Contacts of the helix formed by residues 306 - 318 (chain K) in PDB entry 3HX0
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 GLY 306 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300K CYS* 4.8 4.0 - - - -
305K ILE* 1.3 75.1 - - - +
307K LYS* 1.3 57.4 + - - -
308K ARG 3.1 2.9 - - - -
309K MET* 2.8 2.6 + - - +
310K ALA* 2.7 34.7 + - - +
2N C 3.2 24.0 + - - -
3N C 4.6 6.5 - - - -
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Residues in contact with LYS 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296K TYR* 3.5 25.1 + - + +
300K CYS* 4.8 6.2 - - - -
306K GLY* 1.3 70.1 - - - -
308K ARG* 1.3 61.6 + - + +
310K ALA* 4.4 1.6 - - - -
311K GLU* 3.0 30.1 + - - +
2N C 3.9 0.2 + - - -
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Residues in contact with ARG 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K ARG* 5.2 1.0 - - - +
306K GLY 2.9 1.0 + - - -
307K LYS* 1.3 80.5 - - + +
309K MET* 1.3 63.1 + - - +
311K GLU* 3.9 4.8 + - - +
312K LYS* 2.9 36.5 + - - +
324K LYS* 6.0 1.4 - - - +
1N G 2.7 57.8 + - - -
2N C 3.3 15.4 + - - +
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Residues in contact with MET 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260K LEU* 4.5 18.4 - - + -
279K TYR* 3.5 56.1 - - + +
282K ALA* 4.0 21.3 - - + -
286K LEU* 6.0 0.4 - - + -
305K ILE* 3.6 25.1 - - + -
306K GLY 2.8 2.8 + - - +
308K ARG* 1.3 72.4 - - - +
310K ALA* 1.3 66.5 + - - +
312K LYS* 3.2 8.8 + - - +
313K ILE* 3.1 29.1 + - + +
1N G 3.5 25.4 - - + +
2N C 2.8 18.7 + - - +
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Residues in contact with ALA 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296K TYR* 3.4 29.3 - - + -
299K ALA* 4.0 12.9 - - + +
300K CYS* 3.7 20.2 - - - -
305K ILE* 3.8 2.8 - - + +
306K GLY 2.7 14.8 + - - +
307K LYS 3.9 0.9 - - - +
309K MET* 1.3 75.0 - - - +
311K GLU* 1.3 65.8 + - - +
313K ILE* 2.9 25.3 + - - +
314K ILE* 3.1 11.1 + - - +
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Residues in contact with GLU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K TYR* 3.4 13.9 - - + -
307K LYS 3.0 20.7 + - - +
308K ARG* 4.0 8.5 - - - +
309K MET 3.3 0.4 - - - -
310K ALA* 1.3 76.4 - - - +
312K LYS* 1.3 62.0 + - + +
314K ILE* 3.7 3.8 + - - +
315K GLU* 3.4 20.8 + - - +
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Residues in contact with LYS 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260K LEU* 4.6 10.5 - - + -
263K LEU* 4.4 16.8 - - + -
279K TYR* 3.6 23.3 + - + +
308K ARG* 2.9 25.8 + - - +
309K MET* 3.2 10.6 + - - +
310K ALA 3.1 0.6 - - - -
311K GLU* 1.3 78.0 - - + +
313K ILE* 1.3 62.2 + - - +
315K GLU* 3.8 8.4 + - - +
316K ILE* 3.1 30.4 + - - +
322K LEU* 4.0 20.6 - - + +
324K LYS* 4.8 15.7 - - - +
1N G 2.7 31.5 - - - -
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Residues in contact with ILE 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K ILE* 4.3 25.9 - - + +
260K LEU* 5.1 6.7 - - + -
286K LEU* 4.2 22.2 - - + -
293K VAL* 4.5 9.2 - - + -
295K SER 5.6 0.2 - - - +
299K ALA* 3.7 27.6 - - + -
305K ILE* 3.9 17.0 - - + -
309K MET* 3.1 21.1 - - + +
310K ALA* 2.9 7.7 + - - +
312K LYS* 1.3 79.3 - - - +
314K ILE* 1.3 60.9 + - + +
316K ILE* 3.3 9.6 + - - +
317K LEU* 2.9 40.6 + - + +
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Residues in contact with ILE 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294K THR 4.2 1.3 - - - +
295K SER* 3.5 9.0 - - - +
296K TYR* 3.1 54.3 - - + +
310K ALA 3.1 10.5 + - - +
311K GLU* 4.1 4.7 - - - +
313K ILE* 1.3 75.0 - - + +
315K GLU* 1.3 57.5 + - - +
316K ILE 2.9 5.2 - - - -
317K LEU* 3.9 18.8 - - + +
318K GLU* 2.8 64.0 + - + +
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Residues in contact with GLU 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311K GLU 3.4 15.0 + - - +
312K LYS* 3.9 10.7 - - - +
313K ILE 3.4 0.2 - - - -
314K ILE* 1.3 79.9 - - - +
316K ILE* 1.3 57.0 + - - +
318K GLU* 5.2 2.2 - - - -
319K SER* 3.3 32.4 + - - +
321K HIS* 2.9 16.9 + - + +
322K LEU* 3.2 25.9 + - - +
323K ARG* 2.8 35.2 + - - +
324K LYS* 4.4 1.7 + - - +
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Residues in contact with ILE 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K HIS* 4.1 19.7 - - + +
256K ILE* 4.3 30.1 - - + +
259K LYS* 3.8 26.2 - - + -
260K LEU* 4.4 7.2 - - + -
312K LYS 3.1 18.6 - - - +
313K ILE 3.3 6.5 + - - +
314K ILE 2.9 0.2 - - - -
315K GLU* 1.3 77.1 - - - +
317K LEU* 1.3 61.9 - - - +
318K GLU 3.2 1.6 - - - -
320K GLY* 2.8 29.7 + - - -
321K HIS* 3.1 24.5 - - - +
322K LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K HIS* 5.0 9.9 - - + +
256K ILE* 3.9 22.7 - - + -
293K VAL* 3.4 25.8 - - + +
294K THR* 3.1 32.5 - - - +
295K SER 4.4 0.7 - - - +
313K ILE* 2.9 26.6 + - + +
314K ILE* 3.1 20.6 + - + +
316K ILE* 1.3 77.4 - - - +
318K GLU* 1.3 64.3 + - + +
320K GLY* 4.5 0.5 + - - -
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Residues in contact with GLU 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314K ILE* 2.8 46.4 + - + +
315K GLU* 5.2 1.6 - - - -
317K LEU* 1.3 77.4 - - + +
319K SER* 1.3 63.9 + - - +
320K GLY* 2.8 10.5 + - - -
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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