Contacts of the helix formed by residues 353 - 374 (chain C) in PDB entry 4YCV
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 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C ALA* 1.3 74.6 - - - +
354C TYR* 1.3 67.7 + - + +
355C ASN* 2.9 29.8 + - - +
356C ASP* 2.7 31.2 + - - +
357C LEU* 3.0 19.1 + - - +
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Residues in contact with TYR 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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353C ASP* 1.3 76.0 - - - +
355C ASN* 1.3 57.8 + - - +
357C LEU* 3.0 15.1 + - - +
358C ILE* 2.9 36.7 + - + +
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Residues in contact with ASN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ASP* 2.9 37.3 + - - +
354C TYR* 1.3 73.3 + - - +
356C ASP* 1.3 59.8 + - - +
358C ILE* 3.8 10.8 - - - +
359C LYS* 2.9 38.0 + - + +
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Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C TRP* 4.3 17.0 - - + -
351C TYR 4.1 3.5 - - - +
352C ALA* 3.2 22.7 - - + +
353C ASP* 2.7 42.6 + - - +
355C ASN* 1.3 81.9 + - - +
357C LEU* 1.3 55.5 + - - +
359C LYS* 3.5 7.6 + - - +
360C TRP* 2.9 27.4 + - - +
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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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347C PHE* 4.1 29.6 - - + -
349C TRP* 4.6 14.4 - - + -
352C ALA* 5.3 5.2 - - + +
353C ASP* 3.0 18.6 + - - +
354C TYR* 3.0 15.3 + - - +
356C ASP* 1.3 74.4 - - - +
358C ILE* 1.3 60.0 + - + +
360C TRP* 3.2 7.3 + - - +
361C SER* 2.9 32.1 + - - +
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Residues in contact with ILE 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 TYR* 2.9 23.4 + - + +
355C ASN* 3.8 11.0 - - - +
357C LEU* 1.3 73.4 - - + +
359C LYS* 1.3 68.7 + - + +
361C SER* 3.1 8.2 + - - +
362C GLU* 2.9 45.7 + - + +
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Residues in contact with LYS 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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355C ASN* 2.9 25.1 + - + +
356C ASP* 3.6 8.3 - - - +
358C ILE* 1.3 77.5 - - + +
360C TRP* 1.3 63.0 + - - +
362C GLU* 3.9 10.8 - - - +
363C ASP* 3.0 38.9 + - - +
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Residues in contact with TRP 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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261C LEU* 4.1 13.0 - - + -
264C PHE* 3.6 28.2 - + - -
265C LEU* 3.4 37.4 - - + +
268C ARG* 5.1 8.2 - - - +
270C PHE* 4.5 4.6 - + - -
345C CYS* 6.3 0.4 - - - -
347C PHE* 3.7 33.4 - + + -
349C TRP* 4.0 23.6 - + + -
356C ASP 2.9 14.7 + - - +
357C LEU* 3.2 13.9 - - - +
359C LYS* 1.3 76.7 - - - +
361C SER* 1.3 69.3 + - - +
363C ASP* 3.8 4.1 - - - +
364C PHE* 2.9 61.4 + + + +
365C PHE* 5.3 2.5 - + - -
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Residues in contact with SER 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 2.9 14.1 + - - +
358C ILE* 3.1 9.0 + - - -
360C TRP* 1.3 88.4 - - - +
362C GLU* 1.3 68.2 + - - +
364C PHE 3.3 0.2 + - - -
365C PHE* 2.9 45.6 + - - +
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Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ILE* 2.9 36.9 + - + +
359C LYS* 3.9 10.2 - - - +
361C SER* 1.3 75.6 - - - +
363C ASP* 1.3 64.2 + - - +
365C PHE* 4.3 2.1 - - - +
366C SER* 2.9 32.4 + - - -
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Residues in contact with ASP 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PHE* 4.5 7.6 - - + -
268C ARG* 5.8 4.1 + - - +
359C LYS* 3.0 28.9 + - - +
360C TRP* 3.8 4.5 - - - +
362C GLU* 1.3 78.9 - - - +
364C PHE* 1.3 63.5 + - - +
366C SER* 2.8 20.8 + - - -
367C GLN* 2.9 33.5 + - - +
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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
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257C ILE* 5.3 5.2 - - + -
260C PHE* 3.9 27.8 - + - -
261C LEU* 3.9 33.0 - - + -
264C PHE* 3.7 26.2 - + + -
360C TRP* 2.9 48.6 + + + +
361C SER 3.7 0.9 - - - +
363C ASP* 1.3 72.6 - - - +
365C PHE* 1.3 101.4 + + - +
367C GLN 3.9 0.2 - - - -
368C LEU* 2.9 48.9 + - + +
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Residues in contact with PHE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C TRP* 5.3 2.9 - + - -
361C SER* 2.9 39.1 + - - +
362C GLU* 4.3 2.5 - - - +
364C PHE* 1.3 106.3 - + - +
366C SER* 1.3 68.1 + - - +
368C LEU* 3.6 12.0 - - + +
369C VAL* 3.0 37.2 + - + +
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Residues in contact with SER 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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362C GLU 2.9 16.4 + - - -
363C ASP* 2.8 18.2 + - - -
365C PHE* 1.3 78.8 - - - +
367C GLN* 1.3 70.0 + - - +
369C VAL* 3.4 4.4 + - - +
370C TYR* 2.9 30.1 + - - +
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Residues in contact with GLN 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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260C PHE* 3.8 14.4 - - + -
264C PHE* 3.0 30.3 - - - -
268C ARG* 4.2 13.3 + - - +
363C ASP* 2.9 27.6 + - - +
364C PHE 4.1 0.2 - - - +
366C SER* 1.3 86.4 + - - +
368C LEU* 1.3 56.6 + - - +
370C TYR* 3.7 5.9 - - - +
371C HIS* 2.9 30.0 + - - +
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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
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257C ILE* 4.1 31.6 - - + -
260C PHE* 3.7 39.7 - - + -
364C PHE* 2.9 44.3 + - + +
365C PHE* 3.6 14.4 - - + +
366C SER 3.2 0.2 - - - -
367C GLN* 1.3 73.6 - - - +
369C VAL* 1.3 70.9 + - + +
371C HIS* 3.0 6.9 + - - +
372C LEU* 3.0 37.4 + - + +
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Residues in contact with VAL 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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365C PHE* 3.0 24.1 + - + +
366C SER* 3.9 4.3 - - - +
368C LEU* 1.3 81.8 - - + +
370C TYR* 1.3 57.6 + - - +
372C LEU* 4.8 2.0 - - + -
373C PHE* 2.9 49.2 + - + -
375C THR* 3.2 19.1 - - + +
376C TYR* 4.0 11.4 - - - -
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Residues in contact with TYR 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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366C SER 2.9 17.9 + - - +
367C GLN* 3.9 7.0 - - - +
369C VAL* 1.3 74.8 - - - +
371C HIS* 1.3 62.0 + - - +
374C GLY* 3.0 46.6 + - - +
375C THR* 3.4 25.1 + - - +
376C TYR* 4.4 2.0 - - - -
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Residues in contact with HIS 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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256C LYS* 5.0 15.3 - - + +
260C PHE* 3.2 41.8 - + + +
367C GLN 2.9 17.7 + - - +
368C LEU* 3.3 6.3 + - - +
370C TYR* 1.3 79.2 - - - +
372C LEU* 1.3 75.0 + - + +
374C GLY 4.6 0.5 + - - -
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Residues in contact with LEU 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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253C THR* 4.3 16.2 - - + -
256C LYS* 4.1 32.8 - - + -
257C ILE* 4.0 26.7 - - + +
368C LEU* 3.0 30.4 + - + +
369C VAL* 5.3 0.4 - - - -
371C HIS* 1.3 90.9 - - + +
373C PHE* 1.3 89.3 + - + +
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Residues in contact with PHE 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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253C THR* 5.9 4.3 - - + -
369C VAL* 2.9 37.9 + - + +
372C LEU* 1.3 97.9 - - + +
374C GLY* 1.3 63.1 + - - +
375C THR* 3.0 25.7 + - + +
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Residues in contact with GLY 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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370C TYR* 3.0 43.3 + - - -
371C HIS 4.6 0.4 + - - -
372C LEU 3.6 1.2 - - - -
373C PHE* 1.3 76.5 - - - +
375C THR* 1.3 60.6 + - - +
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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