Contacts of the helix formed by residues 266 - 284 (chain C) in PDB entry 5NTI
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 SER 266 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C TYR 3.3 4.0 + - - -
265C ALA* 1.3 76.0 - - - +
267C LEU* 1.3 64.9 + - - +
268C THR* 3.4 10.3 + - - -
269C GLU* 2.9 35.5 + - - +
270C ILE* 3.1 22.6 + - - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C SER* 1.3 73.9 - - - +
268C THR* 1.3 59.5 + - - +
270C ILE* 3.5 5.9 + - + +
271C GLU* 3.0 44.3 + - - +
452C HIS* 3.9 33.7 - - + +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C SER* 3.2 9.4 + - - -
267C LEU* 1.3 80.3 - - - +
269C GLU* 1.3 58.4 + - + +
271C GLU* 3.3 13.2 + - + +
272C HIS* 2.8 58.6 + - + +
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C TYR 4.2 2.6 - - - +
265C ALA* 3.4 15.7 - - + -
266C SER* 2.9 40.5 + - - +
268C THR* 1.3 80.9 - - + +
270C ILE* 1.3 58.2 + - - +
272C HIS* 3.4 8.8 + - - +
273C LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 3.7 26.7 - - + +
266C SER 3.1 20.0 + - - +
267C LEU* 3.9 6.3 - - + +
269C GLU* 1.3 72.5 - - - +
271C GLU* 1.3 61.5 + - - +
273C LEU* 3.1 8.2 + - + +
274C VAL* 2.9 27.2 + - - +
445C ASN* 3.4 33.4 - - + +
448C LEU* 3.8 24.2 - - + +
449C ALA* 3.7 24.0 - - - +
452C HIS* 4.3 17.0 - - + -
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Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 3.0 36.9 + - - +
268C THR* 3.6 11.1 + - + +
270C ILE* 1.3 77.4 - - - +
272C HIS* 1.3 59.5 + - - +
274C VAL* 3.4 11.8 + - + +
275C GLN* 3.2 30.5 + - - +
452C HIS* 3.3 33.8 + - + +
456C LYS* 3.4 21.4 + - - +
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Residues in contact with HIS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C THR* 2.8 44.5 + - + +
269C GLU* 3.6 8.7 + - - +
270C ILE 3.3 0.2 - - - -
271C GLU* 1.3 74.4 - - + +
273C LEU* 1.3 61.1 + - - +
275C GLN* 3.2 31.4 + - - +
276C SER* 2.8 29.6 + - - -
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLU 2.9 14.1 + - - +
270C ILE* 3.1 13.0 + - + +
272C HIS* 1.3 74.9 - - - +
274C VAL* 1.3 64.8 + - - +
276C SER* 3.8 3.3 - - - -
277C VAL* 3.0 39.7 + - + +
339C SER* 4.1 32.3 - - - +
442C LEU* 5.3 6.3 - - + -
445C ASN* 3.6 44.9 - - + +
446C LEU* 3.9 20.9 - - + +
449C ALA* 4.2 4.9 - - + -
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 2.9 22.4 + - + +
271C GLU* 3.4 13.0 - - - +
273C LEU* 1.3 75.8 - - - +
275C GLN* 1.3 63.5 + - + +
277C VAL* 4.0 0.9 - - - +
278C CYS* 3.1 41.0 + - - -
415C ASP* 5.8 0.2 - - - +
419C LEU* 4.1 10.5 - - + -
449C ALA* 3.5 32.5 - - + +
452C HIS* 4.8 7.6 - - + -
453C HIS* 3.8 29.2 - - + +
456C LYS* 6.3 0.9 - - - +
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Residues in contact with GLN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLU* 3.2 17.9 + - - +
272C HIS* 3.2 33.0 + - - +
274C VAL* 1.3 77.6 - - + +
276C SER* 1.3 58.6 + - - +
278C CYS* 3.3 6.0 + - - +
279C LYS* 2.8 33.4 + - - +
282C ARG* 5.0 1.6 + - - -
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Residues in contact with SER 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C HIS 2.8 20.0 + - - -
273C LEU* 3.8 8.5 - - - -
274C VAL 3.4 0.2 - - - -
275C GLN* 1.3 73.7 - - - +
277C VAL* 1.3 58.2 + - - +
279C LYS* 3.4 10.5 + - - +
280C SER* 3.0 33.7 + - - -
337C ARG 4.7 2.1 + - - -
338C LEU* 5.7 0.4 - - - -
339C SER* 3.4 31.1 + - - -
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Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 3.0 28.4 + - + +
274C VAL 4.1 2.2 - - - +
276C SER* 1.3 75.1 - - - +
278C CYS* 1.3 64.9 + - - +
280C SER* 3.3 3.3 + - - -
281C TYR* 3.1 22.5 + - - +
334C PHE* 4.0 3.2 - - + -
338C LEU* 3.8 24.7 - - + -
339C SER 5.5 1.8 - - - +
418C ALA 3.4 32.1 - - - +
419C LEU* 4.0 11.7 - - + -
422C ALA* 3.7 11.4 - - + -
446C LEU* 3.7 26.2 - - + -
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Residues in contact with CYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C VAL* 3.1 37.8 + - - +
275C GLN* 3.7 5.2 - - - +
277C VAL* 1.3 76.4 - - - +
279C LYS* 1.3 60.0 + - - +
281C TYR* 3.6 2.6 + - - +
282C ARG* 3.2 39.2 + - - +
415C ASP* 3.3 55.4 - - - +
418C ALA* 4.0 9.6 - - + -
419C LEU* 4.5 5.8 - - - -
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLN 2.8 17.6 + - - +
276C SER* 3.5 9.4 - - - +
278C CYS* 1.3 73.8 - - - +
280C SER* 1.3 67.1 + - - +
282C ARG* 3.3 21.9 + - - +
283C GLU* 2.8 63.8 + - + +
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C SER* 3.0 18.8 + - - -
277C VAL* 3.3 6.2 + - - -
279C LYS* 1.3 75.8 - - - +
281C TYR* 1.3 54.9 - - - +
283C GLU* 3.5 7.1 + - - +
284C THR* 2.6 38.4 + - - +
334C PHE* 3.8 15.5 - - - -
337C ARG* 2.9 44.5 + - - +
338C LEU* 4.2 3.8 - - - -
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Residues in contact with TYR 281 (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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277C VAL 3.1 10.3 + - - +
278C CYS 3.7 4.7 - - - +
279C LYS 3.2 0.2 - - - -
280C SER* 1.3 73.9 - - - +
282C ARG* 1.3 68.1 + - + +
284C THR* 3.1 13.3 + - - -
285C CYS* 3.2 36.3 + - - -
334C PHE* 3.6 14.1 - + + -
364C ARG* 4.1 26.0 + - + +
367C ARG* 3.0 27.4 - - - +
414C GLU* 3.5 45.3 - - + -
417C ILE* 3.6 35.2 - - + +
418C ALA* 3.5 28.9 - - + -
421C THR* 4.6 5.4 - - - -
601C C3S 5.0 1.6 + - - -
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Residues in contact with ARG 282 (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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275C GLN 5.0 1.2 + - - -
278C CYS* 3.2 24.6 + - - +
279C LYS* 3.3 27.3 + - - +
281C TYR* 1.3 83.5 - - + +
283C GLU* 1.3 63.0 + - + +
284C THR 3.5 0.3 + - - -
285C CYS* 3.7 8.3 + - - +
288C ARG* 3.5 31.8 + - - +
367C ARG* 6.1 0.4 - - - +
414C GLU* 3.4 25.1 - - + +
415C ASP* 3.8 19.4 + - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LYS* 2.8 56.3 + - + +
280C SER* 3.9 5.0 - - - +
281C TYR 3.2 0.2 - - - -
282C ARG* 1.3 78.1 - - + +
284C THR* 1.3 62.4 + - - +
285C CYS 3.5 2.6 - - - +
330C TYR* 5.3 3.1 - - - -
333C GLU* 5.8 0.3 - - - +
337C ARG* 2.8 36.3 + - - +
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Residues in contact with THR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C SER 2.6 22.7 + - - +
281C TYR 3.1 3.2 + - - -
283C GLU* 1.3 81.0 - - - +
285C CYS* 1.3 59.1 + - - +
330C TYR* 3.2 31.9 - - - +
333C GLU* 3.7 12.8 - - + -
334C PHE* 3.3 27.0 - - - +
337C ARG* 3.7 21.8 - - - +
364C ARG* 2.8 39.6 + - - -
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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
------------------------------------------------------------
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