Contacts of the helix formed by residues 268 - 273 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C ASP* 2.6 44.1 + - - -
266C ASN* 3.4 18.1 + - - +
267C ILE* 1.3 80.4 - - - +
269C LEU* 1.3 64.3 + - - +
270C MET* 4.3 2.5 - - + +
271C LYS* 3.3 24.4 + - + +
272C ALA* 3.2 23.4 + - - +
294C VAL* 5.2 1.1 - - - -
295C GLY* 3.9 16.6 - - - +
296C SER* 3.5 30.5 - - - +
297C MET* 3.4 28.2 - - + +
299C GLU* 6.0 0.2 - - - +
2475C GLU* 3.5 18.8 + - - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA* 3.3 3.7 - - + +
105C MET* 3.9 34.1 - - + -
267C ILE* 5.3 0.7 - - + -
268C LYS* 1.3 69.6 - - - +
270C MET* 1.3 68.8 + - + +
272C ALA 3.3 0.5 + - - -
273C GLY 3.0 20.6 + - - -
274C GLY* 3.0 32.5 + - - +
275C ILE* 3.8 26.5 - - + -
278C ALA* 3.8 16.8 - - + -
294C VAL* 5.6 2.0 - - + -
295C GLY 4.9 2.4 + - - -
296C SER* 5.9 0.6 - - - +
299C GLU* 6.0 0.9 - - - +
306C ALA* 4.0 17.0 - - + -
307C ALA* 4.1 22.9 - - + +
310C PHE* 4.5 12.3 - - + -
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Residues in contact with MET 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU 3.2 24.0 - - - +
48C ALA* 3.7 15.0 - - - -
49C PRO* 3.9 6.5 - - + +
51C THR* 5.6 0.4 - - - +
55C THR* 4.4 4.4 - - + +
97C MET* 3.2 27.0 - - - +
98C SER* 3.5 38.9 + - - +
101C ALA* 3.8 9.9 - - + -
105C MET* 3.4 22.0 - - + -
268C LYS* 3.4 2.1 - - + +
269C LEU* 1.3 79.3 - - + +
271C LYS* 1.3 62.9 + - - +
297C MET* 3.7 30.3 - - + -
299C GLU* 3.7 25.4 + - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 5.5 1.8 - - + -
97C MET* 3.4 15.1 - - - +
244C ASP* 2.5 35.9 + - - +
245C GLU* 4.9 1.3 - - + -
247C VAL 2.5 25.9 + - - +
248C PHE* 3.5 61.4 - - + +
266C ASN 2.8 24.1 + - - -
267C ILE* 4.7 0.4 - - - +
268C LYS* 3.3 28.3 + - + +
269C LEU 3.2 0.8 - - - -
270C MET* 1.3 78.4 - - - +
272C ALA* 1.3 59.9 + - - +
273C GLY 3.2 1.7 + - - -
297C MET* 3.9 21.1 - - + -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLN* 4.0 7.3 + - - +
97C MET* 3.6 11.0 - - - +
248C PHE 3.2 17.0 - - - +
249C THR* 4.8 2.5 - - - +
250C PRO* 5.2 2.1 - - - +
267C ILE* 5.2 0.9 - - + -
268C LYS 3.2 12.3 + - - +
269C LEU 3.3 0.2 + - - -
271C LYS* 1.3 76.9 - - - +
273C GLY* 1.3 61.3 + - - +
274C GLY 3.4 7.9 + - - +
277C GLY* 3.8 16.5 - - - -
278C ALA* 3.5 30.1 - - - +
281C ILE* 4.0 5.4 - - + -
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Residues in contact with GLY 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLN* 2.9 21.9 + - - -
97C MET* 3.1 33.3 - - - +
100C LYS* 3.2 18.9 - - - +
101C ALA* 3.4 7.0 - - - -
104C GLU* 3.2 4.4 - - - +
269C LEU 3.0 3.8 + - - -
270C MET 3.6 0.8 + - - -
271C LYS 3.2 5.9 + - - -
272C ALA* 1.3 78.3 - - - +
274C GLY* 1.3 55.2 + - - +
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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