Contacts of the helix formed by residues 274 - 288 (chain A) in PDB entry 1TKK
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 GLY 274 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 3.4 14.8 - - - +
104A GLU* 3.3 12.3 - - - -
105A MET* 6.2 0.2 - - - -
269A LEU* 2.9 22.4 + - - +
272A ALA* 3.8 4.7 - - - +
273A GLY* 1.3 78.8 - - - +
275A ILE* 1.3 65.3 + - - -
276A SER 3.5 0.4 - - - -
277A GLY 4.0 1.3 + - - -
278A ALA* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.8 7.9 + - - +
105A MET* 4.7 11.9 - - - -
108A TYR* 3.6 39.7 - - + +
119A LEU* 3.9 26.0 - - + -
123A LEU* 4.0 23.3 - - + -
269A LEU* 3.6 23.8 - - + -
274A GLY* 1.3 70.3 - - - -
276A SER* 1.3 59.1 + - - +
278A ALA* 3.1 5.2 + - - +
279A GLU* 2.8 32.9 + - + +
306A ALA* 4.4 8.3 - - + +
310A PHE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.0 22.3 - - - +
90A GLN* 4.5 8.1 + - - +
104A GLU* 2.8 33.6 + - - -
108A TYR* 3.5 20.0 + - - -
275A ILE* 1.3 72.6 - - - +
277A GLY* 1.3 61.8 + - - +
279A GLU* 3.6 9.3 + - - +
280A LYS* 3.2 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 5.7 1.5 - - - +
104A GLU* 4.8 0.2 + - - -
250A PRO* 3.9 17.6 - - - +
272A ALA* 3.9 16.8 + - - -
274A GLY 4.0 3.4 + - - -
275A ILE 3.3 0.4 - - - -
276A SER* 1.3 81.6 + - - +
278A ALA* 1.3 65.6 + - - +
280A LYS* 3.2 6.1 + - - +
281A ILE* 3.1 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 3.5 30.6 - - + +
269A LEU* 3.7 16.8 - - + -
272A ALA* 3.6 7.7 - - + +
274A GLY 3.4 20.6 + - - +
275A ILE* 3.1 5.3 + - - +
277A GLY* 1.3 74.7 - - - +
279A GLU* 1.3 63.9 + - - +
281A ILE* 3.2 6.1 + - - +
282A ASN 3.1 18.5 + - - -
310A PHE* 3.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 4.3 13.7 + - - -
123A LEU* 4.2 16.2 - - - +
275A ILE* 2.8 16.9 + - + +
276A SER* 3.7 7.3 - - - +
278A ALA* 1.3 79.4 - - - +
280A LYS* 1.3 59.9 + - + +
282A ASN* 3.9 2.9 - - - +
283A ALA* 3.3 23.4 + - + +
310A PHE* 3.4 17.0 - - + -
314A LYS* 2.8 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 5.8 1.8 + - - -
86A LEU* 6.0 2.4 - - - +
90A GLN* 6.2 1.2 - - - +
250A PRO* 3.9 25.8 - - + -
276A SER* 3.2 34.6 + - - +
277A GLY* 3.2 10.0 + - - +
279A GLU* 1.3 77.5 - - + +
281A ILE* 1.3 63.9 + - - +
283A ALA* 3.5 5.3 + - - +
284A MET* 3.2 30.7 + - + +
283B ALA* 4.2 29.3 - - + +
286B GLU* 4.5 18.3 + - - +
287B ALA* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 4.5 4.5 - - + +
248A PHE 3.5 25.8 - - - +
249A THR 3.9 6.7 - - - +
250A PRO* 3.7 20.2 - - + -
253A ALA* 3.8 23.3 - - + -
257A LEU* 4.7 1.0 - - - +
265A ILE* 3.8 30.1 - - + -
267A ILE* 3.8 15.0 - - + -
272A ALA* 4.1 7.4 - - + -
277A GLY 3.1 23.8 + - - +
278A ALA* 3.2 7.6 + - - +
280A LYS* 1.3 74.1 - - - +
282A ASN* 1.3 68.5 + - - +
283A ALA 3.2 0.2 + - - -
284A MET* 3.3 3.5 + - - +
285A ALA* 3.0 21.1 + - - +
292A CYS* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 3.7 12.3 - - + +
278A ALA 3.1 14.0 + - - +
279A GLU* 3.9 5.4 - - - +
281A ILE* 1.3 79.9 - - - +
283A ALA* 1.3 53.9 + - - +
285A ALA* 3.3 0.5 + - - +
286A GLU* 2.8 34.3 + - - +
292A CYS* 3.8 10.0 - - - -
310A PHE* 4.3 8.1 - - + -
314A LYS* 3.6 21.7 - - - +
316A ASN* 3.1 37.0 + - - +
317A ILE* 3.2 29.0 - - - +
83B GLU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 3.3 17.3 + - + +
280A LYS* 3.9 5.4 - - - +
281A ILE 3.2 0.8 - - - -
282A ASN* 1.3 80.9 - - - +
284A MET* 1.3 64.0 + - - +
286A GLU* 3.3 11.2 + - - +
287A ALA* 3.1 21.7 + - - +
280B LYS* 4.3 33.9 - - + +
283B ALA* 6.2 2.9 - - + -
284B MET* 5.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 3.6 36.8 - - + +
253A ALA* 4.4 5.2 - - - -
254A PHE* 3.9 28.9 - - + -
257A LEU* 3.7 10.1 - - + -
280A LYS* 3.2 17.4 + - + +
281A ILE 3.7 6.5 - - - +
283A ALA* 1.3 73.3 - - - +
285A ALA* 1.3 66.6 + - - +
287A ALA* 3.3 8.8 + - - +
288A CYS* 3.3 26.2 + - - -
254B PHE* 4.8 4.1 - - + -
283B ALA* 4.8 2.0 - - + +
284B MET* 3.7 36.3 - - + +
287B ALA* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.6 11.9 - - - +
265A ILE* 4.2 9.4 - - + -
281A ILE 3.0 18.6 + - - +
282A ASN 3.4 5.4 - - - +
284A MET* 1.3 75.3 - - - +
286A GLU* 1.3 63.9 + - - +
288A CYS* 3.0 8.3 + - - +
290A VAL* 2.8 50.1 + - + +
292A CYS* 3.6 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASN* 2.8 20.6 + - - +
283A ALA* 3.5 9.7 - - - +
284A MET 3.3 0.2 - - - -
285A ALA* 1.3 76.6 - - - +
287A ALA* 1.3 60.4 + - - +
289A GLY* 3.2 13.3 + - - -
290A VAL 4.1 0.4 - - - +
315A ARG* 4.8 5.9 + - - +
316A ASN* 3.5 39.2 + - + +
83B GLU* 4.7 10.9 - - - +
87B HIS* 4.7 15.8 + - - -
91B HIS* 5.7 1.0 + - - -
280B LYS* 3.4 29.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA 3.1 13.4 + - - +
284A MET 3.6 9.9 - - - +
285A ALA 3.3 0.2 - - - -
286A GLU* 1.3 75.1 - - - +
288A CYS* 1.3 60.5 + - - +
289A GLY 3.5 0.4 + - - -
250B PRO* 4.2 14.1 - - + +
251B ARG* 3.2 33.9 - - - +
254B PHE* 5.5 2.5 - - + -
280B LYS* 6.3 0.7 - - + -
284B MET* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 4.0 26.5 - - + +
260A ARG* 5.9 1.0 + - - -
284A MET 3.3 13.4 + - - +
285A ALA 3.0 9.0 + - - +
287A ALA* 1.3 79.8 - - - +
289A GLY* 1.3 58.7 + - - +
290A VAL* 3.6 7.5 + - + +
251B ARG* 5.0 9.6 - - - +
254B PHE* 3.8 42.2 - - - -
226G ASP* 5.7 1.9 - - - +
----------------------------------------------------------
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