Contacts of the helix formed by residues 346 - 365 (chain N) in PDB entry 1KYO
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 VAL 346 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345N GLU* 1.3 66.6 - - - +
347N PRO* 1.4 74.8 - - + +
348N TYR 3.3 0.4 + - - -
349N VAL* 3.7 15.0 + - - +
350N LEU* 3.9 12.1 + - - +
76S TYR* 4.1 10.3 - - + -
80S LEU* 3.7 25.6 - - + -
81S TYR* 4.3 7.6 - - + +
89S LEU* 4.5 1.6 - - + -
92S VAL* 3.9 26.7 - - + +
93S ASN* 3.3 28.7 - - - +
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Residues in contact with PRO 347 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345N GLU 2.9 11.9 - - - +
346N VAL* 1.4 92.1 - - + +
348N TYR* 1.3 64.5 + - + +
350N LEU* 3.8 4.1 + - + +
351N MET* 3.1 31.9 + - - +
73S GLY* 3.3 35.9 - - - +
76S TYR* 4.0 18.6 - - + -
77S ASN* 3.8 27.8 - - + +
80S LEU* 4.5 0.9 - - + -
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Residues in contact with TYR 348 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N ILE* 3.6 21.0 - - + +
342N CYS* 3.8 15.9 - - + -
343N HIS* 3.8 30.3 - + + +
345N GLU* 2.9 19.9 + - + +
347N PRO* 1.3 75.9 - - + +
349N VAL* 1.3 58.2 + - - +
351N MET* 3.5 13.6 - - - +
352N GLY 2.8 24.4 + - - -
70S TRP* 3.5 33.6 - + - -
73S GLY 4.2 4.9 - - - -
74S ASN* 3.0 39.7 + - - -
77S ASN* 3.5 38.1 + - + +
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Residues in contact with VAL 349 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283N ARG 5.6 5.6 - - - +
284N SER* 4.4 3.4 + - - -
339N ILE* 5.7 0.4 - - - -
344N VAL* 3.8 30.1 - - + -
345N GLU 4.0 18.4 - - - +
346N VAL* 3.7 7.5 + - - +
347N PRO 3.5 0.6 - - - -
348N TYR* 1.3 75.5 - - - +
350N LEU* 1.3 59.5 + - - +
352N GLY* 3.1 3.8 + - - -
353N GLN* 3.0 52.2 + - + +
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Residues in contact with LEU 350 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N VAL 3.9 7.9 + - - +
347N PRO* 3.8 7.8 + - + +
348N TYR 3.4 0.2 - - - -
349N VAL* 1.3 76.0 - - - +
351N MET* 1.3 64.8 + - + +
353N GLN* 3.1 20.8 + - + +
354N ILE* 2.8 56.4 + - + +
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Residues in contact with MET 351 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335N LEU* 4.3 8.9 - - + +
339N ILE* 4.1 12.6 - - + -
347N PRO* 3.1 31.9 + - + +
348N TYR* 3.5 20.0 - - - +
350N LEU* 1.3 79.9 - - + +
352N GLY* 1.3 64.8 + - - +
354N ILE* 3.1 2.9 + - - +
355N ALA* 3.0 25.4 + - - +
69S TRP* 3.6 62.9 - - + +
70S TRP* 3.8 27.8 - - + +
73S GLY* 4.6 12.8 - - - -
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Residues in contact with GLY 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280N ALA* 6.1 0.4 - - - -
284N SER* 3.3 16.1 + - - -
336N LEU* 4.0 5.3 - - - +
339N ILE* 4.1 19.9 - - - +
348N TYR 2.8 15.1 + - - -
349N VAL* 3.1 4.2 + - - -
351N MET* 1.3 75.7 - - - +
353N GLN* 1.3 56.3 + - - +
355N ALA* 3.9 3.7 - - - +
356N THR* 2.9 32.4 + - - -
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Residues in contact with GLN 353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284N SER* 3.2 35.8 + - - +
286N PRO* 4.6 10.3 - - - +
349N VAL* 3.0 29.2 + - - +
350N LEU* 3.1 31.0 + - + +
352N GLY* 1.3 75.7 - - - +
354N ILE* 1.3 65.6 + - - +
356N THR* 3.4 3.9 + - - -
357N PHE* 3.1 21.8 + - - +
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Residues in contact with ILE 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350N LEU* 2.8 46.0 + - + +
351N MET 3.1 4.2 + - - +
353N GLN* 1.3 74.6 - - - +
355N ALA* 1.3 56.5 + - - +
357N PHE* 3.2 10.2 + - + +
358N ILE* 3.0 36.7 + - + +
69S TRP* 3.5 30.7 - - + -
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Residues in contact with ALA 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332N ASN* 3.1 32.7 - - - +
335N LEU* 4.2 15.0 - - + -
336N LEU* 3.4 25.1 - - + -
351N MET 3.0 15.5 + - - +
352N GLY 3.9 0.2 - - - +
354N ILE* 1.3 75.7 - - - +
356N THR* 1.3 54.4 + - - +
358N ILE* 3.0 4.0 + - - -
359N TYR* 2.7 33.3 + - - +
69S TRP* 4.4 1.5 - - + -
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Residues in contact with THR 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N ILE* 3.8 38.5 - - + +
284N SER* 3.7 14.5 + - - -
285N ILE* 4.9 8.3 - - + -
294N THR* 4.5 6.1 - - + -
336N LEU* 4.0 6.5 - - - +
352N GLY 2.9 22.5 + - - -
353N GLN* 3.4 6.9 + - - -
355N ALA* 1.3 75.7 - - - +
357N PHE* 1.3 66.9 + - - +
359N TYR* 3.2 14.3 + - - +
360N PHE* 3.2 27.2 + - + -
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Residues in contact with PHE 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353N GLN 3.1 13.3 + - - +
354N ILE* 3.3 13.2 - - + +
356N THR* 1.3 77.7 - - - +
358N ILE* 1.3 59.4 + - + +
360N PHE* 3.3 4.3 + - + +
361N ALA* 2.7 57.0 + - + +
365N ILE* 4.7 14.8 - - + -
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Residues in contact with ILE 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328N ILE* 4.8 12.8 - - + +
329N PHE* 5.6 2.9 - - - -
332N ASN* 3.5 24.2 - - + +
354N ILE* 3.0 30.3 + - + +
355N ALA* 3.0 7.5 + - - +
357N PHE* 1.3 80.8 - - + +
359N TYR* 1.3 64.7 + - - +
361N ALA* 3.0 8.0 + - - +
362N TYR* 2.8 26.1 + - + +
366N ILE* 5.2 10.5 - - + -
66S TYR* 3.3 22.9 - - - +
69S TRP* 4.5 6.1 - - + -
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Residues in contact with TYR 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278N PHE* 4.4 8.6 - + - -
281N ILE* 4.2 9.0 - - + -
298N ALA* 2.4 43.6 + - + +
301N VAL* 3.8 6.3 - - + -
302N LEU* 3.7 13.5 - - - +
329N PHE* 3.7 31.2 - + - -
332N ASN* 3.6 6.0 + - - +
333N PHE* 3.9 23.3 - + + -
336N LEU* 4.1 23.6 - - + -
355N ALA 2.7 15.6 + - - +
356N THR* 3.2 10.7 + - - +
358N ILE* 1.3 75.0 - - - +
360N PHE* 1.3 77.0 + + - +
362N TYR* 3.2 15.8 + - - +
363N PHE* 3.5 25.9 - + - -
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Residues in contact with PHE 360 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N ILE* 4.3 2.0 - - + -
294N THR* 3.3 33.9 - - + -
297N ALA* 3.7 15.7 - - + -
298N ALA* 3.3 46.9 - - + -
301N VAL* 4.2 17.9 - - + -
356N THR* 3.2 29.7 + - + -
357N PHE* 3.9 5.4 - - + +
359N TYR* 1.3 81.7 - + - +
361N ALA* 1.3 64.4 + - - +
362N TYR 3.0 6.0 + - - -
363N PHE* 3.2 7.2 + - - +
364N LEU* 3.1 36.9 + - + +
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Residues in contact with ALA 361 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357N PHE* 2.7 52.2 + - + +
358N ILE* 3.4 6.3 - - - +
360N PHE* 1.3 73.4 - - - +
362N TYR* 1.3 56.5 + - - +
364N LEU* 4.8 1.3 - - - -
365N ILE* 2.8 40.0 + - + +
366N ILE* 3.0 19.1 + - + +
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Residues in contact with TYR 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N LEU* 4.0 24.5 + - + +
305N LEU* 5.4 0.9 - - + -
316N ASN* 5.0 3.5 + - - -
322N SER 5.2 1.1 + - - -
325N PHE* 3.7 27.1 - - + -
326N PHE* 3.9 23.3 + - - +
329N PHE* 3.5 39.0 - + + -
358N ILE* 2.8 11.9 + - + +
359N TYR 3.2 13.0 - - - +
360N PHE 3.0 0.4 + - - -
361N ALA* 1.3 78.9 - - - +
363N PHE* 1.3 72.7 + + - +
364N LEU 3.7 0.2 + - - -
366N ILE* 4.1 26.5 - - + -
367N VAL* 3.1 59.4 + - + +
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Residues in contact with PHE 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N LEU* 4.5 9.9 - - + -
301N VAL* 3.4 51.8 - - + +
302N LEU* 4.0 23.3 - - + -
304N VAL* 4.9 2.7 - - + -
305N LEU* 3.9 38.4 - - + -
308N THR* 2.9 33.7 + - - +
329N PHE* 3.6 23.8 - + - -
359N TYR* 3.5 32.3 - + - -
360N PHE* 3.2 4.3 + - - +
362N TYR* 1.3 90.1 - + - +
364N LEU* 1.3 61.3 - - + +
367N VAL* 4.6 0.4 - - - +
368N PRO* 3.8 2.9 - - - +
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Residues in contact with LEU 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301N VAL* 4.4 15.7 - - + -
304N VAL* 3.9 24.9 - - + -
308N THR* 4.6 5.8 - - + +
360N PHE* 3.1 29.6 + - + +
361N ALA* 4.8 0.7 - - - -
363N PHE* 1.3 86.7 - - + +
365N ILE* 1.3 68.7 + - + +
368N PRO* 3.2 14.5 - - - +
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Residues in contact with ILE 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357N PHE* 4.7 13.2 - - + -
361N ALA* 2.8 31.4 + - + +
364N LEU* 1.3 83.6 - - + +
366N ILE* 1.3 72.7 + - + +
367N VAL 3.5 0.9 - - - -
368N PRO* 3.1 3.3 - - - +
369N VAL* 3.0 40.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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