Contacts of the helix formed by residues 355 - 370 (chain C) in PDB entry 2Y4T
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 MET 355 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326C ILE* 5.2 3.6 - - - -
350C TYR* 2.6 43.7 + - + +
353C GLU* 3.8 25.6 - - + +
354C GLU* 1.3 76.7 - - - +
356C TYR* 1.3 58.4 + - - +
357C ASP 3.4 2.7 - - - -
358C GLU* 3.0 51.0 + - + +
359C ALA 3.0 9.7 + - - -
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Residues in contact with TYR 356 (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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351C LEU* 4.4 26.0 - - + -
354C GLU* 3.2 51.1 + - + +
355C MET* 1.3 69.7 - - - +
357C ASP* 1.3 65.5 + - - +
359C ALA* 3.1 8.1 + - - +
360C ILE* 3.1 29.6 + - - +
383C ALA* 3.8 18.6 - - - +
386C LEU* 3.6 49.5 - - + +
387C LEU* 3.8 15.3 - - + -
390C SER* 4.0 24.2 - - - -
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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
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355C MET 3.4 0.2 - - - -
356C TYR* 1.3 77.5 - - - +
358C GLU* 1.3 73.4 + - - +
360C ILE* 3.2 34.0 - - - +
361C GLN* 3.5 11.3 + - - +
387C LEU* 4.1 14.9 - - + +
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Residues in contact with GLU 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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350C TYR* 3.6 36.5 - - + +
355C MET* 3.0 48.9 + - + +
357C ASP* 1.3 87.5 - - - +
359C ALA* 1.3 63.5 + - - +
360C ILE 3.5 0.2 - - - -
361C GLN* 3.8 11.0 + - - +
362C ASP* 3.4 21.0 + - - +
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Residues in contact with ALA 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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347C ALA* 3.9 14.7 - - - +
350C TYR* 3.8 17.2 - - + +
351C LEU* 4.1 11.4 - - + +
355C MET 3.0 10.9 + - - +
356C TYR* 3.1 14.5 + - - +
358C GLU* 1.3 75.3 - - - +
360C ILE* 1.3 64.0 + - - +
362C ASP* 3.5 5.2 + - - +
363C TYR* 3.1 30.6 + - + -
383C ALA* 4.1 13.0 - - + -
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Residues in contact with ILE 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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356C TYR 3.1 10.9 + - - +
357C ASP* 3.2 35.4 - - - +
359C ALA* 1.3 75.4 - - - +
361C GLN* 1.3 52.2 + - - +
363C TYR* 3.0 10.9 + - - +
364C GLU* 2.8 54.2 + - - +
380C LEU* 3.7 24.6 - - + +
383C ALA* 3.5 25.1 - - + +
384C GLN* 3.8 24.9 - - - +
387C LEU* 5.4 5.8 - - + -
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Residues in contact with GLN 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 ASP 3.5 13.2 + - - +
358C GLU* 4.0 11.6 + - - +
359C ALA 3.4 0.4 - - - -
360C ILE* 1.3 80.9 - - + +
362C ASP* 1.3 62.1 + - - +
364C GLU* 3.2 17.7 + - - +
365C THR* 3.0 40.8 + - + +
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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
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343C LEU* 3.5 30.1 - - + +
346C ARG* 2.8 57.6 + - - +
347C ALA* 4.1 6.2 + - + -
350C TYR* 3.7 7.1 - - - -
358C GLU 3.4 14.4 + - - +
359C ALA 3.8 8.1 - - - +
360C ILE 3.3 0.4 - - - -
361C GLN* 1.3 83.7 - - - +
363C TYR* 1.3 60.6 + - - +
365C THR* 3.1 17.6 + - - -
366C ALA* 3.3 13.9 + - - +
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Residues in contact with TYR 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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344C LYS* 4.2 24.1 + - + +
347C ALA* 3.5 28.3 - - + +
348C GLU* 4.4 4.0 + - - +
351C LEU* 4.3 16.3 - - + +
359C ALA* 3.1 26.8 + - + -
360C ILE* 3.0 7.6 + - - +
362C ASP* 1.3 76.3 - - - +
364C GLU* 1.3 53.2 + - - +
366C ALA* 3.0 8.0 + - + +
367C GLN* 2.8 38.0 + - - +
375C GLN 4.9 1.9 + - - -
376C ILE* 3.8 35.5 - - + +
379C GLY* 3.5 36.9 - - - -
380C LEU* 3.8 19.5 - - + -
383C ALA* 5.1 0.2 - - + -
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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
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360C ILE* 2.8 40.7 + - - +
361C GLN* 3.2 23.5 + - + +
363C TYR* 1.3 72.1 - - - +
365C THR* 1.3 61.0 + - + +
367C GLN* 3.2 18.9 + - - +
368C GLU* 3.4 16.3 + - - +
380C LEU* 3.8 20.0 - - + +
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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
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337C PRO 5.5 1.1 - - - -
343C LEU* 3.4 19.7 - - - +
361C GLN* 3.0 26.2 + - + +
362C ASP* 3.1 17.7 + - - -
364C GLU* 1.3 76.2 - - + +
366C ALA* 1.3 59.0 + - - +
368C GLU* 3.4 27.2 + - - +
369C HIS* 3.0 29.3 + - - -
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Residues in contact with ALA 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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340C VAL* 4.6 10.9 - - + +
343C LEU* 3.9 24.0 - - + +
344C LYS* 5.4 0.9 - - + -
362C ASP 3.3 14.0 + - - +
363C TYR* 3.0 16.5 + - + +
365C THR* 1.3 79.2 + - - +
367C GLN* 1.3 55.7 + - - +
369C HIS* 3.5 4.5 + - - +
370C ASN* 3.1 30.5 + - - +
376C ILE* 4.3 19.6 - - + +
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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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363C TYR 2.8 13.4 + - - +
364C GLU* 3.2 12.7 + - - +
366C ALA* 1.3 74.5 - - - +
368C GLU* 1.3 63.8 + - - +
370C ASN 3.0 23.7 - - - +
371C GLU* 4.5 8.5 + - - +
376C ILE* 3.7 17.3 - - + +
377C ARG* 3.9 29.1 - - - +
380C LEU* 3.5 28.2 - - - +
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Residues in contact with GLU 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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364C GLU 3.6 11.1 - - - +
365C THR* 3.4 29.1 - - - +
366C ALA 3.3 0.6 - - - -
367C GLN* 1.3 78.5 - - - +
369C HIS* 1.3 68.4 + - + +
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Residues in contact with HIS 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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337C PRO* 3.8 10.7 + - + +
338C ASP* 3.4 52.8 + - + +
340C VAL* 4.7 7.0 - - + -
343C LEU* 4.5 3.4 - - - +
365C THR* 3.0 30.0 + - - -
366C ALA* 3.5 4.5 + - - +
368C GLU* 1.3 86.6 - - + +
370C ASN* 1.3 60.5 + - - +
371C GLU* 4.1 3.3 + - - +
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Residues in contact with ASN 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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340C VAL* 4.1 32.5 - - + +
366C ALA 3.1 13.2 + - - +
367C GLN* 3.0 24.2 - - - +
368C GLU 5.2 0.2 - - - -
369C HIS* 1.3 77.2 - - - +
371C GLU* 1.3 69.7 + - - +
372C ASN* 3.4 21.0 + - - +
373C ASP* 4.1 16.5 + - - +
376C ILE* 4.5 4.4 - - + +
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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