Contacts of the helix formed by residues 407 - 411 (chain A) in PDB entry 3K72
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 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ARG 4.2 1.2 - - - +
383A ASP* 2.6 69.0 + - - +
384A SER* 3.3 10.0 + - - -
385A TYR* 3.3 31.1 - - + -
405A ALA 2.9 1.2 + - - -
406A PRO* 1.3 89.9 - - + +
408A TYR* 1.3 60.6 + - - +
409A GLN 3.4 3.6 + - - -
410A HIS* 3.4 39.4 + - - +
211B PRO* 4.1 11.1 - - - +
245B PHE 2.9 28.3 + - - -
246B HIS* 4.4 6.1 + - - +
247B PHE* 3.4 26.6 - - + -
250B ASP* 3.3 22.4 + - - -
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP* 2.8 40.1 + - + -
381A MET* 4.0 24.5 - - + +
382A ARG 5.6 0.2 - - - -
384A SER* 3.7 10.2 - - - -
405A ALA* 3.4 9.1 + - + +
406A PRO 3.7 0.6 - - - -
407A ARG* 1.3 71.9 - - - +
409A GLN* 1.3 105.1 + - + +
410A HIS 3.2 0.3 + - - -
411A THR* 3.1 18.3 + - - -
412A GLY 3.8 1.4 - - - +
413A LYS* 3.1 64.5 + - + +
431A THR* 4.3 14.6 - - + +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP* 5.3 7.3 - - + +
381A MET 5.9 1.6 - - - +
382A ARG 5.2 4.4 + - - -
407A ARG 3.4 2.8 + - - -
408A TYR* 1.3 108.8 + - + +
410A HIS* 1.3 75.1 + - - +
411A THR* 3.1 18.2 + - + +
431A THR* 5.5 2.1 - - - +
435A ILE* 5.2 1.0 - - - +
307B THR* 4.3 4.7 + - - -
310B LYS* 5.7 2.4 + - - -
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Residues in contact with HIS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG 5.9 1.4 + - - -
383A ASP* 5.8 2.5 - - + -
407A ARG* 3.4 47.8 + - - +
408A TYR 3.0 2.0 - - - -
409A GLN* 1.3 84.0 - - - +
411A THR* 1.3 58.5 + - - +
435A ILE* 3.7 6.9 - - + +
436A GLY* 3.1 18.7 + - - -
211B PRO* 5.1 4.0 - - + -
244B GLY* 4.0 13.7 - - - -
245B PHE* 3.1 41.5 + + + -
247B PHE* 3.8 15.6 - - + -
304B MET* 4.2 12.9 - - - +
307B THR* 3.1 23.4 + - - +
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Residues in contact with THR 411 (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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406A PRO 3.0 11.5 - - - +
408A TYR* 3.1 11.3 + - - -
409A GLN* 3.5 18.2 + - + +
410A HIS* 1.3 79.7 - - - +
412A GLY* 1.3 72.6 + - - +
431A THR* 5.5 1.0 - - - -
432A GLY* 4.1 12.9 + - - -
434A GLN 3.4 17.9 - - - +
435A ILE* 3.6 24.5 - - + +
436A GLY* 3.9 0.8 - - - +
437A SER* 3.3 5.3 + - - -
438A TYR 3.2 22.9 + - - -
439A PHE* 5.0 0.2 - - - -
310B LYS* 5.5 11.0 - - + +
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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