Contacts of the helix formed by residues 351 - 371 (chain C) in PDB entry 4JUO
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 LEU 351 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASN* 3.6 24.5 - - - +
255C PHE* 4.0 24.7 - - + -
336C HIS* 6.3 1.8 - - + +
349C SER* 3.4 1.0 - - - +
350C PRO* 1.3 82.4 - - + +
352C ALA* 1.3 61.6 + - - +
353C ARG 3.3 0.4 - - - -
354C PRO* 3.2 21.5 - - + +
355C VAL* 3.2 28.6 - - + +
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Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 4.3 9.8 - - + -
285C THR* 3.1 21.8 - - - +
286C HIS* 4.1 7.9 - - + +
330C ILE* 4.3 4.5 - - + -
347C LEU* 3.7 20.2 - - + -
349C SER* 3.2 13.1 + - - +
350C PRO 3.0 1.4 + - - -
351C LEU* 1.3 79.0 - - - +
353C ARG* 1.3 60.3 + - - +
355C VAL* 3.1 10.5 - - + +
356C VAL* 3.1 30.1 + - - +
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Residues in contact with ARG 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR* 3.4 26.1 + - - +
288C THR* 4.1 15.9 - - - +
289C GLY* 3.5 21.0 - - - +
292C SER* 5.7 4.8 - - - -
350C PRO* 3.2 10.0 + - - +
352C ALA* 1.3 77.9 - - - +
354C PRO* 1.3 82.8 - - + +
357C ASP* 3.1 32.2 + - + +
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Residues in contact with PRO 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C PRO 3.2 12.6 - - - +
351C LEU* 3.2 28.0 - - + +
353C ARG* 1.3 109.3 - - + +
355C VAL* 1.3 58.3 + - - +
357C ASP* 4.3 6.3 - - + -
358C GLY* 3.5 16.6 + - - -
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ASP* 3.9 28.0 - - + +
253C ASN* 3.9 11.0 - - - +
255C PHE* 3.9 24.9 - - + -
257C VAL* 4.5 4.3 - - + -
330C ILE* 5.8 0.4 - - + -
351C LEU* 3.2 33.9 - - + +
352C ALA* 3.1 20.6 - - - +
354C PRO* 1.3 78.5 - - - +
356C VAL* 1.3 70.8 + - + +
358C GLY* 3.4 1.9 + - - -
359C ILE* 3.0 33.4 + - - +
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Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C VAL* 4.1 11.4 - - + -
286C HIS* 3.5 32.1 - - + +
290C LEU* 3.8 20.0 - - + +
328C LEU* 4.3 11.9 - - + -
330C ILE* 3.7 29.2 - - + -
352C ALA* 3.1 17.4 + - - +
353C ARG 4.4 0.9 - - - +
355C VAL* 1.3 77.6 - - + +
357C ASP* 1.3 65.0 + - - +
358C GLY 3.1 0.9 - - - -
359C ILE* 3.4 0.6 + - - +
360C VAL* 2.9 35.1 + - + +
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Residues in contact with ASP 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C GLY* 3.1 24.0 + - - +
292C SER* 3.4 13.0 - - - +
293C ALA* 3.2 23.0 + - - -
353C ARG* 3.1 21.1 + - + +
354C PRO* 4.3 4.7 - - + -
356C VAL* 1.3 80.1 - - - +
358C GLY* 1.3 63.9 + - - +
361C ALA* 2.9 26.5 + - - +
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Residues in contact with GLY 358 (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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354C PRO 3.5 14.6 + - - -
355C VAL 3.4 6.2 + - - -
356C VAL 3.1 1.4 - - - -
357C ASP* 1.3 84.1 - - - +
359C ILE* 1.3 64.5 + - - +
360C VAL 3.0 0.3 + - - -
361C ALA* 4.1 0.5 - - - +
362C ASP* 3.1 22.0 + - - +
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Residues in contact with ILE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C PHE* 4.7 5.2 - - + +
249C GLU 3.7 22.0 - - - +
250C GLY* 3.8 15.7 - - - +
251C GLU 3.6 24.2 - - - +
252C ASP* 3.6 15.7 - - + -
257C VAL* 3.7 35.7 - - + -
355C VAL 3.0 17.9 + - - +
356C VAL 4.1 0.2 - - - +
358C GLY* 1.3 71.5 - - - +
360C VAL* 1.3 62.4 + - + +
362C ASP* 3.8 3.8 - - - +
363C LYS* 3.3 30.1 + - + +
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Residues in contact with VAL 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C PHE* 4.9 13.8 - - + -
257C VAL* 4.7 3.4 - - + -
259C VAL* 3.7 30.7 - - + -
290C LEU* 3.8 21.5 - - + -
293C ALA* 3.9 16.8 - - + -
294C ILE* 4.9 6.5 - - + -
356C VAL* 2.9 22.5 + - + +
359C ILE* 1.3 75.7 - - + +
361C ALA* 1.3 67.2 + - - +
362C ASP 3.0 3.0 + - - -
363C LYS* 3.1 12.4 + - - +
364C LEU* 3.1 34.8 + - + +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ALA* 4.1 16.5 - - + +
297C VAL* 3.6 7.3 - - + +
357C ASP* 2.9 31.6 + - - +
358C GLY 4.1 0.7 - - - +
360C VAL* 1.3 78.6 - - - +
362C ASP* 1.3 54.3 + - - +
364C LEU* 3.8 8.7 - - - -
365C THR* 2.3 35.0 + - - -
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Residues in contact with ASP 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C GLY 3.1 16.8 + - - +
359C ILE* 3.8 5.4 - - - +
360C VAL 3.0 0.4 - - - -
361C ALA* 1.3 81.4 - - - +
363C LYS* 1.3 73.2 + - + +
364C LEU 3.2 1.0 + - - -
365C THR* 3.2 10.8 + - - -
366C PHE* 3.5 9.2 + - - +
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Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C PHE* 3.4 35.8 - - + -
249C GLU* 3.1 29.2 + - - +
250C GLY* 5.2 1.5 - - - -
359C ILE* 3.3 27.0 + - + +
360C VAL 3.1 2.7 + - - +
362C ASP* 1.3 85.5 - - + +
364C LEU* 1.3 58.0 + - - +
366C PHE* 3.2 10.0 - - - +
367C PHE* 3.0 22.0 + - - +
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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
----------------------------------------------------------
246C LEU* 5.7 4.9 - - + -
248C PHE* 3.5 31.6 - - + -
294C ILE* 4.0 16.8 - - + -
297C VAL* 3.5 32.2 - - + +
298C MET* 4.6 8.1 - - + -
360C VAL* 3.1 44.6 + - + +
361C ALA* 3.8 6.1 - - - -
363C LYS* 1.3 75.0 - - - +
365C THR* 1.3 60.8 + - - +
367C PHE* 3.8 13.5 - - + +
368C LEU* 3.7 33.7 + - + +
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Residues in contact with THR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 3.1 25.2 - - + +
300C ASP* 5.4 7.2 - - + -
301C TYR* 5.6 5.4 - - + +
361C ALA 2.3 30.7 + - - -
362C ASP* 3.2 5.0 + - - -
364C LEU* 1.3 76.9 - - - +
366C PHE* 1.3 64.2 + - - +
368C LEU* 4.1 4.1 - - + +
369C MET* 3.3 23.4 + - - +
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Residues in contact with PHE 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C ASP 3.5 6.2 + - - +
363C LYS* 3.2 15.7 + - - +
365C THR* 1.3 78.0 - - - +
367C PHE* 1.3 60.2 + - - +
369C MET* 3.3 6.1 + - - +
370C GLU* 2.8 32.7 + - - +
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Residues in contact with PHE 367 (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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243C THR* 6.4 0.2 - - - -
244C PRO* 5.4 5.6 - - + -
246C LEU* 3.5 45.8 - - + -
248C PHE* 4.2 14.1 - + + -
363C LYS 3.0 16.4 + - - +
364C LEU* 3.8 11.8 - - + +
365C THR 3.5 0.4 - - - -
366C PHE* 1.3 76.3 - - - +
368C LEU* 1.3 80.8 + - + +
370C GLU* 3.1 20.3 + - + +
371C ASN* 3.3 37.3 + - - -
374C LEU* 5.0 14.8 - - + -
375C ALA* 6.4 0.4 - - + -
378C LEU* 6.0 2.2 - - + -
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Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 5.9 1.1 - - + -
297C VAL 4.4 2.7 - - - +
298C MET* 3.5 45.1 - - + -
301C TYR* 3.7 45.8 + - + -
364C LEU* 3.7 27.6 + - + +
365C THR* 4.2 4.0 - - - +
366C PHE 3.2 0.4 - - - -
367C PHE* 1.3 98.2 - - + +
369C MET* 1.3 65.9 + - - +
370C GLU 3.2 0.5 + - - -
371C ASN 3.5 7.8 + - - +
374C LEU 5.2 0.2 - - - +
375C ALA* 3.5 32.1 - - + +
378C LEU* 5.2 5.8 - - + -
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Residues in contact with MET 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TYR* 4.1 16.3 + - + -
365C THR 3.3 15.9 + - - +
366C PHE* 3.3 5.7 + - - +
368C LEU* 1.3 79.0 - - - +
370C GLU* 1.3 61.7 + - - +
371C ASN* 3.4 1.9 + - - -
372C GLY 4.9 1.0 + - - -
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Residues in contact with GLU 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C PHE* 2.8 19.3 + - - +
367C PHE* 3.3 15.0 - - + +
368C LEU 3.1 0.8 - - - -
369C MET* 1.3 77.7 - - - +
371C ASN* 1.3 68.0 + - - +
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Residues in contact with ASN 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C PHE* 3.3 40.3 + - - +
368C LEU 3.5 3.8 - - - +
369C MET 3.3 0.6 - - - -
370C GLU* 1.3 90.4 - - - +
372C GLY* 1.3 56.7 + - - +
373C GLU* 3.0 15.3 + - + +
374C LEU* 3.9 21.1 + - - +
375C ALA* 3.1 17.7 + - - +
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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