Contacts of the helix formed by residues 359 - 374 (chain C) in PDB entry 5C5B
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 SER 359 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C PRO 3.4 19.3 - - - -
265C ASP* 3.7 5.6 - - - -
266C PRO* 3.7 16.2 - - - +
340C TYR* 3.5 13.7 - - - -
357C ALA* 3.4 2.7 - - - +
358C GLU* 1.3 81.5 - - - +
360C LYS* 1.3 58.2 + - - +
361C LYS* 3.4 8.1 + - - +
362C ASP* 3.1 28.4 + - - +
363C HIS* 2.9 27.7 + - - +
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Residues in contact with LYS 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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265C ASP* 3.6 7.0 + - - +
268C PRO* 6.3 3.4 - - + -
340C TYR* 3.4 33.8 - - + +
359C SER* 1.3 71.4 - - - +
361C LYS* 1.3 67.1 - - - +
363C HIS* 3.3 9.5 - - - +
364C GLU* 2.9 54.1 + - + +
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Residues in contact with LYS 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASP* 5.0 0.8 + - - -
266C PRO* 4.3 20.8 + - + +
271C PHE* 3.2 37.2 - - + +
272C PRO 3.7 11.9 - - - +
273C VAL* 3.9 20.5 - - + +
280C LYS* 4.9 0.6 - - - +
359C SER* 3.2 8.4 + - - +
360C LYS* 1.3 79.6 - - - +
362C ASP* 1.3 66.2 + - - +
365C GLU* 2.9 68.2 + - - +
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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
----------------------------------------------------------
280C LYS* 3.2 24.1 + - - +
283C TYR 5.7 1.4 - - - +
284C LEU* 5.7 0.9 - - + -
357C ALA* 4.1 12.1 - - + -
358C GLU* 4.9 7.4 + - - +
359C SER* 3.1 23.1 + - - +
361C LYS* 1.3 83.8 + - - +
363C HIS* 1.3 61.0 + - - +
365C GLU* 3.6 8.5 - - - +
366C TRP* 2.9 44.3 + - + +
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Residues in contact with HIS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ALA* 3.5 26.3 - - + +
340C TYR* 3.2 43.5 - + + -
341C CYS 3.1 20.8 + - - -
342C PHE* 3.9 17.8 - + + +
357C ALA* 3.9 6.2 - - - +
359C SER 2.9 18.3 + - - +
360C LYS* 3.1 13.1 + - - +
362C ASP* 1.3 78.1 - - - +
364C GLU* 1.3 70.1 + - + +
366C TRP* 3.5 3.8 - - - +
367C ILE* 3.0 38.4 + - + +
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL* 4.6 18.9 - - + +
360C LYS* 2.9 45.8 + - + +
361C LYS 4.5 0.7 - - - +
363C HIS* 1.3 86.3 + - + +
365C GLU* 1.3 61.1 + - - +
367C ILE* 3.8 12.8 - - + +
368C CYS* 2.9 31.2 + - - +
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Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PRO 4.1 0.5 - - - +
273C VAL* 3.7 18.8 - - + -
274C ASN* 3.1 35.1 + - - +
277C LEU* 3.9 12.5 - - + +
280C LYS* 2.9 30.2 + - + +
361C LYS* 2.9 56.2 + - - +
362C ASP* 3.6 3.3 - - - +
364C GLU* 1.3 76.0 - - - +
366C TRP* 1.3 57.0 + - - +
368C CYS* 4.0 3.9 - - - +
369C THR* 2.6 38.6 + - - -
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Residues in contact with TRP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LYS* 3.3 52.2 - - + +
281C ALA 4.1 0.2 - - - -
282C GLY* 3.8 25.2 - - - -
283C TYR 5.2 0.6 + - - -
284C LEU* 3.4 43.6 - - + +
302C TYR* 3.7 20.9 - - + -
304C THR* 4.0 10.1 - - + -
309C LEU* 4.0 19.3 - - + -
342C PHE* 3.7 22.0 - + + -
362C ASP* 2.9 34.4 + - + +
363C HIS 3.5 4.0 - - - +
365C GLU* 1.3 74.2 - - - +
367C ILE* 1.3 66.7 + - - +
369C THR* 3.8 1.7 - - - -
370C ILE* 3.0 47.0 + - + +
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Residues in contact with ILE 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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330C VAL* 3.6 31.0 - - + +
331C MET* 5.3 0.4 - - - -
332C ALA* 4.2 18.4 - - + +
342C PHE* 4.4 15.0 - - + -
363C HIS* 3.0 44.1 + - + +
364C GLU* 3.8 12.6 - - + +
365C GLU 3.4 0.2 - - - -
366C TRP* 1.3 75.7 - - - +
368C CYS* 1.3 58.0 + - - +
370C ILE 3.4 0.2 + - - -
371C ASN* 3.0 49.7 + - - +
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Residues in contact with CYS 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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273C VAL* 5.7 1.1 - - + -
274C ASN 4.9 0.7 - - - +
275C ARG* 3.3 54.3 - - + -
364C GLU 2.9 19.5 + - - +
365C GLU* 4.0 5.6 - - - +
367C ILE* 1.3 77.5 - - + +
369C THR* 1.3 57.7 + - - +
371C ASN* 3.4 8.0 + - - +
372C ASN* 2.9 40.3 + - - +
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Residues in contact with THR 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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274C ASN 5.1 0.9 + - - -
277C LEU* 3.4 42.8 - - - +
279C ARG 4.0 12.8 - - - +
280C LYS* 3.9 26.1 - - + +
304C THR* 4.7 3.6 - - + -
365C GLU 2.6 26.3 + - - -
366C TRP* 3.8 4.0 - - + -
368C CYS* 1.3 73.9 - - - +
370C ILE* 1.3 63.3 + - + +
372C ASN* 3.1 3.4 + - - +
373C ILE* 2.9 46.7 + - + +
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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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304C THR* 5.5 1.1 - - + -
309C LEU* 4.9 4.5 - - + -
325C ILE* 4.3 24.2 - - + +
328C CYS* 3.9 22.9 - - - -
330C VAL* 3.9 19.7 - - + -
342C PHE* 4.1 16.6 - - + -
344C ILE* 3.6 29.4 - - + -
366C TRP* 3.0 40.7 + - + +
367C ILE 3.8 3.4 - - - +
369C THR* 1.3 77.4 - - + +
371C ASN* 1.3 62.6 + - - +
373C ILE* 3.3 7.3 + - - +
374C SER* 3.0 23.7 + - - -
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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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328C CYS 5.1 2.1 - - - +
329C SER* 4.8 5.2 - - - -
330C VAL* 3.4 23.4 + - - +
367C ILE* 3.0 42.9 + - - +
368C CYS* 3.5 8.5 - - - +
370C ILE* 1.3 77.8 - - - +
372C ASN* 1.3 63.2 + - - +
374C SER* 3.3 20.2 + - - +
375C LYS 5.1 2.1 - - - -
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Residues in contact with ASN 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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275C ARG 2.8 31.1 + - - +
276C ASN* 4.0 3.6 - - - +
277C LEU 3.3 24.8 + - - +
278C THR* 5.0 7.4 - - + +
368C CYS* 2.9 28.8 + - - +
369C THR* 3.1 7.8 + - - +
371C ASN* 1.3 79.8 - - - +
373C ILE* 1.3 62.7 + - + +
374C SER 3.7 4.3 - - - +
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Residues in contact with ILE 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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278C THR* 3.4 30.3 - - - +
304C THR* 3.7 35.2 - - + +
306C GLY 4.0 18.8 - - - +
307C GLY* 4.3 9.4 - - - -
325C ILE* 3.8 25.6 - - + +
326C ASP* 4.5 5.3 - - - +
369C THR* 2.9 24.7 + - + +
370C ILE 3.8 4.7 - - - +
371C ASN 3.3 0.2 - - - -
372C ASN* 1.3 79.7 - - - +
374C SER* 1.3 61.2 + - - +
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Residues in contact with SER 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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325C ILE 3.1 19.3 - - - -
326C ASP 3.4 7.4 - - - -
327C ASN* 3.4 2.3 + - - -
328C CYS* 2.9 40.8 + - - -
370C ILE 3.0 16.1 + - - -
371C ASN* 3.3 14.9 + - - +
372C ASN 3.7 4.3 - - - +
373C ILE* 1.3 82.1 - - - +
375C LYS* 1.3 77.2 + - - +
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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