Contacts of the helix formed by residues 339 - 353 (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 ASN 339 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C ARG* 3.0 18.3 + - - +
310C GLU* 3.0 29.9 + - - +
332C VAL* 3.8 10.1 - - + +
333C LEU* 3.9 0.5 - - - +
336C GLU* 3.2 30.8 + - + +
337C PRO 3.3 1.0 - - - -
338C ASP* 1.3 76.0 - - - +
340C VAL* 1.3 64.9 + - - +
341C ASN* 3.0 17.5 + - - +
342C ALA* 3.2 21.6 + - + +
343C LEU* 3.1 25.7 + - - +
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Residues in contact with VAL 340 (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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338C ASP 3.1 10.4 + - - +
339C ASN* 1.3 72.1 + - - +
341C ASN* 1.3 62.5 + - - +
343C LEU* 3.5 9.9 + - - +
344C LYS* 3.0 41.1 + - + +
366C ALA* 4.6 6.3 - - + +
369C HIS* 4.7 10.1 - - + -
370C ASN* 4.1 30.5 - - + +
373C ASP* 5.8 0.7 - - - +
376C ILE* 3.9 27.6 - - + -
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Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C GLU* 3.7 24.4 + - - +
311C ARG* 5.2 6.5 - - - +
339C ASN* 3.0 5.0 + - - +
340C VAL* 1.3 77.7 - - - +
342C ALA* 1.3 55.9 + - - +
343C LEU 3.2 1.3 - - - -
344C LYS* 3.0 26.0 + - - +
345C ASP* 2.7 47.5 + - - +
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Residues in contact with ALA 342 (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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310C GLU* 4.8 4.6 - - + +
313C CYS* 4.2 17.3 - - - -
329C CYS* 4.1 5.4 - - - +
332C VAL* 3.9 19.3 - - + -
333C LEU* 3.9 18.3 - - + +
339C ASN* 3.2 28.3 + - - +
341C ASN* 1.3 75.8 - - - +
343C LEU* 1.3 57.6 + - - +
345C ASP* 4.3 0.9 + - - -
346C ARG* 3.0 30.1 + - - +
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Residues in contact with LEU 343 (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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333C LEU* 3.7 28.0 - - + -
337C PRO 3.5 21.1 - - - +
338C ASP 4.4 3.1 - - - -
339C ASN 3.1 25.7 + - - +
340C VAL* 3.5 5.4 - - - +
341C ASN 3.2 0.2 - - - -
342C ALA* 1.3 76.6 - - - +
344C LYS* 1.3 56.8 + - - +
346C ARG* 3.7 0.8 + - - +
347C ALA* 3.1 28.4 + - - +
362C ASP* 3.5 32.1 - - - +
363C TYR* 5.7 0.2 - - - -
365C THR* 3.4 26.2 - - - +
366C ALA* 3.9 28.7 - - + +
369C HIS* 4.5 1.6 - - - +
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Residues in contact with LYS 344 (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* 3.0 32.3 + - + +
341C ASN* 3.0 27.3 + - - +
343C LEU* 1.3 76.8 - - - +
345C ASP* 1.3 58.6 + - - +
347C ALA* 3.4 7.3 + - - +
348C GLU* 3.1 25.8 + - - +
363C TYR* 4.2 16.5 + - + -
366C ALA* 5.4 1.6 - - + -
373C ASP* 3.6 18.1 + - - -
375C GLN* 2.7 37.3 + - - -
376C ILE* 4.0 20.0 - - + +
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Residues in contact with ASP 345 (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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310C GLU* 4.5 2.6 - - - +
311C ARG* 5.6 0.2 + - - -
313C CYS* 3.8 19.6 - - - -
314C HIS* 3.0 50.2 + - - +
317C SER* 2.8 36.4 + - - -
318C LYS* 5.0 4.3 - - - +
329C CYS* 4.6 1.9 - - - -
341C ASN* 2.7 30.7 + - - +
342C ALA 4.1 0.6 + - - +
344C LYS* 1.3 72.4 - - - +
346C ARG* 1.3 66.4 + - - +
348C GLU* 3.4 2.2 + - - +
349C ALA* 3.3 10.4 + - - +
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Residues in contact with ARG 346 (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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326C ILE* 4.4 13.5 - - + +
329C CYS* 3.8 13.2 - - + -
330C SER* 2.7 54.5 + - - +
333C LEU* 3.7 21.3 - - - +
342C ALA 3.0 19.4 + - - +
343C LEU* 5.2 0.4 - - - +
345C ASP* 1.3 74.1 - - - +
347C ALA* 1.3 65.2 + - - +
349C ALA* 3.3 7.5 + - - +
350C TYR* 3.1 48.0 + - + -
362C ASP* 2.8 35.9 + - - +
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Residues in contact with ALA 347 (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 3.1 19.5 + - - +
344C LYS 3.4 6.3 - - - +
345C ASP 3.3 0.2 - - - -
346C ARG* 1.3 74.0 - - - +
348C GLU* 1.3 63.7 + - - +
350C TYR* 3.2 13.8 + - - +
351C LEU* 3.1 25.7 + - - +
359C ALA* 3.9 13.4 - - - +
362C ASP* 4.1 6.2 + - + -
363C TYR* 3.5 34.3 - - + -
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Residues in contact with GLU 348 (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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317C SER* 3.5 28.3 - - - +
318C LYS* 5.9 7.4 - - + -
344C LYS 3.1 13.4 + - - +
345C ASP* 3.6 3.6 - - - +
346C ARG 3.3 0.2 - - - -
347C ALA* 1.3 75.8 - - - +
349C ALA* 1.3 62.9 + - - +
351C LEU* 3.3 29.7 + - - +
352C ILE* 3.1 33.7 + - + +
363C TYR* 4.4 4.6 + - - +
382C LYS* 5.9 1.0 + - - -
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Residues in contact with ALA 349 (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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317C SER* 4.2 3.3 + - - +
322C PRO* 4.1 11.0 - - + +
325C ALA* 4.0 19.5 - - + -
326C ILE* 4.0 22.7 - - + -
345C ASP 3.3 8.9 + - - +
346C ARG* 3.3 12.7 + - - +
347C ALA 3.2 0.2 - - - -
348C GLU* 1.3 78.5 - - - +
350C TYR* 1.3 57.6 + - - +
352C ILE* 3.0 14.5 + - - +
353C GLU* 2.9 29.3 + - - +
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Residues in contact with TYR 350 (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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326C ILE* 3.9 32.8 - - + +
346C ARG* 3.1 45.7 + - + -
347C ALA* 3.2 6.5 + - - +
349C ALA* 1.3 77.1 - - - +
351C LEU* 1.3 56.0 + - - +
353C GLU* 3.5 1.9 + - - +
354C GLU 3.0 6.4 + - - -
355C MET* 2.6 66.6 + - + +
358C GLU* 3.6 45.5 - - + +
359C ALA* 3.8 7.6 - - + +
362C ASP* 3.7 20.9 - - - -
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Residues in contact with LEU 351 (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 3.1 14.5 + - - +
348C GLU* 3.3 40.4 - - - +
350C TYR* 1.3 74.1 - - - +
352C ILE* 1.3 65.0 + - + +
354C GLU* 3.1 16.5 + - - +
355C MET 4.9 0.4 - - - +
356C TYR* 4.4 17.4 - - + -
359C ALA* 4.1 7.6 - - + -
363C TYR* 4.3 14.4 - - + +
379C GLY* 5.1 3.4 - - - +
382C LYS* 5.0 23.8 - - + +
383C ALA* 4.1 33.7 - - + +
386C LEU* 6.1 2.0 - - + -
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Residues in contact with ILE 352 (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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317C SER* 4.1 12.3 - - - +
320C GLU* 3.9 45.1 - - + +
321C LYS 5.0 0.4 - - - +
322C PRO* 4.1 24.9 - - + -
348C GLU* 3.1 30.4 + - + +
349C ALA* 3.0 11.0 + - - +
351C LEU* 1.3 77.1 - - - +
353C GLU* 1.3 58.7 + - - +
354C GLU* 3.2 10.7 + - - +
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Residues in contact with GLU 353 (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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322C PRO* 3.5 36.0 - - + +
323C VAL* 4.7 9.1 - - - +
326C ILE* 4.4 13.0 - - + -
349C ALA 2.9 12.2 + - - +
350C TYR* 3.5 3.1 + - - +
351C LEU 3.3 0.2 - - - -
352C ILE* 1.3 75.0 - - - +
354C GLU* 1.3 69.2 + - - +
355C MET* 3.8 27.2 - - + +
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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