Contacts of the helix formed by residues 377 - 389 (chain A) in PDB entry 1KU7
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 SER 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A LYS 4.0 0.8 + - - -
376A LEU* 1.3 77.0 - - - +
378A GLU* 1.3 65.2 + - - +
379A ARG* 3.5 8.9 + - - +
380A GLU* 2.7 45.5 + - - +
381A ALA* 2.9 21.3 + - - +
422A LYS* 4.6 1.4 - - - +
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Residues in contact with GLU 378 (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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376A LEU 3.8 1.1 + - - +
377A SER* 1.3 72.8 - - - +
379A ARG* 1.3 52.8 + - - +
381A ALA* 3.0 8.1 + - - +
382A MET* 2.6 40.0 + - - +
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Residues in contact with ARG 379 (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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377A SER* 3.7 8.3 - - - +
378A GLU* 1.3 79.6 - - - +
380A GLU* 1.3 63.9 + - - +
382A MET* 3.2 7.4 + - - +
383A VAL* 2.8 32.4 + - + +
405A PHE* 3.7 44.4 + - + +
407A VAL* 4.7 8.2 - - - +
411A ARG* 4.3 0.6 - - - +
415A ILE* 3.8 26.6 - - - +
1B C 3.5 16.6 - - - -
2B C 2.5 45.4 + - - -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.4 10.1 - - + +
377A SER* 2.7 52.2 + - - +
379A ARG* 1.3 73.6 - - + +
381A ALA* 1.3 63.7 + - - +
383A VAL* 3.2 3.5 + - - +
384A LEU* 3.1 27.7 + - - +
415A ILE* 4.2 23.8 - - + -
418A LYS* 4.0 17.8 - - - +
419A ALA* 4.1 17.5 + - + +
422A LYS* 2.8 40.3 + - - +
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Residues in contact with ALA 381 (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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373A LEU* 4.8 13.5 - - + +
376A LEU* 4.5 17.7 - - + +
377A SER 2.9 13.2 + - - +
378A GLU* 3.4 10.1 - - - +
380A GLU* 1.3 76.1 - - - +
382A MET* 1.3 64.2 + - - +
384A LEU* 3.2 6.9 + - - +
385A LYS* 3.0 43.9 + - - +
390D LEU* 4.7 0.4 - - - +
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Residues in contact with MET 382 (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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378A GLU 2.6 21.2 + - - +
379A ARG* 3.5 4.9 - - - +
381A ALA* 1.3 72.4 - - - +
383A VAL* 1.3 57.5 + - - +
385A LYS* 3.7 6.9 - - - +
386A MET* 2.9 63.9 + - + +
391A ILE* 3.8 33.7 - - + -
404A TYR* 3.8 22.4 - - + +
405A PHE* 3.5 15.7 - - + -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 2.8 23.7 + - + +
380A GLU 3.5 6.3 - - - +
381A ALA 3.2 0.2 - - - -
382A MET* 1.3 77.2 - - - +
384A LEU* 1.3 57.7 + - + +
386A MET* 3.4 1.1 + - - +
387A ARG* 2.9 33.9 + - + +
401A VAL* 4.0 13.6 - - + +
405A PHE* 3.8 21.8 - - + -
412A ILE* 3.6 29.8 - - + +
415A ILE* 4.0 17.0 - - + -
416A GLU* 4.1 25.4 - - + +
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Residues in contact with LEU 384 (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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376A LEU* 4.3 7.2 - - + -
380A GLU 3.1 12.2 + - - +
381A ALA 3.6 3.8 - - - +
383A VAL* 1.3 75.4 - - - +
385A LYS* 1.3 65.9 + - - +
387A ARG* 3.8 1.7 - - - +
388A LYS* 2.9 34.5 + - + +
416A GLU* 3.7 28.5 - - + +
419A ALA* 4.1 17.3 - - + -
420A LEU* 3.5 34.8 - - + -
423A LEU* 4.1 16.4 - - + -
390D LEU* 3.4 34.8 - - + -
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Residues in contact with LYS 385 (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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373A LEU* 5.6 6.3 - - - -
381A ALA* 3.0 33.9 + - + +
382A MET* 3.7 8.3 - - - +
384A LEU* 1.3 75.7 - - - +
386A MET* 1.3 57.0 + - - +
388A LYS* 3.7 0.4 - - - -
389A GLY 2.9 24.4 + - - -
390A LEU* 2.9 34.3 + - + +
391A ILE* 3.8 28.6 + - + -
385D LYS* 5.4 13.6 - - - +
390D LEU* 4.5 14.4 - - + -
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Residues in contact with MET 386 (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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382A MET* 2.9 60.8 + - + +
383A VAL 3.8 4.0 - - - +
385A LYS* 1.3 74.9 - - - +
387A ARG* 1.3 66.6 + - - +
389A GLY* 3.1 9.1 + - - -
391A ILE* 4.1 20.6 - - + -
394A ARG 3.6 0.2 - - - +
396A HIS* 3.3 33.7 + - + -
400A GLU 5.7 0.4 - - - -
401A VAL* 3.8 23.8 - - + -
404A TYR* 3.3 42.8 - - + -
405A PHE* 3.6 7.0 - - + -
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Residues in contact with ARG 387 (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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383A VAL* 2.9 29.0 + - + +
384A LEU* 3.8 2.9 - - - +
386A MET* 1.3 78.4 - - - +
388A LYS* 1.3 65.0 + - + +
395A GLU* 3.2 27.2 - - - +
396A HIS 2.8 37.6 + - - +
397A THR 4.2 0.9 - - - -
398A LEU* 3.1 38.9 - - - +
401A VAL* 4.3 7.4 - - + -
412A ILE* 4.9 0.4 - - - -
416A GLU* 2.9 42.9 + - - +
18C G 2.9 37.5 + - - -
19C T 5.0 2.8 + - - -
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Residues in contact with LYS 388 (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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384A LEU* 2.9 25.2 + - + +
385A LYS 4.2 1.6 - - - +
387A ARG* 1.3 80.1 - - + +
389A GLY* 1.3 58.9 + - - +
390A LEU* 4.7 3.8 - - + -
395A GLU* 3.8 23.7 + - - +
416A GLU* 4.5 15.2 + - - -
420A LEU* 6.1 7.4 - - - -
388D LYS* 3.6 61.2 - - + +
390D LEU* 4.1 9.6 - - + -
395D GLU* 2.7 28.1 + - - +
420D LEU* 6.0 0.7 - - - +
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Residues in contact with GLY 389 (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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385A LYS 2.9 6.3 + - - -
386A MET* 3.1 5.6 + - - -
387A ARG 3.3 0.8 + - - -
388A LYS* 1.3 78.8 - - - +
390A LEU* 1.3 58.8 + - - +
391A ILE 3.2 6.1 - - - -
392A ASP* 4.7 0.2 - - - -
393A GLY* 2.9 31.1 + - - -
394A ARG 3.2 30.1 - - - -
395A GLU* 4.0 0.4 - - - -
396A HIS* 5.4 0.2 - - - -
420D LEU* 4.5 4.4 - - - +
423D LEU* 4.0 3.3 - - - +
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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