Contacts of the helix formed by residues 345 - 365 (chain C) 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 GLU 345 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C HIS* 3.0 30.5 + - + +
344C VAL* 1.3 79.5 - - - +
346C VAL* 1.3 54.1 + - - +
347C PRO* 3.3 1.3 - - - +
348C TYR* 2.8 36.1 + - + +
349C VAL* 3.3 12.5 + - - +
62D MET* 2.9 48.6 + - - +
77H ASN* 3.0 28.3 + - - +
81H TYR* 3.7 24.4 - - + +
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Residues in contact with VAL 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU* 1.3 71.5 - - - +
347C PRO* 1.3 68.2 - - + +
349C VAL* 4.1 10.2 + - - +
350C LEU* 4.5 9.2 + - - +
76H TYR* 4.6 7.0 - - + -
80H LEU* 3.8 17.7 - - + -
81H TYR* 4.6 3.0 + - - +
89H LEU* 4.8 4.7 - - + -
92H VAL* 3.8 30.7 - - + +
93H ASN* 3.8 42.0 - - + +
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Residues in contact with PRO 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU 3.3 3.6 - - - +
346C VAL* 1.3 97.8 - - + +
348C TYR* 1.3 65.8 + - + +
350C LEU* 4.3 2.8 + - - +
351C MET* 3.4 26.4 + - - +
73H GLY* 3.3 23.3 - - - +
76H TYR* 4.0 20.6 - - + -
77H ASN* 3.3 44.2 - - + +
80H LEU* 4.2 9.0 - - + -
81H TYR* 5.3 0.2 - - + -
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Residues in contact with TYR 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 3.9 16.6 - - + +
342C CYS* 3.7 18.8 - - + -
343C HIS* 3.7 26.7 - + - +
345C GLU* 2.8 13.6 + - + +
347C PRO* 1.3 80.9 - - + +
349C VAL* 1.3 58.2 + - - +
351C MET* 3.4 12.5 - - - +
352C GLY* 2.9 24.8 + - - -
70H TRP* 3.4 36.4 - + - -
73H GLY 4.2 5.4 - - - -
74H ASN* 2.4 41.9 + - - -
77H ASN* 3.4 40.6 + - + +
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ARG 5.8 4.0 - - - +
284C SER* 4.4 4.1 + - - +
344C VAL* 3.8 31.4 - - + +
345C GLU* 3.3 21.3 + - - +
346C VAL* 4.5 5.2 - - - +
347C PRO 3.6 0.6 - - - -
348C TYR* 1.3 72.3 - - - +
350C LEU* 1.3 67.4 + - - +
352C GLY* 3.0 12.1 + - - -
353C GLN* 3.1 38.0 + - + +
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C VAL 4.5 7.2 + - - +
347C PRO 4.3 5.3 + - - +
348C TYR 3.5 0.2 - - - -
349C VAL* 1.3 79.4 - - - +
351C MET* 1.3 67.4 + - + +
353C GLN* 3.3 20.1 + - + +
354C ILE* 3.0 56.8 + - + +
69H TRP* 6.0 0.2 - - + -
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Residues in contact with MET 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.2 12.5 - - + +
339C ILE* 4.0 8.5 - - + -
347C PRO 3.4 18.6 + - - +
348C TYR* 3.4 27.2 + - - +
349C VAL 3.1 0.2 - - - -
350C LEU* 1.3 84.0 - - + +
352C GLY* 1.3 62.0 + - - +
354C ILE* 3.3 2.4 + - - +
355C ALA* 2.9 26.3 + - - +
69H TRP* 3.5 63.9 - - + +
70H TRP* 4.0 24.2 - - + -
73H GLY* 4.5 13.5 - - - -
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Residues in contact with GLY 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA 5.6 0.2 - - - -
284C SER* 3.2 17.0 - - - -
336C LEU* 3.9 4.3 - - - +
339C ILE* 4.0 21.7 - - - +
348C TYR 2.9 14.6 + - - -
349C VAL* 3.0 3.5 + - - -
351C MET* 1.3 75.3 - - - +
353C GLN* 1.3 56.7 + - - +
355C ALA* 3.4 3.8 + - - +
356C THR* 2.8 32.6 + - - -
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 3.1 38.3 + - - +
286C PRO* 4.5 9.1 - - - +
349C VAL* 3.1 28.7 + - + +
350C LEU* 3.5 27.9 - - + +
351C MET 3.2 0.2 - - - -
352C GLY* 1.3 74.6 - - - +
354C ILE* 1.3 65.6 + - - +
356C THR* 3.2 5.4 + - - +
357C PHE* 2.9 22.7 + - - +
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Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU* 3.0 50.3 + - + +
351C MET 3.8 3.4 - - - +
353C GLN* 1.3 75.4 - - + +
355C ALA* 1.3 58.7 + - - +
357C PHE* 2.9 12.6 + - + +
358C ILE* 2.9 38.2 + - + +
69H TRP* 3.7 28.0 - - + -
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ASN* 3.1 31.4 - - - +
335C LEU* 3.8 17.9 - - + -
336C LEU* 3.4 24.6 - - + +
351C MET 2.9 17.5 + - - +
352C GLY 3.6 0.7 - - - +
354C ILE* 1.3 72.9 - - - +
356C THR* 1.3 66.4 + - - +
358C ILE* 3.3 3.0 + - - -
359C TYR* 3.0 20.6 + - - +
69H TRP* 4.5 2.2 - - + -
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Residues in contact with THR 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 3.6 40.9 - - + +
284C SER* 4.0 5.9 + - - -
285C ILE* 5.2 9.2 - - + -
294C THR* 4.8 4.9 - - + -
336C LEU* 4.0 6.6 - - - +
352C GLY 2.8 17.6 + - - -
353C GLN* 3.2 11.6 + - - +
355C ALA* 1.3 74.4 - - - +
357C PHE* 1.3 67.4 + - - +
359C TYR* 3.1 16.2 + - - +
360C PHE* 3.2 30.0 + - + -
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C GLN 2.9 12.7 + - - +
354C ILE* 3.1 13.5 - - + +
356C THR* 1.3 79.1 - - - +
358C ILE* 1.3 61.9 + - + +
360C PHE* 3.1 5.8 + - + +
361C ALA* 2.7 55.5 + - + +
365C ILE* 4.5 14.4 - - + -
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Residues in contact with ILE 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ILE* 4.4 15.7 - - + -
329C PHE* 5.5 3.1 - - + -
332C ASN* 3.4 25.6 - - + +
354C ILE* 2.9 33.3 + - + +
355C ALA* 3.5 7.6 - - - +
357C PHE* 1.3 80.1 - - + +
359C TYR* 1.3 64.0 + - - +
361C ALA* 3.0 9.0 + - - +
362C TYR* 2.8 25.5 + - + +
366C ILE* 5.2 8.1 - - + +
66H TYR* 3.4 21.8 - - - +
69H TRP* 4.6 7.0 - - + -
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Residues in contact with TYR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE* 4.3 10.4 - + - -
281C ILE* 4.4 9.4 - - + -
298C ALA* 2.5 46.0 + - + +
301C VAL* 4.0 11.7 - - + -
302C LEU* 4.4 8.0 - - - +
329C PHE* 3.7 30.5 - + - -
332C ASN* 3.4 10.2 + - - +
333C PHE* 4.0 23.7 - + + -
336C LEU* 4.3 17.7 - - + -
355C ALA 3.0 12.9 + - - +
356C THR* 3.2 10.5 - - - +
358C ILE* 1.3 78.0 - - - +
360C PHE* 1.3 76.4 + + - +
362C TYR* 3.2 15.8 + - - +
363C PHE* 3.5 21.7 - + - -
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Residues in contact with PHE 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 4.5 1.8 - - + -
294C THR* 3.3 45.8 - - + -
297C ALA* 3.8 16.6 - - + -
298C ALA* 3.4 30.3 - - + -
301C VAL* 4.2 20.4 - - + -
356C THR* 3.2 25.0 + - + +
357C PHE* 3.1 7.8 + - - +
359C TYR* 1.3 87.0 - + - +
361C ALA* 1.3 62.6 + - - +
362C TYR 3.3 0.3 + - - -
363C PHE* 3.3 6.5 + - - +
364C LEU* 3.2 41.5 + - + +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C PHE* 2.7 47.1 + - + +
358C ILE* 3.0 6.9 + - - +
360C PHE* 1.3 74.8 - - - +
362C TYR* 1.3 54.0 + - - +
364C LEU* 5.1 0.4 - - - -
365C ILE* 2.7 45.3 + - + +
366C ILE* 2.9 18.1 + - + -
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Residues in contact with TYR 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 5.2 9.5 - - + +
305C LEU* 5.5 3.1 - - + -
316C ASN* 5.1 3.1 + - - -
322C SER 4.9 1.6 + - - -
325C PHE* 3.5 30.7 - - + -
326C PHE* 3.6 27.8 - + - +
328C ILE* 6.2 0.7 - - + -
329C PHE* 3.5 42.0 - + + -
358C ILE* 2.8 12.2 + - + +
359C TYR 3.4 11.7 - - - +
360C PHE 3.2 0.4 - - - -
361C ALA* 1.3 77.0 - - - +
363C PHE* 1.3 75.0 + + - +
366C ILE* 3.8 24.7 - - + +
367C VAL* 3.0 60.2 + - + +
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Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.9 6.1 - - + -
301C VAL* 3.9 41.3 - - + -
302C LEU* 3.5 28.0 - - + -
304C VAL* 4.3 3.8 - - + -
305C LEU* 4.0 36.8 - - + -
308C THR* 3.2 31.1 + - - +
329C PHE* 3.6 36.1 - + - -
359C TYR* 3.5 34.3 - + - -
360C PHE* 3.3 5.5 + - - +
361C ALA 3.3 0.2 - - - -
362C TYR* 1.3 89.3 - + - +
364C LEU* 1.3 61.0 + - - +
367C VAL* 4.9 1.8 - - - -
368C PRO* 3.6 4.0 - - - +
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 4.2 8.5 - - + -
304C VAL* 4.1 28.3 - - + -
308C THR* 4.8 5.0 - - + +
360C PHE* 3.2 33.1 + - + +
361C ALA* 5.1 0.4 - - - -
363C PHE* 1.3 82.9 - - + +
365C ILE* 1.3 65.6 + - + +
368C PRO* 3.3 14.8 - - - +
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Residues in contact with ILE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C PHE* 4.5 15.0 - - + -
361C ALA* 2.7 35.1 + - + +
363C PHE 3.7 0.6 - - - -
364C LEU* 1.3 84.1 - - + +
366C ILE* 1.3 72.6 + - + +
368C PRO* 3.1 4.7 - - - +
369C VAL* 3.0 39.3 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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