Contacts of the helix formed by residues 292 - 306 (chain H) 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 ASP 292 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H GLY* 5.2 4.3 - - - -
282H GLY 5.5 0.3 + - - -
283H ALA 3.7 19.1 + - - +
285H PHE* 3.3 41.7 + - + -
291H GLY* 1.3 67.9 - - - +
293H ASN* 1.3 60.7 + - - +
294H GLU 3.7 0.9 - - - -
295H VAL* 3.4 16.7 - - - +
296H GLN* 3.3 23.4 + - - +
303I ARG* 4.1 19.3 - - - +
307I ARG* 3.2 27.4 + - - -
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Residues in contact with ASN 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285H PHE 5.8 1.4 + - - -
286H ASP* 5.5 9.3 + - - +
287H ASP 6.0 0.2 - - - +
290H GLY* 3.4 32.3 - - - +
291H GLY 2.3 26.9 + - - +
292H ASP 1.3 68.6 + - - +
294H GLU* 1.3 66.7 + - - +
295H VAL 3.2 1.3 - - - -
296H GLN* 2.9 17.9 + - - +
297H ARG* 3.1 32.2 + - - +
293M THR* 4.2 23.9 - - - +
296M PHE* 4.6 5.4 - - - -
303M ASP* 4.5 9.6 - - - +
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Residues in contact with GLU 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H VAL* 5.4 3.1 - - + -
247H GLN 4.8 1.4 - - - +
248H LYS 3.6 10.7 - - - +
249H TYR 4.7 0.4 - - - +
250H VAL* 3.3 35.9 - - - +
251H GLY* 4.2 9.9 - - - +
291H GLY 3.8 3.7 + - - +
293H ASN* 1.3 80.0 - - - +
295H VAL* 1.3 67.2 + - + +
297H ARG* 3.6 24.9 + - - +
298H THR* 2.8 24.8 + - - +
260I LEU* 3.2 32.7 - - + +
303M ASP* 3.8 16.5 - - - +
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Residues in contact with VAL 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H VAL* 3.3 28.0 - - + -
279H ALA 3.5 0.2 - - - +
280H ILE 1.9 39.9 - - - +
281H GLY* 4.1 3.1 - - - -
291H GLY 5.5 0.4 - - - +
292H ASP* 3.4 27.8 - - - +
294H GLU* 1.3 77.3 - - + +
296H GLN* 1.3 66.3 + - - +
298H THR* 3.1 11.1 + - - -
299H MET* 2.9 18.9 + - - +
307I ARG* 3.2 32.8 - - - +
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Residues in contact with GLN 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H GLY* 5.4 1.8 - - - -
283H ALA 2.3 12.4 - - - +
284H ARG* 2.1 60.8 - - + +
285H PHE 3.8 0.5 + - - -
292H ASP* 3.3 24.0 + - - +
293H ASN* 2.9 10.6 + - - +
295H VAL* 1.3 77.8 - - - +
297H ARG* 1.3 52.1 + - + +
299H MET* 2.7 49.9 + - - +
300H LEU* 2.7 48.7 + - + +
328H ASP* 3.1 3.2 + - - -
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Residues in contact with ARG 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H VAL* 4.0 11.3 - - - +
251H GLY* 4.1 6.1 - - - +
293H ASN* 3.1 13.6 + - - +
294H GLU* 3.8 38.4 + - - +
296H GLN* 1.3 74.2 - - + +
298H THR* 1.3 55.9 + - - +
300H LEU* 2.5 19.0 + - + +
301H GLU* 2.3 38.7 + - - +
254M PRO* 4.9 8.6 - - + +
257M VAL* 3.4 34.0 - - - +
289M ASP 5.3 0.7 - - - +
290M ALA* 3.4 33.7 + - - +
303M ASP* 2.7 29.9 + - - -
306M VAL* 3.0 20.5 - - - +
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Residues in contact with THR 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H LEU* 4.2 21.8 + - + +
246H VAL* 5.0 3.2 - - + +
251H GLY* 6.0 1.4 - - - -
252H GLU 5.8 0.3 + - - -
253H GLY* 4.2 27.9 + - - +
254H ALA* 4.9 2.7 + - - +
257H VAL* 4.2 5.0 - - + +
280H ILE* 4.0 19.9 - - + +
294H GLU 2.8 15.7 + - - -
295H VAL* 3.1 16.5 + - - -
297H ARG* 1.3 76.9 - - - +
299H MET* 1.3 55.1 + - - +
301H GLU* 3.2 9.9 - - - +
302H LEU* 2.8 27.5 + - - +
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Residues in contact with MET 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H ILE* 4.5 6.8 - - + +
281H GLY* 3.4 35.0 - - - +
282H GLY 4.5 1.1 - - - -
295H VAL 2.9 9.7 + - - +
296H GLN* 2.7 39.5 + - - +
298H THR* 1.3 73.9 - - - +
300H LEU* 1.3 51.1 + - - +
302H LEU* 3.1 9.6 + - + +
303H ILE* 2.4 74.6 + - + +
328H ASP* 2.0 52.5 - - + +
330H ALA* 4.0 2.2 - - + -
331H LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ARG* 3.2 35.0 - - - +
296H GLN* 2.7 28.7 + - + +
297H ARG* 2.5 29.0 + - + +
299H MET* 1.3 69.4 - - - +
301H GLU* 1.3 54.3 + - - +
303H ILE* 3.1 24.2 - - + +
304H ASN* 2.4 38.7 + - - +
254M PRO* 4.7 4.5 - - + -
287M GLU* 4.1 14.0 - - + +
289M ASP* 3.2 27.8 - - + +
290M ALA* 4.1 14.6 - - + +
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Residues in contact with GLU 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H ALA* 3.6 29.4 - - + +
257H VAL* 4.2 10.5 - - + -
258H ARG* 2.7 17.0 + - - +
297H ARG 2.3 25.9 + - - +
298H THR* 3.2 15.5 - - - +
300H LEU* 1.3 67.7 - - - +
302H LEU* 1.3 63.7 + - - +
304H ASN* 3.5 7.9 - - - +
305H GLN* 2.6 57.0 + - - +
252M ALA* 4.8 0.5 - - - +
254M PRO* 2.6 45.3 - - + +
255M GLN* 4.3 4.2 + - - +
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Residues in contact with LEU 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H LEU* 5.4 1.3 - - + -
257H VAL* 3.8 17.1 - - + +
261H PHE* 3.6 22.0 - - + -
274H PHE* 3.7 30.1 - - + -
277H ILE* 5.3 0.2 - - + -
280H ILE* 4.8 21.1 - - + -
298H THR 2.8 14.6 + - - +
299H MET* 3.2 9.9 - - + +
301H GLU* 1.3 73.8 - - - +
303H ILE* 1.3 54.1 + - - +
306H LEU* 2.5 70.4 + - + +
319H MET* 5.2 4.5 - - + -
331H LEU* 4.5 16.8 - - + -
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Residues in contact with ILE 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ARG* 5.7 0.7 - - - +
299H MET* 2.4 77.7 + - + +
300H LEU* 3.1 25.8 - - + +
302H LEU* 1.3 72.8 - - - +
304H ASN* 1.3 69.1 + - - +
306H LEU* 2.9 12.2 + - - +
307H ASP 3.2 8.0 + - - -
330H ALA* 3.5 11.7 - - + -
331H LEU* 4.1 13.9 - - + -
336H ARG* 2.9 47.0 + - - +
287M GLU* 5.2 5.6 - - - +
333M ASN* 5.8 2.2 - - - +
501M ADP 5.8 0.2 - - - +
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Residues in contact with ASN 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H LEU 2.4 22.1 + - - +
301H GLU* 3.5 12.7 - - - +
303H ILE* 1.3 71.1 - - - +
305H GLN* 1.3 63.7 + - + +
308H GLY* 2.9 45.2 + - - +
336H ARG* 5.0 1.3 - - - +
252M ALA* 3.0 30.6 - - - +
255M GLN* 5.1 0.7 + - - -
286M ASP* 3.3 24.7 + - - +
287M GLU* 2.9 27.0 + - - +
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Residues in contact with GLN 305 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H VAL* 4.2 12.1 - - + -
258H ARG* 2.6 53.8 - - - +
261H PHE* 3.9 11.2 - - + +
262H GLU* 4.8 3.3 - - - +
265H ARG* 3.7 27.3 + - - +
301H GLU* 2.6 30.9 + - - +
304H ASN* 1.3 82.6 - - - +
306H LEU* 1.3 60.8 + - - +
307H ASP 3.3 2.4 + - - -
308H GLY 4.9 0.3 + - - -
312H ARG* 4.4 14.7 - - - +
255M GLN* 5.4 6.0 - - - +
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Residues in contact with LEU 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H PHE* 3.0 31.6 - - + -
274H PHE* 3.9 15.3 - - + -
302H LEU* 2.5 57.4 + - + +
303H ILE* 2.9 5.8 + - - +
305H GLN* 1.3 78.3 - - - +
307H ASP* 1.3 65.8 + - - +
312H ARG* 3.0 49.3 + - - +
317H VAL* 3.8 13.9 - - + -
319H MET* 5.7 1.1 - - + -
331H LEU* 5.6 5.2 - - + -
336H ARG* 3.6 12.6 - - + +
337H LEU* 6.5 0.4 - - + -
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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