Contacts of the helix formed by residues 268 - 273 (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 LYS 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASP* 2.6 38.3 + - - -
266A ASN* 2.8 28.3 + - - +
267A ILE* 1.3 73.1 - - - +
269A LEU* 1.3 67.5 + - - +
270A MET* 4.2 3.1 - - + +
271A LYS* 3.4 25.9 + - + +
272A ALA* 3.2 24.1 + - - +
295A GLY* 3.8 6.1 - - - +
296A SER* 3.6 27.1 - - - +
297A MET* 3.6 30.7 - - + -
2471A GLU* 3.5 32.2 + - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.1 6.3 - - + +
105A MET* 4.3 29.2 - - + -
267A ILE* 4.9 1.8 - - + -
268A LYS* 1.3 72.1 - - - +
270A MET* 1.3 66.0 + - + +
272A ALA 4.5 0.2 - - - +
273A GLY 3.1 3.6 + - - -
274A GLY* 2.9 37.9 + - - +
275A ILE* 3.6 31.2 - - + +
278A ALA* 3.7 26.2 - - + -
294A VAL* 5.1 2.9 - - + -
295A GLY 4.9 3.0 + - - -
296A SER* 5.8 0.4 - - - +
299A GLU* 5.9 0.6 + - - +
306A ALA* 4.3 3.6 - - + -
307A ALA* 4.2 33.9 - - + +
310A PHE* 4.5 14.4 - - + -
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Residues in contact with MET 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 3.1 24.7 - - - +
48A ALA* 3.6 27.1 - - + -
49A PRO* 3.8 6.3 - - + -
51A THR* 5.8 0.2 - - - +
55A THR* 4.7 3.3 - - + +
97A MET* 3.2 27.7 - - - +
98A SER* 3.6 24.7 + - - +
101A ALA* 3.6 20.6 - - + -
105A MET* 3.3 23.1 - - + -
268A LYS* 3.3 2.1 - - + +
269A LEU* 1.3 78.5 - - + +
271A LYS* 1.3 60.9 + - - +
297A MET* 3.7 36.3 - - + -
299A GLU* 3.8 15.8 + - - +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 5.5 2.0 - - + -
55A THR* 5.1 0.2 - - - -
97A MET* 3.5 18.0 - - - +
244A ASP* 2.7 45.7 + - - +
245A GLU* 4.8 1.3 - - + -
247A VAL 2.8 13.7 + - - +
248A PHE* 3.5 59.0 - - + +
266A ASN 2.7 26.4 + - - -
267A ILE* 4.7 0.2 - - - +
268A LYS* 3.4 30.6 + - + +
269A LEU 3.3 0.6 - - - -
270A MET* 1.3 78.8 - - - +
272A ALA* 1.3 59.0 + - - +
273A GLY 3.2 4.0 + - - -
297A MET* 4.0 18.2 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 4.1 6.2 + - - +
97A MET* 3.6 11.9 - - - +
248A PHE 3.3 16.6 - - - +
249A THR* 5.1 1.8 - - - +
250A PRO* 5.6 1.9 - - - +
267A ILE* 5.2 0.4 - - + -
268A LYS 3.2 14.1 + - - +
269A LEU 3.5 0.2 + - - -
271A LYS* 1.3 78.4 - - - +
273A GLY* 1.3 62.2 + - - +
274A GLY 3.3 6.6 + - - +
277A GLY* 3.9 16.7 - - - -
278A ALA* 3.6 29.8 - - - +
281A ILE* 4.1 4.0 - - + -
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Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 2.7 26.0 + - - -
97A MET* 3.2 34.3 - - - +
100A LYS* 3.6 8.6 - - - +
101A ALA* 3.4 8.1 - - - -
104A GLU* 3.4 8.3 - - - +
269A LEU 3.1 4.7 + - - -
270A MET 3.6 0.8 + - - -
271A LYS 3.2 6.1 + - - -
272A ALA* 1.3 77.8 - - - +
274A GLY* 1.3 55.7 + - - +
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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