Contacts of the strand formed by residues 344 - 350 (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 GLU 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A PRO* 4.6 15.0 - - + +
343A GLY* 1.3 81.9 - - - -
345A HIS* 1.3 75.1 + - - +
416A TYR* 3.3 33.4 - - + +
417A LEU 3.2 4.7 - - - +
418A SER* 3.7 14.0 + - - +
420A GLY* 5.0 5.5 + - - -
421A ASP* 5.2 1.7 - - - +
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Residues in contact with HIS 345 (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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286A PRO* 4.2 4.5 - - - -
287A ALA 5.8 0.2 - - - -
289A GLU* 2.8 31.5 + - - +
340A LEU* 3.9 37.8 - - + +
341A SER 5.1 0.2 + - - -
342A GLU* 2.7 29.7 + - - -
343A GLY* 3.8 6.7 - - - -
344A GLU* 1.3 85.2 + - - +
346A TYR* 1.3 62.3 + - - +
347A TRP* 4.2 17.5 - - + -
415A LEU 4.3 0.2 - - - -
416A TYR* 3.3 6.1 - - - -
417A LEU* 2.7 40.7 + - + +
419A PHE* 4.5 5.4 - + - -
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Residues in contact with TYR 346 (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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282A ARG* 4.0 5.1 + - - -
285A MET* 3.5 32.5 - - + -
286A PRO* 3.7 36.5 - - + +
287A ALA 4.6 2.2 + - - +
288A LEU* 3.6 15.5 - - + -
289A GLU* 2.7 34.7 + - - +
345A HIS* 1.3 77.6 - - - +
347A TRP* 1.3 56.7 + - - +
348A GLU* 2.6 45.5 + - + +
414A GLY* 3.5 8.1 - - - -
415A LEU 3.2 34.8 - - - -
416A TYR* 4.1 2.0 - - + -
427A TYR* 4.7 3.8 - + - -
435A LEU* 3.5 28.0 - - + +
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Residues in contact with TRP 347 (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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288A LEU* 4.1 6.7 - - + -
289A GLU* 4.1 12.6 - - + +
291A LEU* 3.6 30.7 - - + +
340A LEU* 3.9 25.1 - - + -
345A HIS* 4.2 6.5 - - + -
346A TYR* 1.3 83.7 - - - +
348A GLU* 1.3 66.9 + - - +
349A VAL* 4.1 12.3 - - + -
360A GLY 4.0 2.4 + - - -
361A VAL* 3.8 25.4 - - + -
414A GLY* 3.5 2.1 - - - -
415A LEU* 2.8 83.4 + - + +
417A LEU* 4.0 21.8 - - + -
424A LEU* 4.7 1.8 - - + -
451A PRO* 3.8 22.2 - - + +
453A PHE* 4.2 7.9 - + - -
469A LEU* 4.4 7.2 - - + -
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Residues in contact with GLU 348 (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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282A ARG* 2.8 24.6 + - - -
288A LEU* 3.7 14.5 - - + +
346A TYR* 2.6 39.2 + - + +
347A TRP* 1.3 78.1 - - - +
349A VAL* 1.3 68.0 + - - +
412A ARG* 3.5 32.4 + - - -
413A ILE 3.2 6.7 - - - +
414A GLY* 4.2 2.7 - - - -
429A ALA* 3.5 6.5 - - + +
469A LEU* 3.8 7.1 - - - +
470A VAL* 3.1 43.8 + - + +
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Residues in contact with VAL 349 (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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293A PHE* 5.8 0.2 - - + -
347A TRP* 4.1 12.1 - - + -
348A GLU* 1.3 80.9 - - - +
350A ASP* 1.3 72.3 + - - +
351A VAL* 3.5 7.0 + - + +
359A LEU* 3.9 31.4 - - + -
412A ARG* 3.3 4.6 - - - -
413A ILE* 2.9 34.8 + - - +
415A LEU* 4.2 9.6 - - + -
453A PHE* 3.7 28.7 - - + -
467A LEU* 4.3 7.9 - - + -
468A LEU 3.3 16.8 - - - +
469A LEU* 4.3 3.8 - - + -
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Residues in contact with ASP 350 (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* 1.3 73.9 - - - +
351A VAL* 1.3 59.7 + - - +
352A GLY 4.8 1.8 - - - +
411A THR* 3.6 7.0 + - - +
412A ARG* 2.7 50.6 + - - +
466A PRO 4.2 0.2 - - - +
467A LEU* 3.9 4.3 - - - -
468A LEU* 2.8 57.3 + - + +
470A VAL* 3.8 10.0 - - - +
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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