Contacts of the helix formed by residues 266 - 284 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A TYR 3.4 3.5 + - - -
265A ALA* 1.3 76.2 - - - +
267A LEU* 1.3 61.1 + - - +
268A THR* 3.8 8.8 + - - -
269A GLU* 3.0 34.0 + - - +
270A ILE* 2.9 27.2 + - - +
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Residues in contact with LEU 267 (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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266A SER* 1.3 74.1 - - - +
268A THR* 1.3 58.6 + - - +
270A ILE* 3.8 8.1 - - + -
271A GLU* 3.0 40.9 + - - +
452A HIS* 3.5 35.9 - - + +
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.2 8.6 + - - -
267A LEU* 1.3 77.2 - - - +
269A GLU* 1.3 60.1 + - - +
271A GLU* 3.4 11.2 + - + +
272A HIS* 2.9 53.4 + - + +
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR 3.9 4.5 - - - +
265A ALA* 3.5 20.6 - - + +
266A SER* 3.0 39.8 + - - +
268A THR* 1.3 77.2 - - - +
270A ILE* 1.3 58.5 + - - +
272A HIS* 3.4 8.7 + - - +
273A LEU* 2.9 28.5 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA* 3.7 28.0 - - + +
266A SER 2.9 19.4 + - - +
267A LEU* 3.8 10.1 - - + +
269A GLU* 1.3 74.5 - - - +
271A GLU* 1.3 59.3 + - - +
273A LEU* 3.1 11.1 + - + +
274A VAL* 2.9 32.4 + - - +
445A ASN* 3.9 11.7 - - - +
448A LEU* 3.8 33.2 - - + +
449A ALA* 3.8 20.6 - - - +
452A HIS* 3.9 25.4 - - + +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.0 34.5 + - - +
268A THR* 3.8 13.6 + - + +
270A ILE* 1.3 75.4 - - - +
272A HIS* 1.3 61.2 + - + +
274A VAL* 3.5 10.8 + - - +
275A GLN* 3.3 33.0 + - - +
452A HIS* 3.4 24.8 + - + +
456A LYS* 3.3 23.4 + - - +
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Residues in contact with HIS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 2.9 41.5 + - + +
269A GLU* 3.6 7.9 + - - +
271A GLU* 1.3 75.1 - - + +
273A LEU* 1.3 60.0 + - - +
275A GLN* 3.5 16.7 + - + +
276A SER* 2.9 30.9 + - - -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU 2.9 17.0 + - - +
270A ILE* 3.1 11.4 + - + +
272A HIS* 1.3 74.5 - - - +
274A VAL* 1.3 58.7 + - - +
276A SER* 3.7 3.6 - - - -
277A VAL* 3.0 37.4 + - + +
339A SER* 3.6 36.6 - - - +
442A LEU* 5.2 3.8 - - + -
445A ASN* 3.4 44.4 - - + +
446A LEU* 4.0 23.8 - - + +
449A ALA* 3.8 9.2 - - + -
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Residues in contact with VAL 274 (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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270A ILE 2.9 21.2 + - - +
271A GLU* 3.7 9.0 - - - +
272A HIS 3.3 0.2 - - - -
273A LEU* 1.3 76.5 - - - +
275A GLN* 1.3 65.4 - - + +
277A VAL* 3.3 2.9 + - - +
278A CYS* 3.1 38.8 + - - -
419A LEU* 4.3 9.6 - - + -
449A ALA* 3.4 32.8 - - + +
452A HIS* 4.4 15.0 - - + -
453A HIS* 4.0 28.3 - - + +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 3.3 23.6 + - - +
272A HIS* 3.5 17.9 + - + +
274A VAL* 1.3 83.0 - - + +
276A SER* 1.3 56.2 + - - +
278A CYS* 4.0 4.8 - - - +
279A LYS* 3.1 32.0 + - - +
282A ARG* 4.9 1.2 + - - -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A HIS 2.9 18.7 + - - -
273A LEU* 3.7 7.9 - - - -
274A VAL 3.3 0.2 - - - -
275A GLN* 1.3 76.3 - - - +
277A VAL* 1.3 58.4 + - - +
279A LYS* 4.0 15.3 + - - +
280A SER* 2.8 34.4 + - - -
337A ARG 4.6 2.6 + - - -
339A SER* 3.4 26.6 + - - -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.0 26.6 + - + +
274A VAL 3.8 3.4 - - - +
276A SER* 1.3 75.1 - - - +
278A CYS* 1.3 65.3 + - - +
280A SER* 3.4 7.2 + - - -
281A TYR* 3.1 21.8 + - - +
334A PHE* 4.0 1.9 - - + -
338A LEU* 3.7 22.0 - - + -
339A SER 5.4 1.8 - - - +
418A ALA* 3.5 32.1 - - + +
419A LEU* 3.9 20.2 - - + +
422A ALA* 4.1 5.8 - - + -
446A LEU* 3.7 25.1 - - + -
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Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 3.1 28.5 + - - +
275A GLN* 4.1 4.9 - - - +
277A VAL* 1.3 77.1 - - - +
279A LYS* 1.3 58.1 + - - +
281A TYR* 3.8 2.9 - - - +
282A ARG* 3.1 41.2 + - - +
415A ASP* 3.7 53.5 - - - +
418A ALA* 3.9 10.1 - - + -
419A LEU* 4.2 12.1 - - - -
453A HIS* 5.4 0.4 - - - -
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Residues in contact with LYS 279 (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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275A GLN 3.1 20.1 + - - +
276A SER* 4.0 14.4 + - - +
278A CYS* 1.3 72.6 - - - +
280A SER* 1.3 69.5 + - - +
281A TYR 3.1 1.6 - - - -
282A ARG* 3.3 25.2 + - - +
283A GLU* 3.1 56.2 + - + +
337A ARG* 6.4 0.2 - - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 2.8 20.8 + - - -
277A VAL* 3.6 7.6 - - - -
279A LYS* 1.3 82.3 + - - +
281A TYR* 1.3 55.4 + - - +
283A GLU* 3.6 6.2 + - - +
284A THR* 2.7 38.3 + - - +
334A PHE* 3.8 15.0 - - - -
337A ARG* 2.9 42.8 + - - +
338A LEU* 3.9 4.6 + - - -
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Residues in contact with TYR 281 (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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277A VAL 3.1 9.7 + - - +
278A CYS 3.8 3.8 - - - +
280A SER* 1.3 73.5 - - - +
282A ARG* 1.3 70.5 + - + +
283A GLU 3.2 1.6 - - - -
284A THR* 3.1 11.4 + - - -
285A CYS* 3.3 32.6 + - - -
334A PHE* 3.6 13.0 - + + -
364A ARG* 4.0 24.7 - - + -
367A ARG* 2.8 33.1 + - - -
414A GLU* 3.5 40.5 + - + -
417A ILE* 3.3 28.3 - - + +
418A ALA* 3.4 36.6 - - + -
421A THR* 4.2 7.9 - - - -
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Residues in contact with ARG 282 (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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275A GLN 4.9 1.8 + - - -
278A CYS* 3.1 33.2 + - - +
279A LYS* 3.3 34.4 + - - +
281A TYR* 1.3 84.9 - - + +
283A GLU* 1.3 62.9 + - + +
284A THR 3.6 0.2 + - - -
285A CYS* 4.1 12.3 + - - +
414A GLU* 5.6 10.3 - - + +
415A ASP* 4.5 8.2 + - - +
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Residues in contact with GLU 283 (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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279A LYS* 3.1 47.7 + - + +
280A SER* 4.0 4.0 - - - +
282A ARG* 1.3 80.5 - - + +
284A THR* 1.3 62.0 + - + +
285A CYS 3.6 2.6 - - - +
330A TYR* 5.5 2.3 - - - -
337A ARG* 2.9 39.4 + - - +
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Residues in contact with THR 284 (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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280A SER 2.7 22.8 + - - +
281A TYR 3.1 3.6 + - - -
283A GLU* 1.3 81.4 - - - +
285A CYS* 1.3 60.5 + - - +
330A TYR* 3.3 32.2 - - - +
333A GLU* 3.8 23.8 - - + +
334A PHE* 3.4 26.6 - - - +
337A ARG* 4.1 12.1 - - - +
364A ARG* 2.9 34.0 + - - -
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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