Contacts of the helix formed by residues 300 - 314 (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 THR 300 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G ILE* 3.5 30.7 - - + -
13G VAL* 5.0 2.5 - - + -
29G ALA* 5.7 4.7 - - + +
31G SER* 5.0 1.8 - - - -
47G GLU* 2.7 25.9 + - - +
299G GLU* 1.3 76.8 - - - +
301G LYS* 1.3 64.2 + - - +
302G LEU 3.1 8.0 + - - -
303G GLY 3.2 11.1 + - - -
304G ILE* 3.3 8.7 + - - +
325G PRO* 3.7 3.6 - - - -
328G LEU* 4.1 23.1 - - + -
331G ASP* 5.8 0.4 - - - -
332G VAL* 4.1 10.5 - - + -
333G PHE* 3.3 17.6 - - - -
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Residues in contact with LYS 301 (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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300G THR* 1.3 75.1 - - - +
302G LEU* 1.3 49.8 + - - +
304G ILE* 3.6 1.5 - - - -
305G THR* 2.7 50.9 + - - +
325G PRO* 3.6 21.6 - - + +
331G ASP* 2.9 33.0 + - - +
333G PHE* 2.5 39.4 + - + -
334G ASN* 4.3 0.2 - - - +
335G GLY 2.8 26.5 + - - +
336G GLY* 4.8 0.7 - - - -
337G ILE* 3.5 31.0 + - + +
339G TYR* 4.6 11.9 - - + -
354G ILE* 5.3 0.4 - - - -
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Residues in contact with LEU 302 (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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33G ILE* 4.1 6.7 - - + -
45G TRP* 3.6 33.2 - - + +
46G GLY* 3.5 30.5 - - - +
47G GLU* 3.6 17.7 - - + +
105G MET* 5.5 0.9 - - - -
300G THR* 3.1 3.0 + - - -
301G LYS* 1.3 77.4 - - - +
303G GLY* 1.3 61.6 + - - +
305G THR* 3.3 6.0 + - - -
306G ALA* 3.2 20.3 + - - +
333G PHE* 3.6 43.4 - - + +
352G LEU* 4.3 6.5 - - + -
354G ILE* 3.8 20.2 - - + -
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Residues in contact with GLY 303 (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* 3.0 19.0 + - - -
105G MET* 4.0 18.5 - - - +
299G GLU* 3.1 27.4 - - - +
300G THR 3.2 2.1 + - - -
302G LEU* 1.3 72.6 - - - +
304G ILE* 1.3 60.2 + - - +
306G ALA* 3.6 3.1 + - - +
307G ALA* 3.1 25.5 + - - +
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Residues in contact with ILE 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G SER* 3.2 37.2 - - - +
299G GLU* 4.0 13.2 - - + +
300G THR 3.3 2.2 + - - +
301G LYS* 3.3 7.1 + - - +
302G LEU 3.3 0.4 - - - -
303G GLY* 1.3 76.9 - - - +
305G THR* 1.3 60.2 + - - +
307G ALA* 3.9 3.7 - - - +
308G ALA* 2.8 28.3 + - + +
322G PHE* 3.7 28.8 - - + +
324G ALA* 4.5 0.4 - - + -
325G PRO* 3.1 35.4 - - + -
337G ILE* 4.0 14.8 - - + -
339G TYR* 3.3 19.3 - - - +
344G ILE* 4.9 0.2 - - + -
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Residues in contact with THR 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301G LYS* 2.7 24.9 + - - +
302G LEU* 3.5 9.8 - - - -
304G ILE* 1.3 77.3 - - - +
306G ALA* 1.3 63.0 + - - +
308G ALA* 3.4 0.5 + - - +
309G HIS* 3.0 45.3 + - + -
336G GLY* 3.5 8.2 - - - -
337G ILE* 3.2 36.2 + - - +
352G LEU* 3.4 35.0 - - + +
354G ILE* 4.4 3.3 - - + +
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Residues in contact with ALA 306 (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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105G MET* 3.7 43.1 - - + -
269G LEU* 3.7 13.3 - - + +
275G ILE* 4.5 7.0 - - + +
302G LEU 3.2 7.4 + - - +
303G GLY 3.8 1.1 - - - +
304G ILE 3.3 0.2 - - - -
305G THR* 1.3 80.4 - - - +
307G ALA* 1.3 62.4 + - - +
309G HIS* 3.4 2.3 + - - +
310G PHE* 3.2 21.7 + - - +
352G LEU* 3.6 18.4 - - + +
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Residues in contact with ALA 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G LEU* 3.7 17.7 - - + +
294G VAL* 4.0 12.6 - - + +
295G GLY 4.1 6.7 - - - +
296G SER* 5.3 3.4 - - - -
299G GLU* 5.8 0.2 - - - +
303G GLY 3.1 15.5 + - - +
304G ILE* 3.9 2.7 - - - +
306G ALA* 1.3 78.1 - - - +
308G ALA* 1.3 52.7 + - - +
310G PHE* 3.3 5.5 + - - +
311G ALA* 2.8 34.8 + - - +
322G PHE* 3.4 26.6 - - + -
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G LEU* 4.1 4.3 - - + +
304G ILE* 2.8 24.2 + - + +
305G THR 3.8 3.4 - - - +
307G ALA* 1.3 70.5 - - - +
309G HIS* 1.3 56.1 + - - +
311G ALA* 3.8 1.5 - - - +
312G ALA* 2.7 36.9 + - - +
322G PHE* 3.8 23.7 - - + -
337G ILE* 4.0 20.0 - - + -
344G ILE* 4.5 8.5 - - + -
346G MET* 3.9 8.0 - - - +
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Residues in contact with HIS 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G PRO* 4.4 3.6 - - + -
119G LEU* 3.5 23.2 + - + +
120G TYR* 3.0 53.1 + + - +
123G LEU* 4.5 1.7 - - - +
305G THR* 3.0 46.0 + - + +
306G ALA 3.7 4.5 - - - +
307G ALA 3.3 0.2 - - - -
308G ALA* 1.3 72.7 - - - +
310G PHE* 1.3 66.1 + - - +
313G SER* 3.3 12.0 + - - -
337G ILE* 4.1 4.5 - - + +
346G MET* 3.0 32.3 - - + +
347G PRO* 4.4 12.1 - - + +
349G LYS 5.2 1.1 - - - -
351G GLY 3.5 21.1 - - - -
352G LEU* 4.0 11.4 + - + -
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Residues in contact with PHE 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G LEU* 5.5 0.2 - - - +
123G LEU* 4.1 10.2 - - + +
267G ILE* 4.3 4.0 - - + -
269G LEU* 4.7 5.4 - - + -
275G ILE* 4.2 28.5 - - + -
278G ALA* 3.4 38.8 - - + -
279G GLU* 3.5 28.7 - - + -
282G ASN* 4.3 3.4 - - + -
294G VAL* 3.7 20.9 - - + -
306G ALA 3.2 13.1 + - - +
307G ALA* 3.5 8.5 - - - +
309G HIS* 1.3 73.7 - - - +
311G ALA* 1.3 66.9 + - - +
313G SER* 2.7 27.6 + - - -
314G LYS* 3.8 15.9 + - - +
317G ILE* 3.3 26.2 - - + -
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Residues in contact with ALA 311 (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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127G ARG* 3.0 20.0 + - - -
294G VAL* 3.8 12.8 - - + -
307G ALA 2.8 21.0 + - - +
308G ALA 3.8 3.4 - - - +
310G PHE* 1.3 75.0 - - - +
312G ALA* 1.3 60.6 + - - +
313G SER 3.2 1.0 + - - -
314G LYS 3.5 7.1 + - - +
317G ILE* 3.8 31.9 - - + +
320G PHE* 3.8 19.1 - - + -
322G PHE* 4.0 6.7 - - + -
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Residues in contact with ALA 312 (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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120G TYR* 4.1 7.0 - - + -
126G TYR* 3.3 3.3 + - - +
127G ARG* 3.1 55.2 + - + +
128G ASP 5.7 0.2 - - - -
130G LEU* 4.2 8.9 - - + +
308G ALA 2.7 22.6 + - - +
309G HIS 3.9 4.5 - - - +
311G ALA* 1.3 74.1 - - - +
313G SER* 1.3 60.0 + - - +
314G LYS 3.4 0.7 + - - -
346G MET* 3.8 22.9 - - + -
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Residues in contact with SER 313 (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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120G TYR 3.2 22.2 - - - -
123G LEU* 3.3 29.0 - - - +
124G GLY* 3.7 1.7 - - - -
125G GLY 3.6 9.4 + - - +
126G TYR 3.6 4.9 + - - -
309G HIS 3.3 8.9 + - - -
310G PHE* 2.7 17.3 + - - -
311G ALA 3.1 0.6 - - - -
312G ALA* 1.3 78.8 - - - +
314G LYS* 1.3 71.3 + - - +
83H GLU* 3.4 25.5 - - - +
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Residues in contact with LYS 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G LEU* 2.9 21.5 + - - +
126G TYR* 4.1 3.6 - - - -
127G ARG* 3.1 20.1 + - - -
279G GLU* 2.9 41.0 + - - +
282G ASN* 3.7 25.1 - - - +
286G GLU* 6.1 0.2 - - - +
310G PHE* 3.8 17.3 - - + +
311G ALA 3.5 3.0 + - - +
312G ALA 3.4 1.2 - - - -
313G SER* 1.3 99.1 - - - +
315G ARG* 1.3 64.3 + - - +
316G ASN 4.4 2.5 - - - +
317G ILE* 3.4 24.3 + - + +
82H TYR* 5.3 1.8 + - - -
83H GLU* 3.5 16.1 + - - +
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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
------------------------------------------------------------
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