Contacts of the helix formed by residues 371 - 384 (chain A) in PDB entry 1KKQ
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 ASP 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LYS* 4.6 4.9 - - - -
369A GLU 4.4 0.5 - - - +
370A LEU* 1.3 75.7 - - - +
372A ASP* 1.3 62.1 + - - +
373A SER* 2.5 29.6 + - - +
374A ASP* 2.8 23.8 + - - +
375A ILE* 2.8 32.7 + - - +
415A ASN* 3.4 6.6 - - - +
416A HIS* 3.6 14.6 + - - -
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Residues in contact with ASP 372 (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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211A TYR* 3.5 20.9 + - + +
214A TYR* 2.7 43.7 + - + -
215A LEU* 4.9 3.0 - - + +
221A ASN* 3.2 14.0 - - - +
222A LYS* 3.2 18.1 + - - +
223A VAL* 3.1 31.9 + - - +
371A ASP* 1.3 75.3 - - - +
373A SER* 1.3 51.1 + - - +
375A ILE* 4.1 4.9 - - - +
376A SER* 2.6 38.3 + - - -
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Residues in contact with SER 373 (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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211A TYR* 3.4 32.5 + - - +
371A ASP* 2.5 26.0 + - - -
372A ASP* 1.3 76.2 - - - +
374A ASP* 1.3 58.2 - - - +
376A SER* 2.7 17.6 + - - -
377A LEU* 3.5 17.2 - - - +
411A HIS* 3.5 23.7 + - - -
415A ASN* 4.1 1.9 + - - -
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Residues in contact with ASP 374 (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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370A LEU* 3.4 20.1 - - + +
371A ASP* 2.8 25.1 + - - +
373A SER* 1.3 76.0 - - - +
375A ILE* 1.3 67.0 + - - +
377A LEU* 3.0 8.9 + - - +
378A PHE* 3.0 23.0 + - - +
408A LEU* 4.7 5.4 - - + +
411A HIS* 2.9 20.7 + - - -
412A LEU* 4.6 10.8 - - + +
415A ASN* 2.9 18.4 - - - +
416A HIS* 2.5 34.4 - - - -
426A LEU* 5.7 1.3 - - + -
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Residues in contact with ILE 375 (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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214A TYR* 4.0 19.1 - - + +
222A LYS* 3.9 27.6 - - + +
319A ALA 5.3 3.8 - - - +
320A MET* 4.4 13.7 - - + +
323A SER* 3.9 20.0 - - - +
365A PHE* 5.3 10.3 - - + -
366A ASN* 6.2 0.2 - - - +
370A LEU* 4.1 16.4 - - + -
371A ASP* 2.8 23.1 + - - +
372A ASP* 4.1 4.3 - - - +
374A ASP* 1.3 70.7 - - - +
376A SER* 1.3 56.1 + - - +
378A PHE* 3.4 11.1 - - + +
379A VAL* 2.8 52.1 + - + +
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Residues in contact with SER 376 (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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210A ILE* 3.6 23.5 - - - +
211A TYR* 3.8 8.8 - - - +
214A TYR* 3.6 28.8 - - - -
290A PHE* 3.8 5.8 - - - -
372A ASP 2.6 24.2 + - - -
373A SER* 2.7 21.0 + - - -
375A ILE* 1.3 77.5 - - - +
377A LEU* 1.3 59.0 + - - +
379A VAL* 3.4 3.5 + - - +
380A ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 377 (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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207A ALA* 4.0 22.0 - - + +
210A ILE* 3.5 35.0 - - + -
211A TYR* 6.5 0.2 - - + -
373A SER 3.5 18.2 - - - +
374A ASP* 3.0 5.9 + - - +
376A SER* 1.3 72.8 + - - +
378A PHE* 1.3 66.4 + - - +
380A ALA* 2.9 5.6 + - - +
381A ALA* 2.8 24.9 + - - +
404A ILE* 3.5 8.5 - - + +
407A VAL* 4.3 13.5 - - + +
408A LEU* 4.1 27.8 - - + -
411A HIS* 3.9 32.1 - - + +
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Residues in contact with PHE 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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319A ALA* 4.1 14.6 - - + -
365A PHE* 3.8 33.7 - + - -
370A LEU* 5.5 1.6 - - + -
374A ASP 3.0 13.3 + - - +
375A ILE* 3.4 13.9 - - + +
377A LEU* 1.3 77.9 - - - +
379A VAL* 1.3 57.9 + - + +
381A ALA* 3.2 7.8 + - - +
382A ILE* 2.7 35.1 + - + +
408A LEU* 4.2 15.8 - - + +
426A LEU* 3.4 39.3 - - + -
429A LYS* 4.1 2.0 - - + -
430A MET* 3.3 46.7 - - + -
433A LEU* 4.1 17.5 - - + -
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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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214A TYR* 5.1 1.6 - - + -
218A PHE* 5.2 1.1 - - + -
287A LEU* 4.0 27.1 - - + -
290A PHE* 4.0 10.3 - - + -
316A ALA* 4.0 12.8 - - + +
319A ALA* 4.5 14.1 - - + -
320A MET* 4.0 22.9 - - + -
375A ILE* 2.8 44.9 + - + +
376A SER* 3.7 5.6 - - - +
378A PHE* 1.3 71.2 - - + +
380A ALA* 1.3 60.6 + - - +
382A ILE* 3.7 8.8 + - - +
383A ILE* 3.0 23.2 + - - +
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Residues in contact with ALA 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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210A ILE* 4.2 17.9 - - + -
290A PHE* 4.2 2.5 - - + -
294A ILE* 3.9 26.5 - - + -
376A SER 3.0 13.6 + - - +
377A LEU 2.9 9.5 + - - +
379A VAL* 1.3 77.4 - - - +
381A ALA* 1.3 59.4 + - - +
383A ILE* 3.2 2.0 + - - +
384A CYS* 2.9 34.7 + - - +
404A ILE* 3.8 15.7 - - + -
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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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377A LEU 2.8 10.1 + - - +
378A PHE 3.2 10.3 + - - +
380A ALA* 1.3 78.3 - - - +
382A ILE* 1.3 59.1 + - - +
384A CYS* 3.6 18.1 - - - +
385A CYS* 4.1 1.2 - - - +
401A GLN* 3.7 6.8 + - - -
404A ILE* 3.6 18.5 - - + +
405A VAL* 4.2 15.0 - - + -
408A LEU* 4.2 17.0 - - + -
430A MET* 3.6 20.4 - - - +
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Residues in contact with ILE 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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312A GLY* 3.0 31.9 - - - +
315A GLU* 3.3 35.7 - - + +
316A ALA* 3.6 15.3 - - + +
319A ALA* 6.1 1.1 - - + -
378A PHE* 2.7 38.1 - - + +
379A VAL* 3.7 11.2 - - - +
380A ALA 3.2 0.6 - - - -
381A ALA* 1.3 76.1 - - - +
383A ILE* 1.3 64.5 + - - +
385A CYS* 4.0 3.9 - - - -
388A ARG* 2.6 33.1 + - - +
430A MET* 4.3 21.5 - - + -
433A LEU* 6.1 2.0 - - + -
434A ARG* 6.3 0.2 - - - +
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Residues in contact with ILE 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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287A LEU* 4.1 27.6 - - + +
290A PHE* 4.2 9.2 - - + -
291A ALA* 4.2 8.5 - - + -
294A ILE* 4.7 2.5 - - + -
297A PHE* 4.4 17.0 - - + -
308A LEU* 3.1 43.4 - - - +
309A LEU* 4.0 30.7 - - + -
312A GLY* 4.9 4.3 - - - +
316A ALA* 5.1 2.9 - - + -
379A VAL* 3.0 20.6 - - + +
380A ALA* 3.2 5.6 + - - +
382A ILE* 1.3 89.2 - - + +
384A CYS* 1.3 60.3 + - - +
385A CYS* 2.9 8.7 + - - +
388A ARG* 4.5 2.3 + - - -
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Residues in contact with CYS 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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294A ILE* 4.5 14.8 - - - -
297A PHE* 4.5 15.5 - - - -
308A LEU* 4.3 8.3 - - - -
380A ALA 2.9 16.0 + - - +
381A ALA* 3.6 4.6 - - - +
383A ILE* 1.3 73.3 - - - +
385A CYS* 1.3 59.8 + - - +
397A ILE* 4.2 8.7 - - + +
400A MET* 3.8 24.5 - - - -
401A GLN* 3.0 31.1 + - + +
404A ILE* 3.6 28.9 - - + -
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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