Contacts of the helix formed by residues 268 - 273 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244G ASP* 2.6 32.7 + - - -
266G ASN* 2.8 34.7 + - - +
267G ILE* 1.3 76.2 - - - +
269G LEU* 1.3 68.1 + - - +
270G MET* 4.2 5.2 - - + +
271G LYS* 3.4 23.9 + - + +
272G ALA* 3.1 24.9 + - - +
294G VAL* 5.1 0.9 - - - -
295G GLY* 3.9 15.3 - - - +
296G SER* 3.2 30.7 - - - +
297G MET* 3.7 28.7 - - + +
299G GLU* 6.1 0.2 - - - +
2483G GLU* 3.3 16.7 + - - -
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Residues in contact with LEU 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G ALA* 3.3 5.1 - - + +
105G MET* 3.4 37.0 - - + -
267G ILE* 5.4 0.9 - - + -
268G LYS* 1.3 72.2 - - - +
270G MET* 1.3 65.3 + - + +
273G GLY 3.2 3.8 + - - -
274G GLY* 2.9 50.9 + - - +
275G ILE* 3.9 19.5 - - + +
278G ALA* 3.8 17.0 - - + -
294G VAL* 5.5 1.6 - - + -
295G GLY 5.0 1.8 + - - -
296G SER* 5.9 0.4 - - - +
299G GLU* 5.9 1.1 + - - +
306G ALA* 3.7 9.9 - - + -
307G ALA* 3.7 33.6 - - + +
310G PHE* 4.7 11.4 - - + -
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Residues in contact with MET 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G GLU 3.1 23.8 - - - +
48G ALA* 3.7 7.2 - - - -
49G PRO* 3.7 19.3 - - + +
51G THR* 5.6 0.7 - - - +
55G THR* 4.6 3.2 - - + +
97G MET* 3.0 34.5 - - - +
98G SER* 3.4 33.6 + - - +
101G ALA* 4.0 10.3 - - + -
105G MET* 3.8 20.2 - - + -
268G LYS* 3.3 2.8 - - + +
269G LEU* 1.3 78.5 - - + +
271G LYS* 1.3 56.8 + - - +
297G MET* 3.7 30.3 - - + -
299G GLU* 3.7 25.3 + - - +
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Residues in contact with LYS 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ILE* 5.8 0.7 - - + -
55G THR* 5.2 0.4 - - - -
97G MET* 3.3 21.7 - - - +
244G ASP* 2.3 48.1 + - - +
245G GLU* 4.7 2.2 - - + -
247G VAL 3.2 11.8 + - - -
248G PHE* 3.5 61.5 - - + +
266G ASN* 2.7 29.4 + - - -
267G ILE* 4.7 0.4 - - - +
268G LYS* 3.4 26.8 + - + +
269G LEU 3.3 0.4 - - - -
270G MET* 1.3 78.4 - - - +
272G ALA* 1.3 57.4 + - - +
273G GLY 3.3 4.2 + - - -
297G MET* 3.9 22.2 - - + -
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Residues in contact with ALA 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G GLN* 4.2 5.4 + - - +
97G MET* 3.6 8.8 - - - +
248G PHE 3.3 18.4 - - - +
249G THR* 5.0 2.2 - - - +
250G PRO* 5.4 2.3 - - - +
267G ILE* 5.1 0.9 - - + -
268G LYS 3.1 16.1 + - - +
271G LYS* 1.3 76.9 - - - +
273G GLY* 1.3 58.7 + - - +
274G GLY 3.2 8.1 + - - +
277G GLY* 3.8 17.6 + - - -
278G ALA* 3.5 26.9 - - - +
281G ILE* 4.0 8.1 - - + -
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Residues in contact with GLY 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G GLN* 2.8 26.0 + - - -
97G MET* 3.4 31.8 - - - +
100G LYS* 3.1 20.3 - - - +
101G ALA* 3.5 6.5 - - - -
104G GLU* 3.7 2.5 - - - -
269G LEU 3.2 3.0 + - - -
270G MET 3.6 1.4 + - - -
271G LYS 3.3 6.1 + - - -
272G ALA* 1.3 76.4 - - - +
274G 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