Contacts of the helix formed by residues 268 - 273 (chain F) 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 LYS 268 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 5.9 1.6 - - - +
244F ASP* 2.7 33.5 + - - -
245F GLU* 5.7 1.0 - - - +
266F ASN* 3.4 16.6 - - - +
267F ILE* 1.3 81.6 - - - +
269F LEU* 1.3 67.4 + - - +
270F MET* 4.3 3.4 - - + +
271F LYS* 3.2 25.7 + - + +
272F ALA* 3.0 23.6 + - - +
294F VAL* 5.3 0.7 - - - -
295F GLY* 3.6 19.1 - - - +
296F SER* 3.4 31.9 - - - +
297F MET* 3.9 21.4 - - + +
299F GLU* 6.1 0.2 - - - +
2481F GLU* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F ALA* 3.2 4.0 - - + +
105F MET* 3.8 34.5 - - + -
267F ILE* 5.3 0.9 - - + -
268F LYS* 1.3 73.1 - - - +
270F MET* 1.3 58.1 - - + +
273F GLY 2.9 10.2 + - - -
274F GLY* 2.8 48.9 + - - +
275F ILE* 3.9 24.5 - - + -
278F ALA* 4.1 13.2 - - + -
294F VAL* 5.4 1.3 - - + -
295F GLY 5.0 1.6 + - - -
296F SER* 6.1 0.2 - - - +
299F GLU* 5.9 0.9 - - - +
306F ALA* 3.8 19.7 - - + -
307F ALA* 3.9 27.8 - - + +
310F PHE* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F GLU 3.1 23.6 - - - +
48F ALA* 3.9 1.8 - - - -
49F PRO* 3.9 16.6 - - + -
51F THR* 5.7 0.4 - - - +
55F THR* 4.4 3.8 - - + +
97F MET* 3.1 27.5 - - - +
98F SER* 3.6 41.3 + - - +
101F ALA* 3.6 16.8 - - + -
105F MET* 3.4 23.3 - - + -
268F LYS* 3.3 3.0 - - + +
269F LEU* 1.3 80.2 - - + +
271F LYS* 1.3 60.3 + - - +
273F GLY 3.6 0.2 + - - -
297F MET* 3.9 29.4 - - + -
299F GLU* 3.8 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 5.5 2.0 - - + -
97F MET* 3.3 17.2 - - - +
244F ASP* 2.4 50.3 + - - +
245F GLU* 4.9 1.6 - - + -
247F VAL 3.1 10.7 + - - +
248F PHE* 3.4 59.5 - - + +
266F ASN* 3.1 25.9 + - - -
267F ILE* 4.7 0.4 - - - +
268F LYS* 3.2 32.7 + - + +
270F MET* 1.3 76.9 - - - +
272F ALA* 1.3 61.5 + - - +
273F GLY 3.2 0.2 - - - -
297F MET* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLN* 3.8 8.3 + - - +
97F MET* 3.6 11.2 - - - +
248F PHE 3.2 16.4 - - - +
249F THR* 5.0 1.7 - - - +
250F PRO* 5.5 2.1 - - - +
267F ILE* 5.2 1.3 - - + -
268F LYS 3.0 14.7 + - - +
271F LYS* 1.3 75.2 - - - +
273F GLY* 1.3 62.8 + - - +
274F GLY 3.5 10.7 + - - +
277F GLY* 4.1 12.9 + - - -
278F ALA* 3.6 31.4 - - + +
281F ILE* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLN* 2.7 24.7 + - - -
97F MET* 3.1 34.0 - - - +
100F LYS* 3.5 14.4 - - - -
101F ALA* 3.5 7.2 - - - -
104F GLU* 3.5 2.8 - - - +
269F LEU 2.9 4.3 + - - -
270F MET 3.6 0.8 + - - -
271F LYS 3.2 5.7 + - - -
272F ALA* 1.3 78.2 - - - +
274F GLY* 1.3 56.1 + - - +
276F SER* 5.9 0.2 - - - -
----------------------------------------------------------
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