Contacts of the strand formed by residues 423 - 428 (chain A) in PDB entry 3KB5
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 VAL 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A TYR* 4.3 13.0 - - + -
417A LEU* 3.6 1.2 - - - -
418A SER* 3.0 49.1 + - - -
421A ASP* 4.0 14.4 - - + +
422A GLY* 1.3 80.2 - - - +
424A LEU* 1.3 72.2 + - - +
425A SER* 4.1 6.3 - - - +
440A ALA* 4.2 5.4 - - + -
441A PHE 3.1 15.7 - - - +
442A HIS* 3.6 25.8 - - + +
445A LEU* 3.5 11.3 - - - +
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Residues in contact with LEU 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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347A TRP* 4.7 6.5 - - + -
360A GLY* 4.4 0.4 - - - -
361A VAL* 4.0 24.0 - - + +
381A TRP* 3.6 39.7 - - + +
415A LEU* 4.8 5.2 - - + -
416A TYR 3.3 17.7 - - - +
417A LEU* 4.0 17.0 - - + -
423A VAL* 1.3 76.7 - - - +
425A SER* 1.3 63.3 + - - +
426A PHE* 3.8 22.2 - - + -
440A ALA* 3.4 1.0 - - - -
441A PHE* 2.8 39.5 + - + +
445A LEU* 4.0 14.1 - - + +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLY 3.8 0.3 - - - +
415A LEU* 3.4 5.5 - - - +
416A TYR* 2.8 60.4 + - - +
423A VAL* 4.1 5.6 - - - -
424A LEU* 1.3 75.7 - - - +
426A PHE* 1.3 64.2 + - - +
427A TYR* 3.3 21.9 + - - -
439A PHE 3.4 5.2 - - - -
440A ALA* 3.8 16.6 - - - -
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Residues in contact with PHE 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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359A LEU* 3.4 27.4 - - + -
360A GLY* 4.1 0.2 - - - -
381A TRP 4.1 3.6 - - - -
383A LEU* 3.6 46.2 - - + -
413A ILE* 4.3 5.6 - - + -
414A GLY 3.3 4.5 - - - +
415A LEU* 3.6 29.8 - - + -
424A LEU* 3.8 26.7 - - + -
425A SER* 1.3 75.8 - - - +
427A TYR* 1.3 66.5 + - - +
437A PRO* 3.8 1.2 - - - +
438A LEU* 2.9 26.0 + - + -
439A PHE* 2.8 35.3 + + + +
441A PHE* 3.9 27.8 - + - -
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Residues in contact with TYR 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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281A PHE* 4.3 27.9 - + + -
285A MET* 4.2 20.1 - - + +
346A TYR* 4.7 6.5 - + - -
413A ILE* 3.4 9.2 - - - +
414A GLY* 2.8 42.6 + - - +
416A TYR* 4.0 14.9 - - + +
425A SER* 3.3 34.6 + - - -
426A PHE* 1.3 75.0 - - - +
428A ASP* 1.3 61.6 + - - +
429A ALA 3.4 0.3 + - - -
435A LEU* 4.1 30.7 - - + -
436A VAL 3.2 7.9 - - - +
437A PRO* 3.5 35.7 - - + -
438A LEU* 3.9 6.8 - - - +
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Residues in contact with ASP 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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405A SER 4.9 2.4 - - - +
406A PRO* 5.6 2.6 - - + +
407A GLU* 5.9 1.7 - - - +
408A ARG* 4.1 10.0 + - - +
410A PRO* 3.3 29.4 - - + +
412A ARG 3.8 3.1 - - - -
427A TYR* 1.3 70.8 - - - +
429A ALA* 1.3 57.6 + - - +
430A SER* 2.7 31.7 + - - -
431A ASP 5.1 0.9 + - - -
434A ALA 4.0 1.6 - - - +
435A LEU* 3.6 4.9 - - - -
436A VAL* 2.7 47.8 + - + +
438A LEU* 3.8 18.9 - - + +
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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