Contacts of the helix formed by residues 308 - 321 (chain K) in PDB entry 3J0S
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 308 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K VAL* 3.5 24.0 - - - +
220K ALA 5.1 0.9 - - - +
221K LEU* 5.8 0.9 - - - -
307K PRO* 1.3 72.9 - - - +
309K ILE* 1.3 63.8 + - - +
310K ALA* 3.3 3.5 - - - +
311K ASP* 3.2 23.4 + - - +
312K ARG 3.2 16.5 + - - -
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Residues in contact with ILE 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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153K MET* 5.9 4.3 - - + -
219K VAL* 3.5 21.0 - - + +
258K PRO* 6.3 0.2 - - + -
261K LEU* 5.7 7.6 - - + -
262K PHE* 4.9 15.0 - - + -
299K LEU* 5.3 8.5 - - + -
303K THR 4.5 4.9 - - - +
304K THR* 3.0 55.4 - - + +
306K TYR* 3.1 18.2 - - + +
307K PRO 3.2 3.6 + - - -
308K GLY* 1.3 79.1 - - - +
310K ALA* 1.3 68.8 + - + +
312K ARG* 3.3 2.6 + - - +
313K MET* 3.1 35.3 + - + +
335K ARG* 6.0 2.7 - - - +
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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
----------------------------------------------------------
299K LEU* 4.6 13.0 - - + -
308K GLY 3.3 1.1 - - - +
309K ILE* 1.3 86.8 - - + +
311K ASP* 1.3 64.2 + - - +
313K MET* 3.5 7.8 + - - +
314K GLN* 3.5 21.0 + - - +
329K ILE* 5.5 8.2 - - + +
335K ARG* 5.9 6.5 - - - +
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Residues in contact with ASP 311 (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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221K LEU* 3.5 33.1 - - + +
308K GLY* 3.2 21.5 + - - +
310K ALA* 1.3 81.8 - - - +
312K ARG* 1.3 62.9 + - - +
314K GLN* 3.6 12.2 + - - +
315K LYS* 3.6 15.8 + - - +
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Residues in contact with ARG 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K VAL* 3.4 26.9 - - + -
220K ALA 3.7 19.7 + - - +
221K LEU 4.3 11.3 + - - -
222K ASP* 5.8 0.4 - - - +
223K PHE* 4.9 10.7 - - - +
259K GLU* 2.8 42.2 + - - -
262K PHE* 3.7 35.0 - - + +
263K GLN* 5.4 6.9 + - - +
275K HIS* 5.3 0.8 + - - -
308K GLY 3.2 2.8 + - - -
309K ILE* 3.3 4.7 + - - +
311K ASP* 1.3 78.2 - - - +
313K MET* 1.3 64.8 + - - +
315K LYS* 3.2 9.6 + - - +
316K GLU* 3.1 62.1 + - - +
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Residues in contact with MET 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K MET* 5.1 13.7 - - + -
262K PHE* 3.5 31.6 - - - -
275K HIS* 4.6 16.6 - - + -
278K THR* 6.0 3.1 - - + +
297K THR* 6.1 2.0 - - + -
299K LEU* 4.2 37.0 - - + -
309K ILE* 3.1 28.9 + - + +
310K ALA* 3.7 6.3 - - - +
311K ASP 3.4 0.2 - - - -
312K ARG* 1.3 76.0 - - - +
314K GLN* 1.3 63.2 + - - +
316K GLU* 3.5 1.6 + - - +
317K ILE* 3.1 51.2 + - + +
329K ILE* 5.2 7.0 - - + -
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Residues in contact with GLN 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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310K ALA 3.5 9.3 + - - +
311K ASP* 3.8 10.3 - - - +
312K ARG 3.3 0.4 - - - -
313K MET* 1.3 79.9 - - - +
315K LYS* 1.3 59.1 + - - +
317K ILE* 3.6 2.7 + - - +
318K THR* 2.8 38.3 + - - +
327K ILE* 3.3 36.0 + - - +
329K ILE* 3.6 27.1 - - - +
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Residues in contact with LYS 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221K LEU* 3.3 29.6 + - - +
222K ASP* 4.9 12.1 - - - +
311K ASP 3.6 10.2 + - - +
312K ARG* 3.2 13.3 + - - +
314K GLN* 1.3 80.3 - - - +
316K GLU* 1.3 74.1 + - - +
318K THR* 3.4 6.7 + - - -
319K ALA* 3.2 22.0 + - + +
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Residues in contact with GLU 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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262K PHE* 4.4 5.8 - - + -
275K HIS* 3.2 39.6 + - + +
312K ARG* 3.1 52.7 + - - +
313K MET* 4.3 2.7 - - - +
315K LYS* 1.3 82.9 - - - +
317K ILE* 1.3 61.8 + - + +
319K ALA* 3.3 9.2 + - - +
320K LEU* 2.9 38.2 + - - +
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Residues in contact with ILE 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K HIS* 5.9 5.4 - - + +
279K PHE* 6.1 2.7 - - + -
282K ILE* 6.4 0.4 - - + -
294K TYR* 3.8 20.2 - - + -
297K THR* 5.4 5.6 - - + +
313K MET* 3.1 40.1 + - + +
314K GLN* 4.1 2.9 - - - +
316K GLU* 1.3 76.6 - - + +
318K THR* 1.3 53.8 + - - +
320K LEU* 3.7 10.0 - - + +
321K ALA* 2.8 33.3 + - + +
327K ILE* 3.6 27.6 - - + -
329K ILE* 4.1 26.2 - - + -
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Residues in contact with THR 318 (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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314K GLN* 2.8 30.7 + - - +
315K LYS* 3.7 6.2 - - - -
316K GLU 3.3 0.2 - - - -
317K ILE* 1.3 77.4 - - - +
319K ALA* 1.3 61.6 + - - +
321K ALA* 3.4 16.1 + - - +
323K SER* 5.2 7.7 + - - +
327K ILE* 3.8 20.2 - - + +
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Residues in contact with ALA 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315K LYS* 3.2 12.2 + - + +
316K GLU* 3.7 15.3 - - - +
317K ILE 3.3 0.2 - - - -
318K THR* 1.3 80.8 - - - +
320K LEU* 1.3 64.6 + - + +
321K ALA 3.9 4.3 - - - +
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Residues in contact with LEU 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K HIS* 3.5 35.9 - - + +
276K GLU* 3.8 38.8 - - + +
279K PHE* 3.4 43.5 - - + -
316K GLU* 2.9 22.8 + - - +
317K ILE* 3.7 9.0 - - + +
319K ALA* 1.3 79.1 - - + +
321K ALA* 1.3 62.4 + - - +
322K PRO* 3.9 0.9 - - - +
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Residues in contact with ALA 321 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279K PHE* 4.1 4.7 - - + -
294K TYR* 3.6 25.6 - - + +
317K ILE 2.8 21.5 + - - +
318K THR 3.4 14.5 - - - +
319K ALA 3.4 4.4 - - - +
320K LEU* 1.3 76.3 - - - +
322K PRO* 1.4 76.3 - - + +
323K SER* 3.2 6.7 + - - +
325K MET* 5.8 4.5 - - + -
327K ILE* 4.2 9.6 - - + -
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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