEU* 2.7 43.2 + - + +
431F LEU* 4.3 0.4 - - + +
432F ILE* 1.3 78.2 - - - +
434F HIS* 1.3 57.0 + - - +
440F HIS* 4.5 4.7 - - - -
494F VAL* 2.6 32.8 + - - -
495F PRO 3.7 0.2 - - - -
496F TYR* 3.4 28.4 + - + -
499F PHE* 3.4 36.6 - - + -
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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