Contacts of the helix formed by residues 327 - 341 (chain D) in PDB entry 2IB8
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 ILE 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D THR* 4.3 23.6 - - + +
204D LEU* 4.5 5.8 - - + -
320D VAL* 4.3 6.5 - - + -
324D ASP* 2.9 43.1 + - + +
326D PRO* 1.3 75.7 - - - +
328D ALA* 1.3 67.6 + - - +
329D PRO* 3.3 3.1 - - - -
330D VAL* 2.9 25.9 + - - +
331D TYR* 3.5 28.4 - - + +
362D ALA* 4.9 2.9 - - + -
366D MET* 3.7 30.1 - - + -
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Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA* 3.8 6.9 - - - +
320D VAL* 4.1 9.8 - - + +
324D ASP 3.7 1.0 + - - -
325D PHE 3.3 7.1 + - - +
327D ILE* 1.3 80.0 - - - +
329D PRO* 1.4 65.8 - - + +
330D VAL 3.1 1.0 + - - -
331D TYR* 3.2 14.1 + - - +
332D ALA 3.2 16.1 + - - -
417D GLY 3.8 14.4 - - - +
418D GLY* 3.4 34.3 - - - +
419D ALA* 3.4 6.3 - - + +
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Residues in contact with PRO 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 PHE 3.4 9.9 - - - +
326D PRO 3.3 17.9 - - - +
327D ILE 3.4 1.1 - - - -
328D ALA* 1.4 89.9 - - + +
330D VAL* 1.3 60.3 + - - +
331D TYR 3.4 0.2 - - - -
332D ALA* 3.8 3.7 - - + +
333D ALA* 3.0 26.3 + - - +
352D VAL* 5.1 2.2 - - + -
359D VAL* 4.8 4.3 - - + -
363D ASN* 3.4 18.2 - - - +
411D SER* 3.7 25.8 - - - +
412D ILE* 4.2 0.9 - - - +
413D CYS* 3.7 28.3 - - + +
419D ALA* 3.3 12.3 - - + -
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Residues in contact with VAL 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ILE* 2.9 17.0 + - - +
329D PRO* 1.3 77.1 - - - +
331D TYR* 1.3 68.0 + - + +
333D ALA* 3.6 2.9 - - - +
334D SER* 3.0 34.7 + - - +
362D ALA 5.1 0.2 - - - -
363D ASN* 3.3 29.8 - - + +
366D MET* 3.9 46.0 - - + +
367D LEU* 3.9 26.0 - - + +
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Residues in contact with TYR 331 (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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318D ALA* 4.0 13.9 - - + -
320D VAL* 3.9 29.2 - - + -
327D ILE* 3.5 34.3 - - + +
328D ALA 3.2 6.0 + - - +
330D VAL* 1.3 79.6 - - + +
332D ALA* 1.3 58.8 + - - +
334D SER* 3.2 8.8 + - - -
335D MET* 2.9 37.0 + - + +
366D MET* 4.1 19.3 - - + +
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ALA* 4.0 8.5 - - - +
318D ALA* 3.6 19.6 - - + +
328D ALA 3.2 12.6 + - - +
329D PRO* 4.0 3.1 - - + +
331D TYR* 1.3 76.0 - - - +
333D ALA* 1.3 63.0 + - - +
335D MET* 3.5 8.7 + - - +
336D VAL* 3.2 27.4 + - - +
419D ALA* 4.1 18.6 - - + +
420D SER 4.2 2.5 - - - -
421D ALA* 3.6 19.3 - - + +
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D PRO 3.0 19.9 + - - +
330D VAL 3.6 4.3 - - - +
332D ALA* 1.3 77.6 - - - +
334D SER* 1.3 62.5 + - - +
336D VAL* 3.2 6.0 + - - +
337D LEU* 3.1 27.6 + - - +
350D TRP* 4.2 15.0 - - + -
367D LEU* 4.6 10.3 - - + -
409D LEU* 3.7 24.7 - - + +
411D SER* 4.9 3.1 - - - +
421D ALA* 3.8 8.6 - - + +
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Residues in contact with SER 334 (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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330D VAL* 3.0 21.8 + - - +
331D TYR* 3.2 11.0 + - - -
333D ALA* 1.3 75.8 - - - +
335D MET* 1.3 57.4 + - - +
337D LEU* 3.4 9.6 + - - +
338D LYS* 2.9 33.6 + - - +
367D LEU* 4.0 13.4 - - - +
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Residues in contact with MET 335 (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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145C GLN* 6.3 1.1 - - - +
316D ALA* 3.9 17.7 - - + -
317D ASP 3.4 27.4 - - - +
318D ALA* 4.0 14.8 - - - -
331D TYR* 2.9 23.4 + - + +
332D ALA* 3.6 7.9 - - - +
334D SER* 1.3 75.8 - - - +
336D VAL* 1.3 57.0 + - - +
338D LYS* 3.6 7.9 + - - +
339D ASP* 2.9 32.0 + - - +
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Residues in contact with VAL 336 (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 ALA* 4.2 12.3 - - + -
315D PHE* 3.8 9.0 - - - +
316D ALA* 3.7 28.0 - - + +
332D ALA 3.2 13.9 + - - +
333D ALA 3.2 8.0 + - - +
335D MET* 1.3 74.7 - - - +
337D LEU* 1.3 65.4 + - - +
339D ASP* 3.2 7.0 + - - +
340D VAL* 3.0 23.9 + - - +
409D LEU* 4.3 10.8 - - + -
421D ALA* 4.0 13.2 - - + +
423D LEU* 3.6 36.1 - - + +
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Residues in contact with LEU 337 (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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333D ALA* 3.1 21.7 + - + +
334D SER* 3.9 6.7 - - - +
336D VAL* 1.3 77.8 - - + +
338D LYS* 1.3 57.9 + - - +
340D VAL* 3.3 1.2 + - - -
341D GLY* 2.9 25.6 + - - -
342D LEU* 2.9 38.2 + - + +
343D LYS 4.1 3.8 - - - +
344D LYS* 3.9 34.1 - - + +
347D ILE* 3.8 24.2 - - + -
350D TRP* 4.3 12.1 - - + -
367D LEU* 5.7 3.4 - - + -
409D LEU* 3.8 20.2 - - + -
423D LEU* 5.6 2.0 - - + -
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Residues in contact with LYS 338 (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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334D SER 2.9 18.0 + - - +
335D MET* 3.8 7.4 - - - +
337D LEU* 1.3 76.3 - - - +
339D ASP* 1.3 63.5 + - - +
341D GLY* 3.3 11.9 + - - -
342D LEU 5.2 0.7 - - - -
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Residues in contact with ASP 339 (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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36D LYS* 5.1 10.9 + - - -
314D ALA* 3.8 21.0 - - - +
315D PHE 5.3 3.3 - - - +
335D MET 2.9 19.5 + - - +
336D VAL* 3.5 6.5 - - - +
337D LEU 3.2 0.2 - - - -
338D LYS* 1.3 78.7 - - - +
340D VAL* 1.3 60.4 + - - +
341D GLY 3.6 0.2 + - - -
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Residues in contact with VAL 340 (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 VAL* 3.8 24.7 - - + -
314D ALA* 3.4 32.5 - - + -
336D VAL 3.0 12.4 + - - +
337D LEU* 4.3 2.0 - - - +
339D ASP* 1.3 77.4 - - - +
341D GLY* 1.3 58.8 + - - +
342D LEU* 3.9 27.8 - - + +
407D TYR* 5.6 3.1 - - + +
423D LEU* 4.1 8.3 - - + -
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Residues in contact with GLY 341 (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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337D LEU 2.9 6.5 + - - -
338D LYS* 3.3 8.0 + - - -
339D ASP 3.3 4.2 + - - -
340D VAL* 1.3 78.9 - - - +
342D LEU* 1.3 65.9 + - - +
343D LYS* 5.8 0.3 - - - +
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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