Contacts of the helix formed by residues 274 - 288 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.7 13.9 - - - -
104B GLU* 3.5 10.5 - - - -
105B MET 5.6 0.2 - - - -
269B LEU* 2.9 25.5 + - - +
272B ALA* 3.1 6.8 - - - +
273B GLY* 1.3 80.4 - - - +
275B ILE* 1.3 61.5 + - - -
276B SER 3.7 0.4 - - - -
277B GLY 4.6 0.4 - - - -
278B ALA* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 2.8 7.7 + - - +
105B MET* 4.8 11.4 - - - +
108B TYR* 3.6 51.4 - - + -
119B LEU* 4.1 17.7 - - + -
123B LEU* 4.3 20.0 - - + -
269B LEU* 3.8 33.7 - - + -
274B GLY* 1.3 70.3 - - - -
276B SER* 1.3 64.6 + - - +
277B GLY 3.3 1.3 - - - -
278B ALA* 3.7 2.2 - - - +
279B GLU* 2.9 25.7 + - + +
306B ALA* 4.6 7.6 - - + +
310B PHE* 4.5 12.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
86B LEU* 3.8 19.0 - - - +
90B GLN* 4.5 7.3 + - - +
104B GLU* 2.6 31.3 + - - -
108B TYR* 3.5 20.8 + - - -
275B ILE* 1.3 78.3 - - - +
277B GLY* 1.3 61.3 + - - +
279B GLU* 3.3 8.4 + - - +
280B LYS* 3.1 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN* 6.1 0.6 - - - -
250B PRO* 3.8 18.7 - - - +
272B ALA* 4.0 20.1 + - - -
274B GLY 4.3 2.0 + - - -
276B SER* 1.3 80.8 + - - +
278B ALA* 1.3 60.4 + - - +
280B LYS* 3.2 6.6 + - - +
281B ILE* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.5 29.4 - - + +
269B LEU* 3.8 11.9 - - + -
272B ALA* 3.6 9.4 - - + +
274B GLY 3.3 21.6 + - - +
275B ILE* 3.3 5.5 + - - +
277B GLY* 1.3 75.7 - - - +
279B GLU* 1.3 61.2 + - - +
281B ILE* 3.4 6.1 + - - +
282B ASN 3.2 15.4 + - - -
310B PHE* 3.1 23.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.6 0.9 + - - -
108B TYR* 4.5 12.1 + - - -
123B LEU* 3.9 20.6 - - - +
275B ILE* 2.9 16.9 + - + +
276B SER* 3.4 7.2 - - - +
278B ALA* 1.3 76.5 - - - +
280B LYS* 1.3 63.3 + - + +
282B ASN* 3.5 3.0 + - - +
283B ALA* 3.2 23.6 + - + +
310B PHE* 3.4 14.8 - - + -
314B LYS* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 4.3 30.3 - - + +
286A GLU* 3.4 28.0 + - - +
287A ALA* 6.3 0.4 - - + -
83B GLU* 5.6 4.0 + - - -
250B PRO* 4.0 21.5 - - + -
276B SER* 3.1 32.6 + - - +
277B GLY* 3.2 9.1 + - - +
279B GLU* 1.3 78.3 - - + +
281B ILE* 1.3 61.5 + - - +
283B ALA* 3.9 5.1 - - - +
284B MET* 3.3 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 4.6 4.7 - - + +
248B PHE 3.6 25.1 - - - +
249B THR 3.8 11.4 - - - +
250B PRO* 3.7 19.1 - - + -
253B ALA* 3.9 17.4 - - + +
265B ILE* 4.0 19.7 - - + -
267B ILE* 3.8 25.8 - - + -
272B ALA* 4.1 12.1 - - + -
277B GLY 3.0 20.0 + - - +
278B ALA* 3.7 7.6 - - - +
279B GLU 3.2 0.2 - - - -
280B LYS* 1.3 77.0 - - - +
282B ASN* 1.3 66.0 + - - +
284B MET* 3.6 5.7 + - - +
285B ALA* 3.1 22.2 + - - +
292B CYS* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 5.1 0.7 - - - +
267B ILE* 4.1 8.7 - - + +
278B ALA 3.2 13.1 + - - +
279B GLU* 3.5 5.3 + - + +
280B LYS 3.4 0.2 - - - -
281B ILE* 1.3 81.1 - - - +
283B ALA* 1.3 52.6 + - - +
285B ALA 3.7 0.2 - - - -
286B GLU* 2.8 37.6 + - - +
292B CYS* 3.8 13.3 - - - -
310B PHE* 4.2 7.6 - - + -
314B LYS* 3.5 26.2 - - - +
316B ASN* 2.8 42.2 + - - +
317B ILE* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS* 4.2 33.0 - - + +
283A ALA* 6.2 2.7 - - + -
284A MET* 5.1 2.7 - - + -
279B GLU* 3.2 19.7 + - + +
280B LYS* 3.9 7.4 - - - +
282B ASN* 1.3 75.3 + - - +
284B MET* 1.3 64.4 + - - +
286B GLU* 3.3 11.8 + - - +
287B ALA* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 4.8 1.5 - - + -
283A ALA 5.0 1.8 - - - +
284A MET* 3.7 38.1 - - + +
287A ALA* 3.9 16.6 - - + -
250B PRO* 3.3 48.9 - - + +
253B ALA* 4.5 4.0 - - - -
254B PHE* 3.8 29.6 - - + -
257B LEU* 3.8 9.6 - - + -
280B LYS* 3.3 23.7 + - + +
281B ILE 3.7 4.7 - - - +
283B ALA* 1.3 79.6 - - - +
285B ALA* 1.3 60.7 + - - +
287B ALA* 3.5 3.8 + - - +
288B CYS* 3.3 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.8 17.0 - - + -
265B ILE* 4.4 4.3 - - + -
281B ILE 3.1 16.0 + - - +
282B ASN 3.7 1.3 - - - +
283B ALA 3.2 0.2 - - - -
284B MET* 1.3 77.6 - - - +
286B GLU* 1.3 64.5 + - - +
288B CYS* 3.0 7.4 + - - -
290B VAL* 2.8 50.2 + - + +
292B CYS* 3.6 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 4.6 12.7 - - - +
87A HIS* 4.4 17.2 + - - -
280A LYS* 4.5 19.8 + - - +
282B ASN* 2.8 23.5 + - - +
283B ALA* 3.5 7.7 - - - +
285B ALA* 1.3 77.2 - - - +
287B ALA* 1.3 56.9 + - - +
289B GLY* 3.0 20.0 + - - +
290B VAL 4.7 0.2 - - - +
315B ARG* 4.9 6.4 + - - +
316B ASN* 3.6 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 4.3 16.6 - - + -
251A ARG* 3.3 27.5 - - + +
254A PHE* 5.7 0.9 - - + -
280A LYS* 6.2 1.8 - - + -
284A MET* 3.6 26.5 - - + -
283B ALA 3.1 9.1 + - - +
284B MET 3.5 10.1 - - - +
285B ALA 3.3 0.2 - - - -
286B GLU* 1.3 75.5 - - - +
288B CYS* 1.3 59.6 + - - +
289B GLY 3.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG* 5.2 7.9 - - - +
254A PHE* 3.5 45.3 - - - -
257B LEU* 4.0 24.9 - - + +
260B ARG* 5.3 9.3 + - - +
284B MET 3.3 14.5 + - - +
285B ALA 3.0 8.9 + - - +
287B ALA* 1.3 77.4 - - - +
289B GLY* 1.3 61.7 + - - +
290B VAL* 3.2 8.1 + - + +
226F ASP* 4.9 11.2 - - - +
----------------------------------------------------------
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