Contacts of the helix formed by residues 268 - 273 (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 LYS 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP* 2.8 36.7 + - - -
266B ASN* 3.0 23.0 + - - +
267B ILE* 1.3 78.9 - - - +
269B LEU* 1.3 65.2 + - - +
270B MET* 4.2 2.7 - - + +
271B LYS* 3.2 25.3 + - + +
272B ALA* 3.1 24.4 + - - +
294B VAL* 5.4 0.4 - - - -
295B GLY* 4.4 4.7 - - - +
296B SER* 3.6 34.1 - - - +
297B MET* 3.7 24.5 - - + +
2473B GLU* 3.3 30.7 + - - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA* 3.1 5.8 - - - +
105B MET* 4.1 24.5 - - + -
267B ILE* 4.9 1.1 - - + +
268B LYS* 1.3 71.7 - - - +
270B MET* 1.3 62.3 + - + +
273B GLY 3.1 2.4 + - - -
274B GLY* 2.9 50.3 + - - +
275B ILE* 3.8 29.4 - - + -
278B ALA* 3.8 14.6 - - + -
294B VAL* 5.8 2.6 - - + +
295B GLY 5.0 3.2 + - - -
296B SER* 5.8 1.0 - - - +
299B GLU* 5.8 1.7 + - - +
303B GLY 5.8 0.2 - - - +
306B ALA* 3.8 13.7 - - + -
307B ALA* 3.7 37.0 - - + +
310B PHE* 4.6 11.7 - - + -
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Residues in contact with MET 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 3.0 26.0 - - - +
48B ALA* 3.8 2.9 - - - -
49B PRO* 3.7 15.9 - - + +
55B THR* 4.7 3.6 - - + +
97B MET* 3.1 27.5 - - - +
98B SER* 3.6 40.3 + - - +
101B ALA* 3.8 14.6 - - + -
105B MET* 3.2 23.8 - - + -
268B LYS* 3.2 1.2 - - + +
269B LEU* 1.3 79.3 - - + +
271B LYS* 1.3 61.2 + - - +
297B MET* 3.7 29.2 - - + -
299B GLU* 3.6 27.5 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 5.4 1.8 - - + -
97B MET* 3.4 21.3 - - - +
244B ASP* 2.3 53.0 + - - +
245B GLU* 4.8 1.6 - - + -
247B VAL 3.0 14.1 + - - +
248B PHE* 3.4 52.6 - - + +
266B ASN 2.8 23.4 + - - -
267B ILE* 4.7 0.2 - - - +
268B LYS* 3.2 24.3 + - + +
270B MET* 1.3 78.9 - - - +
272B ALA* 1.3 59.8 + - + +
273B GLY 3.2 4.6 + - - -
297B MET* 3.7 24.9 - - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN* 4.2 6.6 + - - +
97B MET* 3.8 9.4 - - - +
248B PHE 3.1 15.9 + - - +
249B THR* 5.0 1.6 - - - +
250B PRO* 5.3 2.4 - - - +
267B ILE* 5.1 0.7 - - + -
268B LYS 3.1 13.1 + - - +
271B LYS* 1.3 76.9 - - - +
273B GLY* 1.3 60.8 - - - +
274B GLY 3.3 17.3 + - - +
277B GLY* 4.0 15.4 + - - -
278B ALA* 3.6 22.9 - - - +
281B ILE* 4.1 6.1 - - + -
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Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLN* 2.7 25.7 + - - -
97B MET* 3.3 33.0 - - - -
100B LYS* 3.3 6.7 - - - +
101B ALA* 3.3 17.5 + - - -
104B GLU* 3.5 1.6 - - - +
269B LEU 3.1 4.0 + - - -
270B MET 3.7 0.2 + - - -
271B LYS 3.2 5.3 + - - -
272B ALA* 1.3 79.1 - - - +
274B GLY* 1.3 55.9 + - - +
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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