Contacts of the helix formed by residues 266 - 284 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR 4.0 1.0 + - - -
265B ALA* 1.3 74.8 - - - +
267B LEU* 1.3 65.1 + - - +
268B THR* 3.4 11.3 + - - -
269B GLU* 2.9 36.0 + - - +
270B ILE* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 1.3 73.9 - - - +
268B THR* 1.3 57.4 + - - +
270B ILE* 3.4 8.9 + - + +
271B GLU* 3.0 30.8 + - + +
452B HIS* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 3.2 9.3 + - - -
267B LEU* 1.3 75.6 - - - +
269B GLU* 1.3 61.4 + - + +
271B GLU* 3.4 6.7 + - + +
272B HIS* 2.9 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR 4.1 4.0 - - - +
265B ALA* 3.3 17.4 - - + -
266B SER* 2.9 40.5 + - - +
268B THR* 1.3 79.7 - - + +
270B ILE* 1.3 58.5 + - - +
272B HIS* 3.5 7.9 + - - +
273B LEU* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 3.8 23.8 - - + +
266B SER 3.0 22.4 + - - +
267B LEU* 3.7 10.1 - - + +
269B GLU* 1.3 74.8 - - - +
271B GLU* 1.3 59.3 + - - +
273B LEU* 3.2 9.5 + - + +
274B VAL* 3.0 27.1 + - - +
445B ASN* 3.9 25.6 - - + +
448B LEU* 3.9 30.5 - - + +
449B ALA* 3.8 22.4 - - - +
452B HIS* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.0 19.9 + - + +
268B THR* 3.8 6.7 - - + +
270B ILE* 1.3 76.7 - - - +
272B HIS* 1.3 65.2 + - + +
274B VAL* 3.5 13.9 + - - +
275B GLN* 3.3 38.0 + - - +
452B HIS* 4.8 11.5 + - - +
456B LYS* 3.2 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 2.9 42.1 + - + +
269B GLU* 3.8 8.5 + - - +
271B GLU* 1.3 80.1 - - + +
273B LEU* 1.3 58.9 + - - +
275B GLN* 3.6 17.1 + - - +
276B SER* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLU 3.0 15.2 + - - +
270B ILE* 3.2 13.4 + - + +
272B HIS* 1.3 74.9 - - - +
274B VAL* 1.3 59.2 + - - +
276B SER* 3.1 4.2 + - - -
277B VAL* 2.9 44.6 + - + +
339B SER* 3.8 35.2 - - - +
442B LEU* 5.4 3.6 - - + -
445B ASN* 3.4 42.6 - - + +
446B LEU* 4.1 17.3 - - + +
449B ALA* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE 3.0 22.0 + - - +
271B GLU* 3.6 20.6 - - - +
273B LEU* 1.3 75.4 - - - +
275B GLN* 1.3 60.2 + - + +
277B VAL* 3.4 2.4 + - - +
278B CYS* 3.1 42.7 + - - -
419B LEU* 4.2 11.6 - - + +
449B ALA* 3.4 33.0 - - + +
452B HIS* 4.6 9.4 - - + -
453B HIS* 3.7 32.1 - - + +
456B LYS* 5.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLU* 3.3 36.5 + - - +
272B HIS* 3.9 18.2 - - - +
273B LEU 3.3 0.4 - - - -
274B VAL* 1.3 80.1 - - + +
276B SER* 1.3 60.5 + - - +
278B CYS* 3.9 5.7 - - - +
279B LYS* 3.0 31.6 + - - +
282B ARG* 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B HIS 2.9 20.1 + - - -
273B LEU* 3.5 9.2 - - - -
275B GLN* 1.3 76.3 - - - +
277B VAL* 1.3 60.2 + - - +
279B LYS* 3.8 7.0 - - - +
280B SER* 2.9 29.5 + - - -
337B ARG 4.8 2.6 + - - -
339B SER* 3.7 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 2.9 28.4 + - + +
274B VAL 3.9 3.6 - - - +
276B SER* 1.3 73.1 - - - +
278B CYS* 1.3 66.4 + - - +
280B SER* 3.4 3.7 + - - -
281B TYR* 3.1 22.2 + - - +
334B PHE* 3.9 1.8 - - + -
338B LEU* 3.8 20.9 - - + -
339B SER 5.5 1.8 - - - +
418B ALA 3.5 30.7 - - - +
419B LEU* 3.9 14.1 - - + -
422B ALA* 3.9 12.1 - - + -
446B LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.1 37.0 + - - +
275B GLN* 3.9 6.5 - - - +
277B VAL* 1.3 76.8 - - - +
279B LYS* 1.3 56.4 + - - +
281B TYR* 3.6 3.1 + - - +
282B ARG* 3.1 44.1 + - - +
415B ASP* 3.2 52.7 - - - +
418B ALA* 3.9 9.4 - - - -
419B LEU* 4.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLN 3.0 18.9 + - - +
276B SER* 3.8 7.9 - - - +
277B VAL 3.2 0.2 - - - -
278B CYS* 1.3 74.8 - - - +
280B SER* 1.3 64.9 + - - +
282B ARG* 3.4 23.8 + - - +
283B GLU* 2.8 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER 2.9 15.1 + - - -
277B VAL* 3.4 8.9 + - - -
279B LYS* 1.3 77.2 - - - +
281B TYR* 1.3 56.7 + - - +
283B GLU* 3.4 5.7 + - - -
284B THR* 2.7 38.3 + - - +
334B PHE* 3.8 15.9 - - - -
337B ARG* 3.0 43.6 + - - +
338B LEU* 4.0 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL 3.1 8.2 + - - +
278B CYS 3.7 3.6 - - - +
279B LYS 3.2 0.2 - - - -
280B SER* 1.3 79.7 - - - +
282B ARG* 1.3 70.4 + - + +
284B THR* 3.3 3.0 + - - -
285B CYS* 3.3 41.7 + - - -
334B PHE* 3.6 13.2 - + + -
364B ARG* 4.0 26.2 - - + -
367B ARG* 2.6 33.4 + - - -
414B GLU* 3.4 45.3 + - + -
417B ILE* 3.3 26.7 - - + +
418B ALA* 3.5 29.4 - - + -
421B THR* 4.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLN 4.9 2.2 + - - -
278B CYS* 3.1 36.8 + - - +
279B LYS* 3.6 30.8 - - - +
281B TYR* 1.3 85.3 - - + +
283B GLU* 1.3 63.6 + - + +
284B THR 3.5 0.7 + - - -
285B CYS* 3.8 15.4 + - - +
288B ARG* 5.0 18.3 + - - +
414B GLU* 5.6 9.6 - - + +
415B ASP* 4.1 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LYS* 2.8 59.3 + - + +
280B SER* 3.9 4.8 - - - +
281B TYR 3.2 0.2 - - - -
282B ARG* 1.3 78.5 - - + +
284B THR* 1.3 61.9 + - + +
285B CYS 3.6 2.2 - - - +
330B TYR* 5.4 2.4 - - - -
337B ARG* 3.3 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER 2.7 22.7 + - - +
281B TYR 3.3 2.8 + - - -
282B ARG 3.3 0.6 - - - -
283B GLU* 1.3 80.5 - - - +
285B CYS* 1.3 60.2 + - - +
330B TYR* 3.3 33.3 - - - +
333B GLU* 3.7 23.3 - - + -
334B PHE* 3.4 26.3 - - - +
337B ARG* 3.8 11.2 - - - +
364B ARG* 2.9 37.0 + - - -
----------------------------------------------------------
Back to top of page
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