Contacts of the helix formed by residues 359 - 377 (chain C) in PDB entry 3BRW
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 359 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C GLY* 1.4 83.6 - - - +
360C GLU* 1.3 68.9 + - + +
361C PHE 3.3 1.5 + - - -
362C GLN* 3.4 28.0 + - + +
363C GLU* 3.9 6.2 + - - +
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Residues in contact with GLU 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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355C PHE* 3.9 31.5 - - + +
356C ARG 5.3 4.0 - - - +
357C LYS 3.7 16.2 - - - +
359C PRO* 1.3 83.6 - - + +
361C PHE* 1.3 65.6 + - + +
363C GLU* 3.9 14.2 + - - +
364C PHE* 4.2 6.4 + - - +
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Residues in contact with PHE 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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226C PHE* 3.5 27.6 - + + -
320C VAL* 5.8 6.7 - - + -
332C TYR* 4.8 13.7 - + + -
333C LYS 5.1 5.8 - - - -
334C VAL* 4.7 16.6 - - + -
353C ALA 6.4 0.2 - - - -
355C PHE* 3.6 40.4 - + + -
356C ARG 3.4 25.6 - - - +
357C LYS 4.3 0.8 + - - +
358C GLY 4.2 2.0 + - - -
359C PRO 3.3 0.4 - - - -
360C GLU* 1.3 76.1 - - + +
362C GLN* 1.3 63.8 + - - +
363C GLU 3.1 2.9 - - - -
364C PHE* 3.2 38.7 + + + +
365C LEU* 3.1 39.4 + - + +
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C PHE* 3.4 31.9 + - + +
227C LEU* 3.4 33.6 + - + +
228C GLY 4.5 0.2 + - - -
257C CYS* 4.5 9.7 - - - +
259C PHE* 5.0 1.3 - - - -
358C GLY 4.8 0.2 - - - +
359C PRO* 3.4 25.2 + - + +
361C PHE* 1.3 77.8 - - - +
363C GLU* 1.3 61.4 + - - +
365C LEU* 4.2 2.2 - - - -
366C LEU* 3.4 46.9 + - + +
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Residues in contact with GLU 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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78C LYS 4.7 12.1 + - - -
79C VAL* 5.1 9.1 - - + +
259C PHE* 3.8 21.5 - - + -
260C ARG* 4.4 10.7 + - - +
359C PRO 3.9 5.4 + - - +
360C GLU 3.9 11.1 + - - +
361C PHE 3.1 0.4 - - - -
362C GLN* 1.3 78.1 - - - +
364C PHE* 1.3 61.5 + - - +
365C LEU 3.3 0.2 - - - -
367C THR* 2.8 32.4 + - + +
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Residues in contact with PHE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 6.4 0.7 - - - -
334C VAL* 4.9 13.7 - - + -
347C PRO* 3.3 46.2 - - + +
348C PRO 3.7 7.2 - - - -
349C LEU* 4.6 2.2 - - - -
350C PRO* 3.8 27.8 - - + -
355C PHE* 5.4 11.0 - + + -
360C GLU* 4.2 5.2 + - - +
361C PHE* 3.2 48.6 + + + +
363C GLU* 1.3 79.3 - - - +
365C LEU* 1.3 62.6 + - + +
367C THR* 3.0 14.6 + - - -
368C LYS* 3.6 15.1 + - + +
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Residues in contact with LEU 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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223C PHE* 5.2 7.6 - - + -
226C PHE* 4.1 12.8 - - + -
227C LEU* 3.7 30.5 - - + -
295C VAL* 5.5 7.0 - - + -
318C VAL* 3.9 32.1 - - + -
320C VAL* 4.7 10.3 - - + -
361C PHE* 3.1 34.5 + - + +
362C GLN* 4.3 3.1 - - - +
363C GLU 3.3 0.2 - - - -
364C PHE* 1.3 78.0 - - + +
366C LEU* 1.3 66.7 + - + +
368C LYS* 2.9 18.1 + - + +
369C LEU* 3.0 26.7 + - + +
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Residues in contact with LEU 366 (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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195C PHE* 5.3 1.1 - - + -
227C LEU* 4.8 7.0 - - + -
257C CYS* 4.2 14.6 - - - -
259C PHE* 3.7 36.8 - - + -
264C ILE* 3.8 20.6 - - + -
266C PHE* 3.9 26.7 - - + -
362C GLN* 3.4 45.2 + - + +
365C LEU* 1.3 79.0 - - + +
367C THR* 1.3 63.0 + - - +
369C LEU* 3.2 16.6 + - + +
370C ILE* 3.2 27.1 + - - +
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Residues in contact with THR 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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79C VAL* 4.4 17.3 - - + +
80C LYS 5.7 0.4 - - - -
81C LEU* 4.4 16.2 - - + +
259C PHE* 3.5 25.1 - - + -
260C ARG* 3.7 12.8 - - - +
347C PRO* 3.2 20.7 - - - +
363C GLU* 2.8 19.9 + - + +
364C PHE* 3.0 15.6 + - - -
366C LEU* 1.3 75.1 - - - +
368C LYS* 1.3 58.7 + - - +
370C ILE* 3.7 4.7 + - - +
371C ASN* 3.2 30.7 + - - +
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Residues in contact with LYS 368 (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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318C VAL* 6.1 6.1 - - + -
334C VAL* 6.4 1.1 - - - -
335C SER 6.0 0.2 - - - -
336C VAL* 4.2 24.0 - - - +
344C PHE* 4.3 6.5 - - - -
345C PHE* 2.7 44.8 + - + +
346C GLY* 3.7 10.8 - - - -
347C PRO* 3.6 30.2 + - + +
349C LEU* 4.2 16.2 - - - +
364C PHE* 3.7 16.8 - - + +
365C LEU* 2.9 12.3 + - + +
367C THR* 1.3 78.0 + - - +
369C LEU* 1.3 56.5 + - - +
371C ASN* 3.7 1.0 - - - +
372C ALA* 2.8 35.6 + - + +
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Residues in contact with LEU 369 (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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195C PHE* 3.7 40.1 - - + -
266C PHE* 4.4 10.3 - - + -
293C VAL* 3.6 25.5 - - + +
295C VAL* 4.1 12.1 - - + -
318C VAL* 4.0 23.8 - - + -
365C LEU* 3.0 26.1 + - + +
366C LEU* 3.2 37.2 + - + +
368C LYS* 1.3 76.7 - - - +
370C ILE* 1.3 61.5 + - - +
372C ALA* 3.1 19.4 - - - +
373C GLU 3.3 5.2 + - - -
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Residues in contact with ILE 370 (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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81C LEU* 4.3 24.9 - - + -
193C PHE* 3.5 48.2 - - + -
195C PHE* 4.1 14.4 - - + -
259C PHE* 4.3 22.0 - - + -
262C LYS* 4.7 6.3 - - + -
264C ILE* 4.6 11.0 - - + -
366C LEU 3.2 17.2 + - - +
367C THR* 4.1 3.6 - - - +
369C LEU* 1.3 71.2 - - - +
371C ASN* 1.3 66.1 + - - +
373C GLU* 2.9 23.1 + - - +
374C TYR* 3.0 24.9 + - + -
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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
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79C VAL* 5.6 0.2 - - - +
80C LYS 3.4 21.2 + - - -
81C LEU* 3.5 11.2 - - - +
82C GLU* 2.9 48.2 + - - +
345C PHE* 3.4 12.6 - - - +
346C GLY* 3.3 32.6 - - - +
347C PRO* 4.1 2.8 - - - +
367C THR* 3.2 17.9 + - - +
368C LYS 4.0 0.2 - - - +
370C ILE* 1.3 77.4 - - - +
372C ALA* 1.3 64.6 + - - +
374C TYR* 3.8 6.0 - - - +
375C ALA 3.1 17.0 + - - -
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Residues in contact with ALA 372 (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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293C VAL* 3.8 19.3 - - + -
316C ALA* 4.1 8.1 - - + -
342C VAL* 5.0 0.2 - - - +
345C PHE* 3.6 26.3 - - + -
368C LYS* 2.8 16.0 + - + +
369C LEU* 3.1 14.8 - - - +
371C ASN* 1.3 74.7 - - - +
373C GLU* 1.3 64.1 + - - +
375C ALA* 3.2 13.3 + - - +
376C CYS* 3.1 20.2 + - - -
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Residues in contact with GLU 373 (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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190C SER* 4.4 4.5 + - - -
192C ASN 5.2 1.2 - - - +
193C PHE* 3.2 38.8 - - + +
194C LYS 4.9 5.0 + - - +
195C PHE* 4.1 11.7 - - + -
292C ILE* 3.9 26.7 + - + +
293C VAL* 3.6 16.1 + - + +
369C LEU 3.3 4.1 + - - +
370C ILE* 2.9 11.4 + - - +
372C ALA* 1.3 78.1 - - - +
374C TYR* 1.3 63.5 + - + +
376C CYS* 3.2 16.4 + - - +
377C TYR* 3.2 43.4 + - + -
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Residues in contact with TYR 374 (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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81C LEU* 5.7 3.1 - - + -
82C GLU* 3.3 30.7 - - + +
83C CYS* 3.5 32.6 - - + +
84C ASN 4.8 2.7 - - - -
188C VAL 4.0 13.9 - - - -
189C ILE* 3.7 8.0 - - - +
190C SER* 3.6 28.9 + - - -
193C PHE* 3.9 24.2 - + - -
262C LYS* 5.8 2.3 - - - -
370C ILE* 3.0 30.2 + - + +
371C ASN* 3.8 12.6 - - - +
372C ALA 3.2 0.4 - - - -
373C GLU* 1.3 78.1 - - + +
375C ALA* 1.3 62.5 + - - +
377C TYR* 3.4 21.8 + + + +
378C LYS 4.5 1.0 + - - -
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Residues in contact with ALA 375 (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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82C GLU* 5.0 2.6 + - - +
342C VAL* 4.1 6.7 - - + +
343C PRO* 3.8 28.9 - - + +
344C PHE 4.9 0.2 - - - +
345C PHE* 3.8 27.4 - - + -
371C ASN 3.1 13.4 + - - +
372C ALA 3.5 8.5 - - - +
374C TYR* 1.3 75.3 - - - +
376C CYS* 1.3 63.0 - - - +
377C TYR 3.1 1.6 + - - -
378C LYS* 3.2 20.4 + - - +
379C ALA 4.1 1.2 + - - -
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Residues in contact with CYS 376 (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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292C ILE* 4.0 20.4 - - + -
315C HIS* 3.7 28.5 - - + -
316C ALA* 4.2 12.8 - - - -
342C VAL* 3.8 19.3 - - - -
345C PHE* 6.3 0.2 - - - -
372C ALA 3.1 27.8 + - - -
373C GLU* 3.2 12.7 + - - +
375C ALA* 1.3 78.6 - - - +
377C TYR* 1.3 56.7 + - + +
378C LYS 3.2 0.4 - - - -
379C ALA* 3.1 26.2 + - - +
382C PHE* 3.4 12.7 - - + -
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Residues in contact with TYR 377 (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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292C ILE* 4.0 19.6 - - + +
373C GLU* 3.2 49.2 + - + -
374C TYR* 3.4 16.5 + + + +
375C ALA 3.1 2.2 + - - -
376C CYS* 1.3 78.6 - - + +
378C LYS* 1.3 60.6 + - - +
382C PHE* 3.6 27.5 - + + +
383C ALA* 3.5 20.8 + - - -
385C LEU* 4.9 7.9 - - + -
386C GLU* 3.6 38.7 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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