Contacts of the helix formed by residues 423 - 430 (chain A) in PDB entry 3BKL
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 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A LEU 3.7 13.2 - - - +
420A SER 2.8 16.3 + - - +
422A SER* 1.3 79.9 - - - +
424A PRO* 1.3 68.8 - - - +
425A LYS* 3.3 18.5 - - - +
426A HIS* 3.3 14.0 + - - +
427A LEU* 2.9 26.5 + - - +
446A PHE* 3.7 7.6 - - + -
534A HIS* 6.2 0.2 - - - +
548A HIS 3.7 19.7 - - - +
550A CYS 3.6 24.7 - - - +
551A ASP* 4.1 2.3 - - - +
595A TYR* 5.6 0.9 - - + +
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Residues in contact with PRO 424 (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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422A SER 3.6 1.3 - - - +
423A THR* 1.3 85.6 - - - +
425A LYS* 1.3 65.9 + - - +
427A LEU* 3.3 3.1 + - + +
428A HIS* 2.9 25.9 + - - +
433A LEU* 4.2 19.3 - - + +
437A GLY 4.7 7.9 - - - +
442A HIS* 3.7 31.9 - - + +
446A PHE* 3.6 41.5 - - + -
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Residues in contact with LYS 425 (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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423A THR* 3.3 19.1 - - - +
424A PRO* 1.3 84.8 - - - +
426A HIS* 1.3 73.2 + - - +
428A HIS* 3.1 7.0 + - - +
429A SER* 3.0 20.3 + - - -
549A LYS* 2.9 52.7 + - - +
551A ASP* 4.2 16.4 - - + +
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Residues in contact with HIS 426 (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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318A GLU* 4.5 3.8 + - - -
322A PHE* 3.6 26.7 - + - -
420A SER 3.3 23.8 - - - +
421A VAL* 3.8 17.9 - - + +
423A THR* 3.1 6.7 + - - +
425A LYS* 1.3 83.1 - - - +
427A LEU* 1.3 62.2 + - - +
429A SER* 2.7 31.3 + - - -
430A LEU* 3.1 32.6 + - + +
551A ASP* 2.9 24.2 + - - +
553A TYR* 3.7 27.8 - + - +
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Residues in contact with LEU 427 (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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301A THR* 4.9 3.6 - - - +
375A LEU* 3.8 38.4 - - + -
378A LEU* 5.6 0.2 - - + -
421A VAL* 3.4 21.3 - - + +
422A SER 3.3 22.4 - - - +
423A THR 2.9 12.6 + - - +
424A PRO* 3.9 4.5 - - + +
426A HIS* 1.3 76.2 - - - +
428A HIS* 1.3 58.6 + - - +
430A LEU* 3.1 16.2 + - + +
432A LEU* 3.0 49.6 + - + +
433A LEU* 3.4 26.4 + - + -
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Residues in contact with HIS 428 (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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424A PRO 2.9 18.6 + - - +
425A LYS* 3.6 5.9 + - - +
427A LEU* 1.3 73.0 - - - +
429A SER* 1.3 64.1 + - - +
430A LEU 3.0 0.4 - - - -
431A ASN* 2.9 22.3 + - - +
433A LEU* 3.3 28.7 - - + +
434A SER* 3.2 29.5 + - - -
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Residues in contact with SER 429 (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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425A LYS 3.0 12.6 + - - -
426A HIS* 2.7 35.6 + - - -
428A HIS* 1.3 81.1 + - - +
430A LEU* 1.3 61.7 + - - +
431A ASN* 3.1 4.4 + - - +
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Residues in contact with LEU 430 (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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308A GLN* 4.8 0.7 - - - +
310A TRP* 4.2 33.3 + - + -
314A ARG* 5.1 4.7 + - - +
318A GLU* 4.4 19.3 - - + -
378A LEU* 5.0 2.5 - - + -
421A VAL* 4.5 12.1 - - + -
426A HIS* 3.1 35.8 + - + +
427A LEU* 3.1 14.6 + - + +
428A HIS 3.0 1.0 - - - -
429A SER* 1.3 82.9 + - - +
431A ASN* 1.3 64.9 + - - +
432A LEU* 2.9 32.2 + - + +
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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