Contacts of the strand formed by residues 412 - 418 (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 ARG 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ARG* 5.9 1.2 - - - +
348A GLU* 3.5 32.0 + - + -
349A VAL 3.3 13.0 - - - +
350A ASP* 2.7 36.0 + - - +
351A VAL* 4.2 0.4 - - - +
410A PRO* 3.6 0.4 - - - +
411A THR* 1.3 83.5 + - - +
413A ILE* 1.3 70.7 + - - +
428A ASP* 3.7 3.6 - - - +
429A ALA* 2.8 53.3 + - + +
430A SER* 3.4 9.1 + - - +
432A ALA* 5.8 6.3 - - - +
470A VAL* 3.6 22.1 - - - +
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Residues in contact with ILE 413 (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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348A GLU* 3.2 2.9 - - - -
349A VAL 2.9 36.3 + - - +
351A VAL* 4.3 8.1 - - + -
357A TRP* 3.8 33.7 - - + -
359A LEU* 3.9 20.4 - - + -
383A LEU* 4.5 6.5 - - + -
391A LEU* 5.5 0.7 - - + -
410A PRO* 4.1 20.6 - - + -
412A ARG* 1.3 81.8 - - - +
414A GLY* 1.3 71.1 + - - +
415A LEU* 3.8 14.5 - - + +
426A PHE* 4.3 15.0 - - + -
427A TYR 3.4 12.1 - - - +
429A ALA* 4.3 2.7 - - - -
438A LEU* 4.1 13.5 - - + -
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Residues in contact with GLY 414 (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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346A TYR* 3.5 25.6 - - - -
347A TRP 3.5 6.7 - - - -
348A GLU* 4.2 2.0 - - - -
413A ILE* 1.3 77.9 - - - +
415A LEU* 1.3 60.2 + - - -
416A TYR 4.2 0.2 - - - -
425A SER 3.8 0.2 - - - +
426A PHE* 3.3 5.9 - - - -
427A TYR* 2.8 38.6 + - - -
429A ALA* 4.0 4.4 - - - +
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Residues in contact with LEU 415 (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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346A TYR* 3.2 10.1 - - - -
347A TRP* 2.8 81.9 + - + +
349A VAL* 4.2 10.5 - - + -
359A LEU* 4.3 6.3 - - + -
360A GLY* 3.7 24.2 - - - +
413A ILE* 3.8 22.2 - - + +
414A GLY* 1.3 77.6 - - - +
416A TYR* 1.3 59.9 + - - +
424A LEU* 4.8 6.1 - - + -
425A SER 3.4 4.9 - - - +
426A PHE* 3.6 31.9 - - + -
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Residues in contact with TYR 416 (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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284A LEU 5.7 0.9 - - - -
285A MET* 3.8 31.0 - - + -
286A PRO* 3.9 20.4 - - + -
344A GLU* 3.3 32.0 - - + +
345A HIS 3.3 11.9 - - - -
346A TYR* 4.2 1.1 - - + -
414A GLY 4.2 0.4 - - - -
415A LEU* 1.3 73.0 - - - +
417A LEU* 1.3 60.1 + - - +
418A SER* 3.6 25.1 + - - -
421A ASP* 4.4 4.9 + - - -
423A VAL* 3.8 11.8 - - + +
424A LEU* 3.3 6.9 - - - +
425A SER* 2.8 56.0 + - - +
427A TYR* 4.0 13.2 - - + -
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Residues in contact with LEU 417 (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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340A LEU* 3.6 28.0 - - + -
343A GLY 3.7 1.0 - - - +
344A GLU* 3.2 4.0 - - - +
345A HIS* 2.7 42.4 + - + +
347A TRP* 4.0 20.6 - - + -
361A VAL* 4.6 7.0 - - + -
415A LEU 4.1 0.2 - - - -
416A TYR* 1.3 75.2 - - - +
418A SER* 1.3 61.6 + - - +
419A PHE* 3.7 29.6 - - + -
423A VAL 3.6 2.9 - - - +
424A LEU* 4.0 13.2 - - + -
445A LEU* 3.4 33.2 - - + -
449A VAL* 3.9 17.0 - - + -
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Residues in contact with SER 418 (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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343A GLY 3.7 4.0 - - - -
344A GLU* 3.7 12.9 + - - +
416A TYR* 3.6 27.3 - - - -
417A LEU* 1.3 75.8 - - - +
419A PHE* 1.3 59.4 + - - +
420A GLY* 3.9 2.4 + - - -
421A ASP* 2.8 28.3 + - - -
422A GLY* 2.8 22.5 + - - -
423A VAL* 3.0 27.9 + - - +
445A LEU* 4.6 0.9 - - - +
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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