Contacts of the helix formed by residues 365 - 381 (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 ILE 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ILE 366 (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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325C PHE* 3.8 51.8 - - + -
328C ILE* 5.5 4.3 - - + -
358C ILE* 5.2 10.3 - - + +
361C ALA* 2.9 20.3 + - + +
362C TYR* 3.8 32.3 - - + +
365C ILE* 1.3 78.6 - - + +
367C VAL* 1.3 66.5 + - - +
369C VAL* 4.8 2.2 - - - -
370C ILE* 2.9 37.8 + - + +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 5.2 1.8 - - - +
305C LEU* 4.2 14.1 - - + -
308C THR* 3.9 12.1 - - - +
309C ASP* 3.8 30.1 - - + +
362C TYR* 3.0 59.4 + - + +
363C PHE 4.4 0.9 - - - +
366C ILE* 1.3 72.9 - - + +
368C PRO* 1.3 57.4 - - + +
370C ILE* 5.0 3.4 - - - -
371C SER* 2.5 40.4 + - - +
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Residues in contact with PRO 368 (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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308C THR* 3.1 29.6 - - + +
310C ARG* 3.4 8.6 - - + +
363C PHE 3.6 15.3 - - - +
364C LEU 3.3 20.9 - - - +
365C ILE* 3.1 19.7 - - - +
367C VAL* 1.3 93.5 - - + +
369C VAL* 1.3 54.5 + - + +
371C SER* 3.0 8.8 + - - +
372C THR* 2.7 28.2 + - - -
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Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C ILE* 3.0 32.3 + - + +
366C ILE* 3.0 4.2 + - - +
368C PRO* 1.3 75.9 - - + +
370C ILE* 1.3 71.4 + - + +
372C THR* 3.0 8.3 + - - -
373C ILE* 2.9 38.5 + - + +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C LEU* 3.6 38.6 - - + +
322C SER* 4.1 11.4 - - - +
325C PHE* 4.1 25.4 - - + -
366C ILE* 2.9 38.5 + - + +
367C VAL* 4.4 2.5 - - - +
369C VAL* 1.3 77.6 - - + +
371C SER* 1.3 58.6 + - - +
373C ILE* 3.2 13.2 + - + +
374C GLU* 2.8 42.2 + - + +
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Residues in contact with SER 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ASP* 4.0 7.4 - - - -
310C ARG* 3.0 20.6 + - - +
311C SER* 3.5 25.4 - - - -
319C LYS* 4.9 2.9 - - - -
322C SER* 5.5 0.7 - - - -
367C VAL* 2.5 26.4 + - - -
368C PRO 3.0 12.5 + - - -
370C ILE* 1.3 76.7 - - - +
372C THR* 1.3 62.0 + - - +
374C GLU* 4.1 10.1 - - - +
375C ASN* 3.2 29.1 + - - +
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Residues in contact with THR 372 (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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310C ARG* 3.6 14.7 + - - +
368C PRO 2.7 18.9 + - - -
369C VAL* 3.0 9.8 + - - -
371C SER* 1.3 79.6 + - - +
373C ILE* 1.3 64.9 + - + +
375C ASN* 2.9 20.1 + - - +
376C VAL* 3.3 10.8 + - + +
3G GLN* 3.8 28.9 - - - +
11G ILE* 4.9 13.0 - - + -
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Residues in contact with ILE 373 (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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321C LEU* 4.2 15.3 - - + -
369C VAL* 2.9 31.6 + - + +
370C ILE* 3.6 14.8 - - + +
372C THR* 1.3 78.3 - - + +
374C GLU* 1.3 64.2 + - - +
375C ASN 3.2 0.3 + - - -
376C VAL* 3.2 8.7 + - - +
377C LEU* 2.9 45.8 + - + +
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Residues in contact with GLU 374 (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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311C SER* 6.6 0.2 - - - -
319C LYS* 3.3 30.5 + - + +
320C VAL 3.4 3.5 + - - -
321C LEU* 3.2 34.5 + - + -
322C SER* 2.6 27.4 + - - -
370C ILE* 2.8 33.3 + - + +
371C SER* 4.1 5.4 - - - +
373C ILE* 1.3 73.6 - - - +
375C ASN* 1.3 63.9 + - - +
377C LEU* 3.6 8.7 - - - +
378C PHE* 3.0 35.1 + - + -
32G PHE* 3.6 18.6 - - + -
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Residues in contact with ASN 375 (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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310C ARG 3.1 18.6 + - - -
311C SER* 3.5 8.5 + - - -
312C VAL* 3.4 24.5 + - - +
313C VAL* 5.7 0.5 - - - +
371C SER 3.2 18.2 + - - +
372C THR 2.9 11.2 + - - +
374C GLU* 1.3 78.1 - - - +
376C VAL* 1.3 62.5 + - + +
378C PHE* 3.4 13.3 - - - +
379C TYR* 3.2 14.6 + - - +
3G GLN* 2.7 31.2 + - - +
8G ILE* 3.6 34.4 - - + +
45G PHE* 5.6 1.2 - - - -
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Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C THR* 3.5 19.5 - - + +
373C ILE* 3.2 7.4 + - - +
375C ASN* 1.3 73.7 - - + +
377C LEU* 1.3 59.3 + - + +
378C PHE 3.0 1.8 - - - -
379C TYR* 2.7 26.8 + - + -
380C ILE* 2.9 21.8 + - + +
3G GLN* 5.4 1.1 - - - +
8G ILE* 4.3 8.5 - - + +
11G ILE* 4.0 27.1 - - + -
12G GLY* 3.9 19.5 - - - +
15G ILE* 3.8 29.6 - - + -
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Residues in contact with LEU 377 (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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321C LEU* 4.5 8.7 - - + -
373C ILE* 2.9 39.7 + - + +
374C GLU* 3.6 9.6 - - - +
376C VAL* 1.3 76.7 - - + +
378C PHE* 1.3 62.1 + - - +
380C ILE* 4.1 17.5 - - + -
381C GLY* 3.1 19.1 + - - -
25G CYS* 5.5 2.9 - - + +
28G VAL* 4.8 16.8 - - + -
29G ALA* 3.4 19.6 - - + +
32G PHE* 3.7 43.5 - - + -
33G ILE* 4.1 2.6 - - - +
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Residues in contact with PHE 378 (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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311C SER* 6.0 0.9 - - - -
313C VAL* 4.9 9.6 - - + -
318C PHE* 3.7 26.5 - - + -
319C LYS* 4.5 14.8 - - + -
374C GLU* 3.0 25.6 + - + -
375C ASN* 3.4 13.2 - - - +
376C VAL 3.0 0.6 - - - -
377C LEU* 1.3 78.3 - - - +
379C TYR* 1.3 58.0 + - - +
381C GLY 3.7 2.3 + - - -
382C ARG* 2.6 29.6 + - - +
32G PHE* 3.7 28.3 - + - -
33G ILE* 3.9 17.5 - - + +
36G ALA* 4.4 4.0 - - + -
38G TYR* 3.9 17.9 - + - -
45G PHE* 3.2 52.5 - + + -
48G LEU* 5.6 0.7 - - + -
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Residues in contact with TYR 379 (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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375C ASN 3.2 2.0 + - - +
376C VAL* 2.7 13.7 + - - +
378C PHE* 1.3 77.1 - - - +
380C ILE* 1.3 63.9 + - + +
381C GLY 3.1 1.0 + - - -
382C ARG* 3.4 10.2 + - - +
383C VAL* 3.2 57.8 + - + +
385C LYS* 3.6 18.0 + - - -
5G PHE* 6.2 1.6 - + - -
8G ILE* 3.6 29.8 - - + -
9G ALA* 3.6 22.0 - - + +
12G GLY* 3.7 18.6 - - - -
13G ASP* 2.9 48.3 + - - -
16G LEU* 4.6 0.9 - - + -
104G LEU* 4.1 22.4 - - + -
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL* 2.9 30.1 + - + +
377C LEU* 3.8 12.8 - - + +
379C TYR* 1.3 73.5 - - + +
381C GLY* 1.3 62.0 + - - +
382C ARG* 3.2 2.4 + - - -
383C VAL 4.1 5.4 + - - +
12G GLY* 3.5 41.1 - - - +
15G ILE* 4.5 11.2 - - + -
16G LEU* 4.0 29.8 - - + +
25G CYS* 3.9 29.6 - - + -
26G VAL* 4.3 13.2 - - + +
29G ALA* 3.5 19.9 - - + +
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Residues in contact with GLY 381 (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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377C LEU 3.1 9.5 + - - -
379C TYR 3.1 1.4 - - - -
380C ILE* 1.3 77.8 - - - +
382C ARG* 1.3 59.1 + - - +
29G ALA* 3.6 11.0 - - - -
30G ASN* 3.0 28.1 + - - -
33G ILE* 3.4 26.8 - - - +
39G LYS* 5.8 1.0 + - - -
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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