Contacts of the strand formed by residues 357 - 363 (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 TRP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A VAL* 3.6 28.5 - - + +
354A LYS* 3.5 40.5 + - + -
356A ARG* 1.3 75.0 - - - +
358A ALA* 1.3 69.6 + - - +
359A LEU* 3.8 20.0 - - + -
383A LEU* 3.7 24.7 - - + -
384A GLY* 3.2 7.0 - - - -
385A LEU* 2.9 58.6 + - + +
391A LEU* 4.0 20.0 - - + -
409A ARG* 5.6 0.2 - - - +
410A PRO* 5.7 2.2 - - + -
413A ILE* 3.8 31.2 - - + -
454A ASP 3.4 14.6 - - - +
456A CYS* 3.6 8.8 - - - -
467A LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 358 (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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357A TRP* 1.3 78.6 - - - +
359A LEU* 1.3 68.6 + - - +
382A LEU* 4.6 15.3 - - + -
383A LEU 3.3 9.6 - - - +
384A GLY* 4.4 3.8 - - - -
394A HIS* 5.4 5.6 - - + -
452A PHE* 4.6 4.2 - - + -
454A ASP* 2.8 48.2 + - + +
456A CYS* 5.3 1.8 - - - -
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Residues in contact with LEU 359 (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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349A VAL* 3.9 24.9 - - + -
351A VAL* 4.1 4.3 - - + -
357A TRP* 3.8 20.6 - - + -
358A ALA* 1.3 82.8 - - - +
360A GLY* 1.3 59.9 + - - +
382A LEU* 3.3 7.6 - - - -
383A LEU 2.8 33.6 + - - +
413A ILE* 3.9 32.1 - - + -
415A LEU* 4.3 10.3 - - + -
426A PHE* 3.4 9.6 - - + -
452A PHE 3.7 3.4 - - - +
453A PHE* 3.7 29.8 - - + -
467A LEU* 4.1 16.8 - - + -
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Residues in contact with GLY 360 (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* 4.0 6.8 + - - -
359A LEU* 1.3 79.1 - - - +
361A VAL* 1.3 69.9 + - - +
381A TRP 3.1 12.3 - - - -
382A LEU* 3.8 1.9 - - - +
415A LEU* 3.7 15.1 - - - +
424A LEU* 4.4 1.3 - - - -
426A PHE* 4.1 5.2 - - - -
451A PRO* 3.6 2.8 - - - +
452A PHE* 2.9 27.4 + - - +
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Residues in contact with VAL 361 (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* 3.8 25.1 - - + -
360A GLY* 1.3 79.5 - - - +
362A ILE* 1.3 61.2 + - - +
380A LEU* 3.7 4.3 - - - +
381A TRP* 3.1 50.1 + - + +
382A LEU* 4.1 1.1 - - - +
417A LEU* 4.6 7.6 - - + -
424A LEU* 4.0 23.8 - - + -
445A LEU* 5.9 2.7 - - + -
449A VAL* 4.0 29.2 - - + -
450A TYR 3.2 12.8 - - - +
451A PRO* 4.3 2.2 - - + -
452A PHE* 3.9 4.5 - - - +
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Residues in contact with ILE 362 (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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328A PHE* 4.0 26.7 - - + -
335A VAL* 3.6 29.4 - - + -
361A VAL* 1.3 74.7 - - - +
363A ALA* 1.3 74.7 + - - +
366A ALA* 3.8 8.3 - - + -
367A PRO 4.2 11.2 - - - +
368A ARG* 4.1 18.8 - - + +
372A LEU* 4.9 1.6 - - + -
379A GLY 3.2 11.4 - - - +
380A LEU* 3.7 22.7 - - + -
381A TRP* 4.5 0.2 - - - -
449A VAL* 3.3 3.2 - - - -
450A TYR* 2.8 40.1 + - + +
452A PHE* 4.1 5.8 - - + -
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Residues in contact with ALA 363 (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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362A ILE* 1.3 79.4 - - - +
364A ALA* 1.3 65.5 + - - +
365A GLU* 4.2 4.7 - - + +
366A ALA* 3.0 25.0 + - + +
368A ARG* 5.5 2.3 + - - -
379A GLY* 2.8 21.2 + - - +
381A TRP* 3.7 22.3 - - + -
446A PRO* 4.5 9.2 - - + -
448A PRO 3.8 9.0 - - - +
449A VAL* 4.1 4.5 - - - -
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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