Contacts of the helix formed by residues 313 - 330 (chain D) in PDB entry 4AY6
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 CYS 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D SER* 1.3 74.6 - - - +
314D PRO* 1.3 67.5 - - - +
315D THR* 3.4 14.6 - - - -
316D HIS* 2.9 44.6 - - + -
317D ALA* 3.1 18.4 + - - +
346D VAL* 3.2 14.1 - - + +
347D PHE* 4.6 1.6 - - - -
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Residues in contact with PRO 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D SER 3.2 12.1 - - - +
313D CYS* 1.3 83.5 - - + +
315D THR* 1.3 54.4 + - - +
317D ALA* 3.5 2.1 + - - +
318D ASP* 2.7 38.7 + - - +
347D PHE* 3.9 38.4 - - + -
350D PHE* 5.2 0.3 - - - -
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Residues in contact with THR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D CYS* 3.3 9.8 - - - -
314D PRO* 1.3 76.5 - - - +
316D HIS* 1.3 70.9 + - - +
318D ASP* 3.2 8.6 + - + +
319D SER* 3.0 21.1 + - - -
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Residues in contact with HIS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D CYS* 2.9 31.4 - - + +
315D THR* 1.3 72.4 - - - +
317D ALA* 1.3 64.8 + - - +
319D SER* 2.9 20.9 + - - -
320D LEU* 3.1 28.2 + - + +
342D LYS* 5.7 5.5 - - + +
346D VAL* 3.6 29.3 - - + +
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D CYS 3.1 3.9 + - - +
314D PRO* 3.7 5.4 - - + +
316D HIS* 1.3 78.9 - - - +
318D ASP* 1.3 64.0 + - - +
320D LEU* 3.0 16.9 + - - +
321D ASN* 2.9 23.2 + - - +
343D ALA* 3.4 25.5 - - - +
346D VAL* 3.9 3.5 - - + +
347D PHE* 3.7 23.6 - - + -
350D PHE* 3.9 14.5 - - + -
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Residues in contact with ASP 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D PRO* 2.7 23.0 + - - +
315D THR* 3.3 12.1 - - + +
316D HIS 3.1 0.2 - - - -
317D ALA* 1.3 73.0 - - - +
319D SER* 1.3 60.5 + - - +
321D ASN* 3.5 4.3 - - - +
322D ASN* 3.0 33.2 + - - +
350D PHE* 3.4 26.6 - - - -
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D THR* 3.0 11.2 + - - -
316D HIS* 2.9 14.3 + - - -
318D ASP* 1.3 74.2 - - - +
320D LEU* 1.3 68.7 + - - +
322D ASN* 3.0 15.7 + - - +
323D LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D HIS* 3.1 24.4 + - + +
317D ALA* 3.0 17.6 + - - +
319D SER* 1.3 80.4 - - - +
321D ASN* 1.3 56.6 + - - +
323D LEU* 3.0 15.0 + - + +
324D ALA* 2.8 30.4 + - - +
339D LEU* 4.3 24.3 - - + +
342D LYS* 4.1 27.8 - - + +
343D ALA* 3.7 34.3 - - + +
346D VAL* 4.1 12.6 - - + -
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Residues in contact with ASN 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ALA 2.9 11.9 + - - +
318D ASP 3.5 9.4 - - - +
320D LEU* 1.3 75.0 - - - +
322D ASN* 1.3 64.1 + - - +
323D LEU 3.0 0.2 + - - -
324D ALA* 3.1 5.2 + - - +
325D ASN* 3.0 41.3 + - - +
340D TYR* 3.4 29.1 - - - -
343D ALA* 4.3 4.7 - - + +
350D PHE* 3.9 20.3 - - + -
352D ALA* 4.6 4.2 - - - +
353D ALA* 3.6 16.9 - - - +
356D ASN* 3.4 21.1 + - - +
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Residues in contact with ASN 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ASP* 3.0 28.4 + - - -
319D SER* 3.0 13.6 + - - +
321D ASN* 1.3 77.9 + - - +
323D LEU* 1.3 63.9 + - + +
325D ASN* 3.9 12.3 + - - +
326D ILE* 3.4 27.2 + - + +
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Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D SER* 2.9 20.9 + - - +
320D LEU* 3.3 19.1 - - + +
321D ASN 3.0 0.2 - - - -
322D ASN* 1.3 77.4 - - + +
324D ALA* 1.3 65.9 + - - +
326D ILE* 2.9 32.2 + - + +
327D LYS* 3.0 20.3 + - + +
339D LEU* 3.9 17.0 - - + -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D LEU 2.8 11.8 + - - +
321D ASN* 3.1 4.7 + - - +
323D LEU* 1.3 76.1 - - - +
325D ASN* 1.3 57.8 + - - +
327D LYS* 2.8 20.8 + - - +
328D ARG* 2.9 14.0 + - - +
336D ALA* 3.7 11.0 - - - +
339D LEU* 3.6 28.1 - - + +
340D TYR* 3.5 35.0 - - + +
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D ASN* 3.0 33.0 + - - +
322D ASN* 4.1 12.4 + - - +
324D ALA* 1.3 73.7 - - - +
326D ILE* 1.3 61.9 + - + +
328D ARG* 3.6 6.6 + - - +
329D GLU* 3.2 29.4 + - - +
340D TYR* 2.9 28.7 + - - -
356D ASN* 3.8 10.3 + - - +
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ASN* 3.4 16.9 + - + +
323D LEU* 2.9 28.3 + - + +
325D ASN* 1.3 79.6 - - + +
327D LYS* 1.3 65.4 + - + +
329D GLU* 2.9 25.5 + - - +
330D GLN* 3.2 34.6 + - + +
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Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D LEU* 3.0 19.4 + - - +
324D ALA 2.8 8.1 + - - +
326D ILE* 1.3 81.1 - - + +
328D ARG* 1.3 61.4 + - - +
330D GLN* 3.5 28.4 + - - +
332D ASN* 3.1 37.0 + - + +
335D GLU* 4.3 18.6 - - + -
336D ALA* 4.0 17.3 - - - +
339D LEU* 3.7 19.3 - - + -
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Residues in contact with ARG 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA 2.9 10.4 + - - +
325D ASN* 3.6 11.4 - - - +
327D LYS* 1.3 75.9 - - - +
329D GLU* 1.3 70.1 + - - +
331D GLY* 2.9 22.4 + - - -
332D ASN 4.5 4.0 - - - +
333D ILE* 4.6 14.6 - - + +
336D ALA* 4.1 11.8 - - + +
340D TYR* 4.1 15.8 + - - +
356D ASN* 4.0 14.6 + - - +
359D SER* 3.2 34.6 + - - -
360D VAL* 3.5 24.5 - - + +
363D GLN* 3.4 23.6 + - - -
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Residues in contact with GLU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ASN* 3.2 15.9 + - - +
326D ILE* 2.9 13.4 + - - +
328D ARG* 1.3 89.0 - - - +
330D GLN* 1.3 57.6 + - + +
331D GLY* 2.8 11.2 + - - -
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Residues in contact with GLN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ILE* 3.2 29.7 + - + +
327D LYS* 3.5 34.7 + - - +
328D ARG 3.3 0.2 - - - -
329D GLU* 1.3 72.9 - - + +
331D GLY* 1.3 49.1 + - - +
332D ASN* 2.6 25.5 + - + +
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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