Contacts of the helix formed by residues 378 - 389 (chain A) in PDB entry 5K9S
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 LEU 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 3.8 33.9 - - + +
340A PHE* 3.9 7.9 - - + -
341A PRO* 3.6 43.5 - - + -
344A LEU* 4.5 8.5 - - + +
359A MET* 3.6 30.1 - - + -
373A VAL* 3.2 23.1 + - + +
376A HIS* 3.9 13.7 - - + +
377A GLY* 1.3 77.1 - - - +
379A VAL* 1.3 66.5 + - - +
380A PRO 3.4 0.4 - - - -
381A PHE* 2.9 16.9 + - + +
382A LEU* 3.1 15.4 + - + +
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Residues in contact with VAL 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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373A VAL* 4.6 6.3 - - + -
374A VAL* 4.2 12.8 - - + -
377A GLY* 3.5 0.4 - - - -
378A LEU* 1.3 76.5 - - - +
380A PRO* 1.3 72.0 - - + +
382A LEU* 3.0 21.8 + - + +
383A VAL* 3.0 13.7 + - + +
401A ILE* 6.2 0.4 - - + -
404A TYR* 4.1 26.0 - - + +
415A TYR* 3.6 23.1 - - + -
416A LEU* 3.9 27.1 - - + -
419A CYS* 3.7 23.1 - - + -
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Residues in contact with PRO 380 (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 GLY* 3.5 20.2 - - - +
379A VAL* 1.3 95.2 - - + +
381A PHE* 1.3 61.4 + - + +
383A VAL* 3.6 9.8 + - + +
384A GLY* 3.0 21.8 + - - -
415A TYR* 3.9 15.5 - - - +
419A CYS* 4.3 13.0 - - + +
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Residues in contact with PHE 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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341A PRO* 3.9 37.2 - - + -
344A LEU* 3.9 20.1 - - + +
345A THR* 4.1 24.6 - - + +
376A HIS 5.6 0.4 - - - -
377A GLY 3.3 27.8 - - - -
378A LEU* 2.9 12.4 + - + +
380A PRO* 1.3 79.9 - - + +
382A LEU* 1.3 62.0 + - - +
384A GLY* 3.3 2.5 + - - +
385A VAL* 2.9 31.9 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.3 18.6 - - + -
356A THR* 4.5 13.9 - - + -
359A MET* 4.0 46.4 - - + -
363A THR* 4.8 6.3 - - + -
373A VAL* 4.8 6.3 - - + -
378A LEU 3.1 15.1 + - - +
379A VAL* 3.0 15.2 + - + +
381A PHE* 1.3 72.6 - - - +
383A VAL* 1.3 61.5 + - - +
385A VAL* 3.3 5.3 + - + +
386A LEU* 2.9 29.5 + - - +
397A ALA* 4.3 6.9 - - + +
400A ALA* 4.6 17.0 - - + +
401A ILE* 4.7 18.8 - - + +
404A TYR* 6.0 3.4 - - + -
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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
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379A VAL* 3.0 19.5 + - + +
380A PRO* 3.7 9.0 - - + +
382A LEU* 1.3 77.3 - - + +
384A GLY* 1.3 62.3 + - - +
386A LEU* 3.2 8.5 + - - +
387A SER* 2.9 30.2 + - - +
401A ILE* 5.6 0.4 - - + -
416A LEU* 4.9 0.7 - - + -
419A CYS* 4.0 34.8 - - + +
420A GLY 4.0 13.5 - - - +
421A ILE* 4.0 24.5 - - + -
424A PRO* 4.1 11.9 - - + -
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Residues in contact with GLY 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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380A PRO 3.0 15.3 + - - -
381A PHE* 3.6 4.5 - - - -
382A LEU 3.3 0.4 - - - -
383A VAL* 1.3 76.2 - - - +
385A VAL* 1.3 61.3 + - - +
387A SER* 3.0 4.9 + - - -
388A LYS* 2.9 45.0 + - - +
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Residues in contact with VAL 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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344A LEU* 3.6 43.1 - - + +
345A THR* 6.0 0.9 - - + -
352A GLN* 5.2 1.8 - - + +
356A THR* 3.7 8.5 - - + +
381A PHE 2.9 17.9 + - - +
382A LEU* 3.3 9.8 + - + +
384A GLY* 1.3 73.3 - - - +
386A LEU* 1.3 65.0 + - - +
389A ALA* 3.0 34.8 + - + +
393A THR* 3.4 33.9 - - + +
394A GLN* 3.7 3.3 - - - +
397A ALA* 3.8 14.6 - - + -
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Residues in contact with LEU 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 LEU 2.9 17.4 + - - +
383A VAL* 3.2 6.0 + - - +
385A VAL* 1.3 77.3 - - - +
387A SER* 1.3 57.5 + - - +
394A GLN* 3.0 27.7 + - - +
397A ALA* 3.8 7.2 - - + -
398A ALA* 3.6 29.8 - - + +
401A ILE* 4.5 3.4 - - + -
421A ILE* 3.8 22.9 - - + -
424A PRO* 4.1 12.5 - - + +
425A LEU* 3.7 37.7 - - + +
428A LEU* 3.5 31.8 - - + +
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Residues in contact with SER 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 18.7 + - - +
384A GLY* 3.0 8.1 + - - -
386A LEU* 1.3 79.2 - - - +
388A LYS* 1.3 67.0 + - - +
389A ALA 3.8 0.4 - - - -
394A GLN* 3.8 10.0 + - - -
424A PRO* 3.2 26.1 - - - +
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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 GLY* 2.9 26.9 + - - +
385A VAL* 5.5 0.2 - - - -
387A SER* 1.3 87.3 - - - +
389A ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 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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352A GLN* 4.0 14.4 - - - +
384A GLY 4.2 0.2 + - - -
385A VAL* 3.0 25.7 + - + +
387A SER 3.8 0.2 - - - -
388A LYS* 1.3 84.4 - - - +
390A ASP* 1.3 67.4 + - - +
393A THR* 3.8 28.5 - - + -
394A GLN* 3.2 15.9 + - + +
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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