Contacts of the helix formed by residues 281 - 298 (chain K) in PDB entry 5GJQ
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 ALA 281 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K VAL* 5.5 0.2 - - - +
279K THR* 3.0 14.3 - - - +
280K GLY* 1.3 80.0 - - - +
282K ASP* 1.3 68.0 + - - +
283K ARG 3.2 1.3 - - - -
284K GLU* 3.4 14.3 + - - +
285K VAL* 3.3 17.5 - - - +
208L ILE* 5.0 13.1 - - + +
248L SER* 5.0 2.5 - - - +
252L GLU* 3.7 27.1 - - + +
255L ARG* 5.2 4.0 + - - +
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Residues in contact with ASP 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K ARG 5.4 0.4 - - - -
275K PHE* 3.4 10.9 - - + -
276K ASP* 2.3 71.8 + - - +
277K ALA* 4.0 0.7 - - - +
279K THR* 3.4 0.2 + - - -
281K ALA* 1.3 77.1 - - - +
283K ARG* 1.3 56.2 + - - +
285K VAL* 2.8 31.0 + - - +
286K GLN* 2.9 17.1 + - - +
248L SER* 2.6 31.6 + - - +
251L ARG* 5.1 4.9 + - - +
255L ARG* 5.1 4.3 + - - -
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Residues in contact with ARG 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ALA* 4.1 26.7 - - + -
278K GLN* 4.1 14.9 + - - +
280K GLY* 3.4 40.4 + - - +
282K ASP* 1.3 75.6 - - - +
284K GLU* 1.3 52.9 + - - +
285K VAL 3.4 0.2 + - - -
286K GLN* 3.7 10.2 + - - +
287K ARG* 2.6 46.2 + - - +
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Residues in contact with GLU 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236K VAL* 4.4 11.9 - - + -
239K TYR 3.9 18.1 - - - +
240K LEU* 3.5 25.3 - - - +
241K GLY 5.2 1.1 - - - +
244K PRO* 5.4 0.5 - - - +
280K GLY 4.0 11.1 + - - +
281K ALA 3.4 11.1 + - - +
282K ASP 3.1 0.4 + - - -
283K ARG* 1.3 81.1 - - - +
285K VAL* 1.3 60.3 + - - +
287K ARG* 3.5 25.9 + - - +
288K ILE* 2.9 30.4 + - + +
208L ILE* 2.8 50.1 - - + +
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Residues in contact with VAL 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236K VAL* 4.3 12.1 - - + -
269K ALA 4.1 7.2 - - - +
270K ILE* 2.9 38.1 - - + +
272K THR* 5.2 2.2 - - - +
275K PHE* 4.1 12.6 - - + -
281K ALA 3.3 19.1 - - - +
282K ASP* 2.8 11.7 + - - +
284K GLU* 1.3 76.1 - - - +
286K GLN* 1.3 68.5 + - - +
288K ILE* 2.6 26.1 + - + +
289K LEU* 2.8 10.4 + - - -
255L ARG* 3.9 23.1 - - - +
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Residues in contact with GLN 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218J GLU 4.6 1.3 - - - -
219J LEU* 3.3 33.3 + - + +
222J LYS* 3.1 47.4 - - - +
275K PHE* 3.6 34.8 - - + +
277K ALA* 4.0 20.3 + - - +
282K ASP 2.9 12.4 + - - +
283K ARG* 3.8 11.2 - - - +
285K VAL* 1.3 78.4 - - - +
287K ARG* 1.3 52.8 + - + +
289K LEU* 2.8 9.7 - - - +
290K LEU* 2.7 40.5 + - + +
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Residues in contact with ARG 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222J LYS* 5.8 6.5 - - - +
240K LEU* 4.0 28.7 + - - +
241K GLY* 4.2 5.2 - - - +
244K PRO* 4.7 17.2 - - + +
283K ARG* 2.6 36.2 + - - +
284K GLU* 3.5 30.2 + - - +
286K GLN* 1.3 72.1 - - + +
288K ILE* 1.3 55.3 + - - +
290K LEU* 2.5 22.0 + - + +
291K GLU* 2.3 39.7 + - + +
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Residues in contact with ILE 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K PHE* 4.1 17.3 - - + -
236K VAL* 3.0 46.2 - - + +
243K GLY* 4.1 18.6 - - - -
244K PRO* 4.5 4.2 - - + +
247K VAL* 4.5 5.5 - - + +
270K ILE* 3.4 35.4 - - + -
284K GLU* 2.9 22.0 - - + +
285K VAL* 2.6 16.6 + - - +
287K ARG* 1.3 73.2 - - - +
289K LEU* 1.3 54.6 + - - -
291K GLU* 3.2 11.1 - - - +
292K LEU* 2.8 28.3 + - + +
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Residues in contact with LEU 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J LEU* 4.2 13.7 - - + -
270K ILE* 3.9 13.5 - - + +
271K ALA* 3.1 39.0 - - + -
275K PHE* 2.7 41.5 - - + -
285K VAL 2.8 6.6 + - - +
286K GLN 2.8 15.0 + - - +
288K ILE* 1.3 72.8 - - - +
290K LEU* 1.3 50.9 + - - +
292K LEU* 3.1 17.5 + - + +
293K LEU* 2.4 49.3 + - + +
318K ASP* 4.5 8.7 - - + -
320K ALA* 6.2 0.4 - - + -
321K LEU* 4.7 5.8 - - + -
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Residues in contact with LEU 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL* 4.3 9.0 - - + -
219J LEU* 4.7 13.5 - - + +
222J LYS* 4.4 12.8 - - - +
223J PHE* 3.7 42.4 - - + -
286K GLN* 2.7 24.4 + - + +
287K ARG* 2.5 30.4 + - + +
289K LEU* 1.3 67.4 - - - +
291K GLU* 1.3 53.3 + - - +
293K LEU* 3.6 22.2 - - + -
294K ASN* 2.3 53.7 + - - +
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Residues in contact with GLU 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244K PRO* 3.0 47.9 - - + +
247K VAL* 3.9 12.4 - - + +
248K ARG* 3.2 28.8 + - - -
287K ARG* 2.3 24.5 + - + +
288K ILE* 3.2 13.5 - - - +
290K LEU* 1.3 66.9 - - - +
292K LEU* 1.3 64.0 + - - +
294K ASN* 3.7 13.3 + - - +
295K GLN* 2.5 62.9 + - - +
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Residues in contact with LEU 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K PHE* 6.5 0.9 - - + -
247K VAL* 3.9 12.9 - - + +
251K PHE* 3.8 21.3 - - + -
264K ILE* 4.4 14.1 - - + -
267K ILE* 5.3 2.5 - - + -
270K ILE* 4.8 9.4 - - + -
271K ALA* 5.5 0.2 - - + -
288K ILE* 2.8 17.5 + - + +
289K LEU* 3.3 22.7 - - + +
291K GLU* 1.3 72.5 - - - +
293K LEU* 1.3 51.5 + - - +
295K GLN 3.7 0.3 - - - -
296K MET* 2.3 56.2 + - - +
307K VAL* 5.6 0.4 - - + -
309K MET* 3.7 28.7 - - + -
321K LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 293 (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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140J VAL* 4.0 28.7 - - + -
219J LEU* 4.1 8.5 - - + -
289K LEU* 2.4 36.3 + - + +
290K LEU* 3.2 22.2 - - + +
292K LEU* 1.3 73.8 - - + +
294K ASN* 1.3 66.3 + - - +
296K MET* 3.0 15.3 - - + +
297K ASP* 3.4 7.4 + - - +
320K ALA* 3.6 26.2 - - + +
321K LEU* 4.7 12.8 - - + -
326K ARG* 2.1 51.8 + - + +
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Residues in contact with ASN 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL* 6.1 0.9 - - - +
248K ARG* 5.9 0.4 - - - +
290K LEU* 2.3 48.0 + - - +
291K GLU* 3.7 17.6 + - - +
293K LEU* 1.3 72.1 - - - +
295K GLN* 1.3 62.9 + - + +
297K ASP* 3.3 1.6 + - - +
298K GLY* 3.0 25.7 + - - -
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Residues in contact with GLN 295 (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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127K ASN* 5.1 3.2 - - - +
247K VAL* 2.7 36.9 - - - +
248K ARG* 2.8 28.1 + - - +
251K PHE* 2.9 33.6 - - + +
291K GLU* 2.5 36.6 + - - +
292K LEU 3.7 0.4 - - - -
294K ASN* 1.3 78.5 - - + +
296K MET* 1.3 62.0 + - - +
297K ASP 3.4 0.4 - - - -
298K GLY* 3.8 7.9 + - - +
299K PHE* 3.5 25.1 - - - -
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Residues in contact with MET 296 (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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200K ARG* 5.0 7.1 + - + +
201K GLY* 4.8 0.4 - - - +
251K PHE* 4.7 5.6 - - - -
292K LEU* 2.3 52.5 + - + +
293K LEU* 3.0 15.3 - - + +
294K ASN 2.9 0.4 - - - -
295K GLN* 1.3 80.6 - - - +
297K ASP* 1.3 60.4 + - - +
299K PHE* 4.0 13.2 - - - -
307K VAL* 3.7 34.1 - - + -
309K MET* 5.1 2.9 - - + -
321K LEU* 5.2 2.2 - - + -
325K GLY 4.7 2.5 - - - +
326K ARG* 2.6 61.1 - - + +
327K LEU* 4.7 4.5 - - + -
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Residues in contact with ASP 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 2.8 46.1 + - - +
200K ARG* 5.6 3.6 + - - +
293K LEU 3.4 6.9 + - - +
294K ASN 3.3 2.5 + - - +
296K MET* 1.3 77.0 - - - +
298K GLY* 1.3 57.7 + - - +
299K PHE* 3.1 12.0 + - - -
300K ASP 5.1 0.7 + - - -
325K GLY* 3.6 19.1 - - - +
326K ARG* 3.9 17.7 + - + +
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Residues in contact with GLY 298 (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 LYS* 5.2 3.3 + - - -
294K ASN 3.0 17.4 + - - -
295K GLN* 3.8 8.3 - - - -
296K MET 3.6 1.4 - - - -
297K ASP* 1.3 76.7 - - - +
299K PHE* 1.3 64.5 + - - +
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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
------------------------------------------------------------
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