Contacts of the helix formed by residues 466 - 474 (chain A) in PDB entry 2B50
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 HIS 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLN* 2.7 20.9 + - + +
287A CYS* 6.5 0.4 - - - -
290A VAL* 3.8 31.8 - - + +
294A ARG* 5.3 3.4 + - - -
464A SER 4.3 0.2 - - - -
465A LEU* 1.3 71.4 - - - +
467A PRO* 1.4 82.4 - - + +
468A LEU* 3.1 40.4 + - + +
469A LEU* 2.9 27.5 + - + +
470A GLN 3.1 9.5 + - - -
310B PHE* 4.3 13.8 - + - -
401B MET* 5.4 2.2 - - + -
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Residues in contact with PRO 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU 3.4 3.3 - - - +
466A HIS* 1.4 99.3 - - + +
468A LEU* 1.3 60.5 + - - +
470A GLN* 3.2 18.6 + - + +
471A GLU* 3.0 25.7 + - + +
401B MET* 3.6 28.3 - - + +
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Residues in contact with LEU 468 (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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290A VAL* 4.1 15.9 - - + -
293A VAL* 3.7 25.6 - - + -
466A HIS* 3.1 20.2 + - + +
467A PRO* 1.3 76.3 - - - +
469A LEU* 1.3 63.9 + - + +
471A GLU* 3.2 5.6 + - - +
472A ILE* 3.1 27.9 + - + +
921A B7G 3.6 20.0 - - + -
310B PHE* 3.6 28.3 - - + -
312B ASN* 3.5 31.2 - - - +
401B MET* 3.5 19.0 - - + -
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Residues in contact with LEU 469 (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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286A GLN* 3.7 35.7 - - + +
289A THR* 4.1 3.1 - - - +
290A VAL* 3.8 31.9 - - + +
293A VAL* 5.2 3.1 - - + -
323A HIS* 4.5 4.9 - - + -
465A LEU* 3.6 14.4 - - + -
466A HIS* 2.9 11.1 + - + +
468A LEU* 1.3 80.7 - - + +
470A GLN* 1.3 65.0 + - - +
472A ILE* 3.2 21.8 + - + +
473A TYR* 3.1 36.8 + - + -
1001A VCA 3.5 31.2 - - - +
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Residues in contact with GLN 470 (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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457A LYS* 5.6 10.5 + - + +
465A LEU* 2.6 53.3 + - + +
466A HIS 3.1 7.0 + - - +
467A PRO* 3.2 19.3 + - + +
469A LEU* 1.3 74.7 - - - +
471A GLU* 1.3 62.3 + - + +
473A TYR* 4.1 2.4 - - - +
474A LYS* 3.2 24.9 + - - +
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Residues in contact with GLU 471 (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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319A LYS* 4.1 0.9 + - - -
467A PRO* 3.0 17.3 + - + +
468A LEU 3.5 8.3 - - - +
469A LEU 3.2 0.2 - - - -
470A GLN* 1.3 76.0 - - + +
472A ILE* 1.3 66.9 + - - +
474A LYS* 2.7 42.0 + - - +
921A B7G 2.9 52.6 + - + +
312B ASN* 4.1 15.0 - - - +
399B GLY* 3.8 18.9 - - - +
401B MET* 4.2 11.6 - - + +
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Residues in contact with ILE 472 (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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293A VAL* 4.6 6.3 - - + -
319A LYS* 3.5 33.0 - - - +
322A VAL* 4.1 15.3 - - + -
323A HIS* 4.0 34.3 - - + +
468A LEU* 3.1 26.1 + - + +
469A LEU* 3.2 17.9 + - + +
471A GLU* 1.3 79.9 - - - +
473A TYR* 1.3 66.9 + - + +
474A LYS 3.4 6.9 - - - +
476A MET* 3.4 23.3 - - + +
921A B7G 3.6 25.6 - - + -
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Residues in contact with TYR 473 (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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323A HIS* 2.9 32.9 + + - -
446A VAL* 5.4 3.1 - - + -
449A HIS* 2.9 18.5 - + - -
450A ALA* 3.6 37.7 - - + +
453A MET* 3.9 25.6 - - + -
454A GLN* 3.5 19.9 + - + +
465A LEU* 5.3 5.8 - - + -
469A LEU* 3.1 33.7 + - + +
470A GLN* 4.5 2.5 - - - +
472A ILE* 1.3 78.5 - - + +
474A LYS* 1.3 65.8 + - - +
475A ASP 3.4 0.3 + - - -
476A MET* 3.1 28.6 + - - +
1001A VCA 2.6 29.9 + - - -
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Residues in contact with LYS 474 (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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319A LYS* 3.8 6.8 + - - -
470A GLN 3.2 18.2 + - - +
471A GLU* 2.7 32.9 + - - +
472A ILE 3.4 9.9 - - - +
473A TYR* 1.3 76.8 - - - +
475A ASP* 1.3 91.8 + - - +
476A MET* 3.3 0.4 - - - +
921A B7G 2.8 34.0 + - - -
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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