Contacts of the helix formed by residues 347 - 365 (chain C) in PDB entry 3H1J
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 PRO 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C HIS* 1.3 103.1 - - + +
348C PHE* 1.3 69.2 + - + +
349C ILE 3.3 2.9 - - - -
350C ILE* 2.8 23.7 - - + +
351C ILE* 3.0 10.5 - - + +
61G TRP* 3.5 28.9 - - + -
62G GLY* 3.5 38.8 - - - +
65G GLU* 4.1 9.6 - - + -
66G PHE* 3.8 18.6 - - + +
69G LEU* 5.0 0.2 - - + -
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Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ARG* 5.9 1.1 - - - +
338C TRP* 3.3 38.1 - + - -
339C ILE* 3.6 18.4 - - + +
342C GLN* 3.3 47.6 - - + -
343C PRO* 3.7 22.4 - - + +
345C GLU 3.0 12.1 + - - +
347C PRO* 1.3 82.0 - - + +
349C ILE* 1.3 62.4 + - - +
351C ILE* 3.1 2.5 + - + +
352C GLY* 2.8 22.5 + - - -
62G GLY 3.8 12.3 - - - -
63G THR* 4.8 5.6 - - + -
66G PHE* 3.7 42.2 - + + -
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ARG 6.1 0.7 - - - +
284C SER* 4.8 1.6 + - - +
339C ILE* 6.0 0.4 - - - -
344C VAL* 3.5 27.4 - - + +
345C GLU* 2.9 48.2 + - - +
346C HIS* 3.9 4.5 - - + +
347C PRO 3.3 0.2 - - - -
348C PHE* 1.3 75.0 - - - +
350C ILE* 1.3 65.6 + - + +
352C GLY* 3.1 1.6 + - - -
353C GLN* 2.9 43.7 + - + +
173R LYS* 5.5 12.8 - - - +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C HIS* 3.9 20.6 + - + +
347C PRO* 2.8 30.0 + - + +
349C ILE* 1.3 77.2 - - + +
351C ILE* 1.3 70.8 + - + +
353C GLN* 3.0 21.9 + - + +
354C MET* 2.9 46.5 + - + +
61G TRP* 5.9 1.6 - - + -
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Residues in contact with ILE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ILE* 4.4 7.6 - - + -
338C TRP* 3.9 27.8 - - + -
339C ILE* 3.9 11.4 - - + -
347C PRO* 3.0 26.6 + - + +
348C PHE* 3.5 6.7 - - - +
350C ILE* 1.3 79.9 - - + +
352C GLY* 1.3 58.2 + - - +
354C MET* 3.1 11.0 + - + +
355C ALA* 2.8 28.8 + - + +
58G LEU* 3.8 34.5 - - + -
61G TRP* 3.9 26.5 - - + -
62G GLY* 4.2 1.1 - - - -
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Residues in contact with GLY 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 5.8 0.7 - - - -
284C SER* 3.5 9.9 - - - -
336C LEU* 4.0 3.2 - - - +
339C ILE* 4.0 26.0 - - - +
348C PHE 2.8 17.4 + - - -
349C ILE* 3.5 4.5 - - - -
351C ILE* 1.3 73.1 - - - +
353C GLN* 1.3 54.9 + - - +
355C ALA* 3.1 6.3 + - - +
356C SER* 2.8 31.5 + - - -
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 3.4 41.0 + - - +
286C PRO* 5.1 6.7 - - - +
349C ILE* 2.9 26.2 + - + +
350C ILE* 3.3 34.1 - - + +
352C GLY* 1.3 73.9 - - - +
354C MET* 1.3 70.2 + - + +
356C SER* 3.5 1.4 - - - -
357C LEU* 2.9 24.6 + - - +
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Residues in contact with MET 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 2.9 40.3 + - + +
351C ILE* 3.3 10.8 - - + +
353C GLN* 1.3 83.9 - - + +
355C ALA* 1.3 53.3 + - - +
357C LEU* 2.8 23.8 + - + +
358C SER* 2.5 37.9 + - - -
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ASN* 3.1 16.3 - - - +
335C ILE* 4.0 21.3 - - + -
336C LEU* 3.5 24.2 - - + -
351C ILE 2.8 16.7 + - - +
352C GLY* 3.5 8.7 - - - +
354C MET* 1.3 70.5 - - - +
356C SER* 1.3 52.3 + - - +
358C SER* 3.0 8.0 - - - -
359C TYR* 2.6 33.4 + - - +
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Residues in contact with SER 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 3.5 32.3 - - - -
284C SER* 3.3 20.3 + - - -
285C ILE* 5.7 2.2 - - - -
336C LEU* 3.5 11.1 - - - +
352C GLY 2.8 21.6 + - - -
353C GLN* 3.5 5.6 - - - -
355C ALA* 1.3 69.1 - - - +
357C LEU* 1.3 68.9 + - - +
359C TYR* 3.0 16.6 + - - +
360C PHE* 3.2 19.2 + - - -
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C GLN 2.9 13.5 + - - +
354C MET* 2.8 28.9 + - + +
356C SER* 1.3 74.3 - - - +
358C SER* 1.3 65.3 + - - +
360C PHE* 3.4 7.0 + - + +
361C THR* 2.9 32.7 + - - +
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Residues in contact with SER 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ASN* 2.6 21.6 + - - +
354C MET 2.5 17.0 + - - -
355C ALA* 3.0 14.8 - - - -
357C LEU* 1.3 71.8 - - - +
359C TYR* 1.3 64.7 + - - +
361C THR* 3.0 16.7 + - - -
362C ILE* 3.0 25.7 + - - +
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Residues in contact with TYR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 5.6 1.8 - + - -
281C ILE* 3.8 11.2 - - + -
298C SER* 2.7 30.7 + - - -
301C ILE* 3.8 4.5 - - + +
329C LEU* 3.8 19.3 - - + -
332C ASN* 2.9 14.4 - - - +
333C LEU* 3.6 30.3 - - + -
336C LEU* 4.0 11.2 - - + -
355C ALA 2.6 15.8 + - - +
356C SER* 3.0 9.4 + - - +
358C SER* 1.3 71.8 - - - +
360C PHE* 1.3 105.1 + + - +
361C THR 3.1 1.0 + - - -
362C ILE* 3.3 9.7 + - - +
363C LEU* 3.3 40.9 + - + +
2007C PEE 3.8 19.2 - - + +
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Residues in contact with PHE 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 3.8 21.8 - - + -
294C ALA* 3.7 15.3 - - + -
297C ALA* 3.8 17.9 - - + -
298C SER* 3.6 38.6 - - - -
301C ILE* 4.1 15.5 - - + -
356C SER* 3.2 18.4 + - - -
357C LEU* 4.2 7.0 - - + +
359C TYR* 1.3 96.7 - + - +
361C THR* 1.3 59.2 + - - +
363C LEU* 4.0 4.3 - - - +
364C LEU* 3.0 45.7 + - + +
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Residues in contact with THR 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU* 2.9 23.6 + - - +
358C SER* 3.0 11.9 + - - -
360C PHE* 1.3 76.5 - - - +
362C ILE* 1.3 68.0 + - + +
363C LEU 3.1 1.6 - - - -
365C ILE* 2.8 45.4 + - + +
366C LEU* 3.1 29.0 + - + -
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Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C LEU* 3.4 36.1 - - + +
328C LEU* 4.5 15.3 - - + -
329C LEU* 3.9 28.9 - - + +
332C ASN* 3.5 27.4 - - + +
358C SER* 3.0 16.2 + - - +
359C TYR 3.3 4.5 + - - +
361C THR* 1.3 75.4 - - - +
363C LEU* 1.3 58.4 + - - +
366C LEU* 4.0 17.5 - - + -
367C PHE* 3.1 47.5 + - + -
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 4.6 5.8 - - + -
301C ILE* 3.7 31.2 - - + -
302C LEU* 6.0 2.5 - - + -
305C ILE* 3.9 26.2 - - + +
308C LEU* 2.8 24.3 - - - +
329C LEU* 3.8 27.6 - - + -
359C TYR* 3.3 49.4 + - + +
360C PHE 4.2 0.2 - - - +
361C THR 3.1 0.8 - - - -
362C ILE* 1.3 80.6 - - - +
364C LEU* 1.3 59.5 + - - +
367C PHE* 4.2 15.7 - - + +
368C PRO* 4.0 6.3 - - - +
2007C PEE 6.0 3.4 - - + -
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 3.6 29.6 - - + -
304C LEU* 4.2 16.8 - - + -
308C LEU* 3.9 23.2 - - + +
360C PHE* 3.0 33.7 + - + +
363C LEU* 1.3 76.9 - - - +
365C ILE* 1.3 71.1 + - + +
368C PRO* 3.4 13.6 - - - +
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Residues in contact with ILE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C THR* 2.8 35.2 + - + +
363C LEU 3.6 0.2 - - - -
364C LEU* 1.3 84.6 - - + +
366C LEU* 1.3 73.5 + - + +
367C PHE 3.5 1.3 - - - -
368C PRO* 3.2 4.3 - - - +
369C THR* 2.5 40.9 + - - +
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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