Contacts of the helix formed by residues 307 - 322 (chain N) in PDB entry 3HOU
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 307 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302N CYS* 4.0 5.3 - - - -
304N ASP* 3.6 20.8 + - + +
305N VAL 3.4 2.2 - - - -
306N ASN* 1.3 78.0 - - - +
308N TRP* 1.3 64.5 + - - +
309N GLN* 2.7 14.0 + - - +
310N MET* 2.9 49.4 + - - +
311N LEU* 3.2 13.2 + - - +
392N ARG* 3.4 25.1 + - - -
52U ILE* 4.9 3.8 - - - +
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Residues in contact with TRP 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305N VAL 4.9 0.2 + - - -
306N ASN* 3.5 11.1 - - - +
307N ASP* 1.3 76.3 - - - +
309N GLN* 1.3 76.9 + - + +
311N LEU* 3.7 14.5 - - - +
312N GLU* 2.5 43.5 + - + +
2U THR* 3.4 46.5 - - + +
3U THR* 4.3 17.0 - - - +
4U PHE* 6.1 1.3 - - + -
45U ARG* 3.1 57.2 - - + -
47U GLU* 3.5 32.5 - - + -
52U ILE* 4.5 10.9 - - + +
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Residues in contact with GLN 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307N ASP* 2.7 5.9 + - - +
308N TRP* 1.3 100.2 - - + +
310N MET* 1.3 64.8 + - - +
312N GLU* 3.2 6.8 + - - +
313N MET* 3.1 22.2 + - - +
390N LEU* 4.4 17.0 - - + +
392N ARG* 3.4 22.7 + - - +
46U HIS 4.0 17.2 + - - -
47U GLU* 3.9 11.7 + - - -
50U THR* 4.1 11.0 + - - +
52U ILE* 2.8 41.2 - - + +
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Residues in contact with MET 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301N ILE* 4.6 2.5 - - - +
302N CYS* 3.9 23.3 - - - -
307N ASP* 2.9 38.6 + - - +
309N GLN* 1.3 76.8 - - - +
311N LEU* 1.3 65.4 + - - +
313N MET* 3.0 24.5 + - - +
314N LEU* 3.1 19.9 + - + +
383N ASN* 3.5 27.4 - - - +
386N LEU* 3.7 28.0 - - + -
387N LEU* 4.1 17.0 - - + +
390N LEU* 4.2 6.0 - - + +
392N ARG* 3.5 20.2 - - - +
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Residues in contact with LEU 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298N LEU* 4.8 14.9 - - + +
302N CYS* 3.8 29.8 - - + -
304N ASP 4.4 1.8 - - - +
305N VAL* 3.9 29.6 - - + +
307N ASP 3.3 18.2 - - - +
308N TRP* 3.4 17.0 - - + +
309N GLN 3.2 0.2 - - - -
310N MET* 1.3 76.2 - - - +
312N GLU* 1.3 57.1 + - - +
314N LEU* 2.5 38.0 + - + +
315N LYS* 3.1 11.1 + - - +
3U THR* 6.1 1.1 - - + -
4U PHE* 4.1 31.0 - - + +
6U PHE* 6.4 1.6 - - + -
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Residues in contact with GLU 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261M LYS* 6.1 0.5 - - - -
308N TRP* 2.5 26.2 + - + +
309N GLN* 3.2 9.0 - - - +
311N LEU* 1.3 72.5 - - - +
313N MET* 1.3 65.9 + - + +
315N LYS* 3.1 49.7 + - - +
316N PRO* 3.4 4.5 - - - +
2U THR* 4.1 18.9 + - - +
4U PHE* 5.4 0.2 - - - -
43U VAL 5.1 0.3 - - - +
44U TYR* 3.9 37.3 - - + +
45U ARG 4.6 7.0 + - - +
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Residues in contact with MET 313 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N LEU* 6.1 2.0 - - - -
267N ARG* 4.2 16.3 - - + +
269N ILE* 5.7 1.4 - - + +
309N GLN 3.1 6.3 + - - +
310N MET* 3.0 13.3 + - - +
311N LEU 3.0 0.6 - - - -
312N GLU* 1.3 79.3 - - + +
314N LEU* 1.3 59.6 + - - +
316N PRO* 2.8 26.8 - - - +
317N CYS* 4.0 5.4 - - - -
386N LEU* 3.3 40.4 - - + -
389N ALA* 4.9 5.6 - - - +
390N LEU* 3.2 53.2 - - + -
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Residues in contact with LEU 314 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N ILE* 4.6 0.9 - - + -
282N ILE* 4.5 1.3 - - + -
298N LEU* 3.4 31.9 - - + -
301N ILE* 3.6 42.0 - - + -
302N CYS* 4.5 8.3 - - + -
310N MET* 3.1 20.8 + - + +
311N LEU* 2.5 21.4 + - + +
313N MET* 1.3 71.4 - - - +
315N LYS* 1.3 63.0 + - - -
316N PRO 3.4 0.2 - - - -
317N CYS* 2.9 30.4 + - + +
318N VAL* 3.1 15.1 + - - +
382N ILE* 4.5 6.1 - - + -
386N LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 315 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311N LEU 3.1 7.2 + - - +
312N GLU* 3.1 44.2 + - - +
314N LEU* 1.3 76.2 - - - +
316N PRO* 1.3 66.5 - - + +
318N VAL* 3.0 21.3 + - - +
319N GLU* 3.0 24.4 + - - +
2U THR* 5.7 4.2 + - - +
4U PHE* 4.0 47.6 - - + +
13U MET* 4.2 17.6 - - + +
14U LEU 5.6 3.2 + - - -
43U VAL 4.7 11.3 + - - -
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Residues in contact with PRO 316 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266N ALA* 5.0 5.8 - - - -
267N ARG* 3.7 35.2 - - + +
268N THR* 4.7 4.6 - - - +
312N GLU 3.4 6.7 - - - +
313N MET* 2.8 30.7 - - - +
315N LYS* 1.3 87.2 - - + +
317N CYS* 1.3 56.3 + - - +
319N GLU* 3.4 9.7 + - + +
320N ASP* 2.9 27.1 + - - +
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Residues in contact with CYS 317 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267N ARG 4.7 2.5 - - - -
268N THR* 5.1 0.6 - - - +
269N ILE* 3.8 32.1 - - - +
281N PRO* 6.3 0.2 - - - -
282N ILE* 3.6 28.7 - - + -
283N VAL* 3.0 23.2 - - + +
313N MET 4.0 5.8 - - - -
314N LEU* 2.9 27.5 + - + +
316N PRO* 1.3 73.5 - - - +
318N VAL* 1.3 60.1 + - + +
320N ASP* 2.6 34.4 + - - +
321N GLY 3.1 0.3 + - - -
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Residues in contact with VAL 318 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283N VAL* 4.0 13.4 - - + +
287N ARG* 5.3 3.6 + - - +
294N ASP* 3.1 33.4 - - + +
297N ILE* 6.5 0.4 - - + -
298N LEU* 4.2 28.0 - - + -
314N LEU 3.4 15.5 - - - +
315N LYS* 3.0 9.4 + - - +
317N CYS* 1.3 82.4 - - + +
319N GLU* 1.3 63.8 + - - +
321N GLY* 3.2 2.6 + - - -
322N PHE* 3.1 20.4 + - + +
13U MET* 4.4 18.6 - - + -
15U TYR* 4.4 9.2 - - - +
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Residues in contact with GLU 319 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258M HIS* 4.7 13.7 - - - -
315N LYS* 3.0 24.4 + - - +
316N PRO* 3.7 11.7 - - + +
318N VAL* 1.3 79.9 - - - +
320N ASP* 1.3 63.5 + - - +
322N PHE* 3.3 19.5 + - + +
323N VAL* 5.8 0.5 - - - +
13U MET* 3.8 13.0 - - + +
15U TYR* 3.9 32.9 - - + +
30U ARG* 5.2 2.1 + - - +
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Residues in contact with ASP 320 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N THR* 3.1 23.9 + - - +
269N ILE 4.8 0.2 - - - +
270N LYS* 3.1 13.5 + - - -
281N PRO* 3.0 31.5 - - + +
284N ILE* 5.7 0.5 - - - +
316N PRO 2.9 13.6 + - - +
317N CYS* 2.6 25.4 + - - +
319N GLU* 1.3 74.8 - - - +
321N GLY* 1.3 55.8 + - - +
322N PHE 3.5 0.2 + - - -
323N VAL* 4.7 6.6 + - - +
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Residues in contact with GLY 321 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N PRO* 5.1 0.7 - - - -
283N VAL* 4.1 19.1 - - - +
284N ILE* 4.3 16.8 - - - -
287N ARG* 3.1 15.1 + - - -
317N CYS 3.1 10.1 + - - -
318N VAL 3.2 4.0 + - - -
320N ASP* 1.3 75.7 - - - +
322N PHE* 1.3 65.8 + - - +
323N VAL 2.9 5.0 + - - -
324N ILE* 3.0 15.6 + - - +
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Residues in contact with PHE 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287N ARG* 4.4 4.5 - - - +
318N VAL* 3.1 12.1 + - + +
319N GLU* 3.5 18.4 - - + +
320N ASP 3.3 2.2 - - - -
321N GLY* 1.3 75.1 - - - +
323N VAL* 1.3 69.7 + - + +
324N ILE 2.8 6.9 + - - -
325N GLN* 2.9 33.8 - - - +
15U TYR* 3.4 26.7 - + - -
30U ARG* 3.5 41.1 - - + -
31U THR* 4.5 9.4 - - - -
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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