Contacts of the helix formed by residues 266 - 283 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264D TYR 3.5 2.7 + - - -
265D ALA* 1.3 75.3 - - - +
267D LEU* 1.3 65.2 + - - +
268D THR* 3.7 9.7 + - - -
269D GLU* 2.7 36.5 + - - +
270D ILE* 3.0 22.4 + - - +
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D SER* 1.3 72.5 - - - +
268D THR* 1.3 56.9 + - - +
270D ILE* 3.3 9.6 + - + +
271D GLU* 2.9 33.8 + - + +
452D HIS* 3.7 37.5 - - + +
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Residues in contact with THR 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D SER* 3.2 9.0 + - - -
267D LEU* 1.3 78.2 - - - +
269D GLU* 1.3 59.5 + - + +
271D GLU* 3.4 4.0 + - - +
272D HIS* 2.9 57.1 + - + +
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Residues in contact with GLU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D TYR 4.4 1.6 - - - +
265D ALA* 3.4 15.8 - - + -
266D SER* 2.7 44.9 + - - +
268D THR* 1.3 79.4 - - + +
270D ILE* 1.3 58.8 + - - +
272D HIS* 3.5 7.8 + - - +
273D LEU* 3.0 27.0 + - - +
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ALA* 3.8 26.0 - - + +
266D SER 3.0 21.0 + - - +
267D LEU* 3.7 12.6 - - + +
269D GLU* 1.3 74.8 - - - +
271D GLU* 1.3 60.3 + - - +
273D LEU* 3.1 8.6 + - + +
274D VAL* 2.9 27.5 + - + +
445D ASN* 3.7 26.9 - - + +
448D LEU* 3.9 25.6 - - + +
449D ALA* 3.7 24.9 - - - +
452D HIS* 4.3 16.6 - - + -
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 2.9 18.4 + - + +
268D THR* 3.9 4.9 - - - +
270D ILE* 1.3 74.8 - - - +
272D HIS* 1.3 62.6 + - + +
274D VAL* 3.5 11.4 + - - +
275D GLN* 3.0 53.5 + - - +
452D HIS* 3.4 24.5 + - - +
456D LYS* 3.1 30.3 + - - -
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Residues in contact with HIS 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D THR* 2.9 44.0 + - + +
269D GLU* 3.6 9.2 - - - +
271D GLU* 1.3 78.6 - - + +
273D LEU* 1.3 55.9 + - - +
275D GLN* 3.2 19.6 + - - +
276D SER* 2.8 30.4 + - - -
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D GLU 3.0 15.2 + - - +
270D ILE* 3.1 11.4 + - + +
272D HIS* 1.3 72.5 - - - +
274D VAL* 1.3 60.8 + - - +
276D SER* 3.9 3.3 - - - -
277D VAL* 3.0 38.2 + - + +
339D SER* 4.0 35.2 - - - +
442D LEU* 4.6 8.5 - - + -
445D ASN* 3.6 44.9 - - + +
446D LEU* 3.8 25.8 - - + -
449D ALA* 4.1 6.3 - - + -
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ILE* 2.9 19.4 + - + +
271D GLU* 3.6 26.7 - - - +
273D LEU* 1.3 76.8 - - - +
275D GLN* 1.3 59.6 + - + +
277D VAL* 3.3 1.0 + - - +
278D CYS* 3.0 47.1 + - - -
419D LEU* 4.1 11.9 - - + -
449D ALA* 3.5 35.2 - - + +
452D HIS* 5.1 1.8 - - + -
453D HIS* 3.9 29.2 - - + +
456D LYS* 4.3 1.8 - - - +
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Residues in contact with GLN 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D GLU* 3.0 43.7 + - - +
272D HIS* 3.2 22.2 + - - +
274D VAL* 1.3 76.9 - - + +
276D SER* 1.3 60.6 - - - +
278D CYS* 4.3 3.4 - - - +
279D LYS* 3.3 26.2 + - - +
282D ARG* 4.8 2.3 + - - -
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Residues in contact with SER 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D HIS 2.8 17.5 + - - -
273D LEU* 3.9 3.6 - - - -
275D GLN* 1.3 75.7 - - - +
277D VAL* 1.3 58.9 + - - +
279D LYS* 3.6 6.0 + - - +
280D SER* 2.7 35.3 + - - -
337D ARG 4.6 2.3 + - - -
338D LEU* 4.8 0.2 - - - +
339D SER* 2.9 41.6 + - - -
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D LEU* 3.0 31.5 + - + +
274D VAL 3.3 3.3 + - - +
276D SER* 1.3 75.3 - - - +
278D CYS* 1.3 65.1 + - - +
280D SER* 3.5 3.3 + - - -
281D TYR* 3.2 21.7 + - - +
334D PHE* 4.1 2.3 - - + -
338D LEU* 3.8 22.4 - - + -
339D SER 5.5 0.2 - - - +
418D ALA* 3.5 32.3 - - + +
419D LEU* 3.9 14.6 - - + +
422D ALA* 3.9 11.0 - - + -
446D LEU* 3.7 26.9 - - + -
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Residues in contact with CYS 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D VAL* 3.0 34.1 + - - +
275D GLN* 4.4 4.3 - - - +
277D VAL* 1.3 73.8 - - - +
279D LYS* 1.3 59.9 + - - +
281D TYR* 3.5 3.3 + - - +
282D ARG* 3.0 43.1 + - - +
415D ASP* 3.5 54.1 - - - +
418D ALA* 4.1 8.7 - - - -
419D LEU* 4.6 6.5 - - - -
453D HIS* 5.2 0.4 - - - -
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLN 3.3 18.8 + - - +
276D SER* 3.8 5.8 - - - +
278D CYS* 1.3 75.8 - - - +
280D SER* 1.3 66.4 + - - +
282D ARG* 3.2 23.8 + - - +
283D GLU* 2.8 63.1 + - + +
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Residues in contact with SER 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D SER 2.7 21.0 + - - -
277D VAL 3.8 4.7 - - - -
278D CYS 3.4 0.2 - - - -
279D LYS* 1.3 77.5 - - - +
281D TYR* 1.3 54.3 + - - +
283D GLU* 3.4 7.3 + - - +
284D THR* 2.7 38.2 + - - +
334D PHE* 3.9 9.4 - - - -
337D ARG* 3.1 40.2 + - - +
338D LEU* 3.8 16.7 - - - +
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Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D VAL 3.2 7.6 + - - +
278D CYS 3.7 3.8 - - - +
280D SER* 1.3 77.5 - - - +
282D ARG* 1.3 71.2 + - + +
284D THR* 3.1 16.6 + - - -
285D CYS* 3.5 33.8 - - - -
334D PHE* 3.8 9.3 - + + -
364D ARG* 4.1 25.4 - - + -
367D ARG* 2.6 35.2 + - - +
414D GLU* 3.3 41.9 + - + -
415D ASP* 5.6 0.7 - - - -
417D ILE* 3.4 27.5 - - + +
418D ALA* 3.5 28.7 - - + -
421D THR* 4.3 7.9 - - - -
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Residues in contact with ARG 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLN 4.8 2.4 + - - -
278D CYS* 3.0 38.5 + - - +
279D LYS* 3.2 33.3 + - - +
281D TYR* 1.3 82.9 - - + +
283D GLU* 1.3 62.7 + - + +
284D THR 3.6 0.7 + - - -
285D CYS* 4.3 9.4 + - - +
414D GLU* 5.8 8.1 - - + +
415D ASP* 3.8 13.3 + - - +
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LYS* 2.8 60.6 + - + +
280D SER* 4.0 4.5 - - - +
281D TYR 3.2 0.4 - - - -
282D ARG* 1.3 79.2 - - + +
284D THR* 1.3 61.7 + - + +
285D CYS 3.8 1.7 - - - +
330D TYR* 5.2 2.9 - - - -
337D ARG* 2.8 42.4 + - - +
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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
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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