Contacts of the helix formed by residues 327 - 342 (chain D) in PDB entry 2DB3
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 THR 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325D SER* 2.7 22.1 + - - -
326D PRO* 1.3 83.8 + - - +
328D ARG* 1.3 63.3 + - - +
329D GLU* 3.5 12.1 - - + +
330D LEU* 3.1 34.3 - - + +
331D ALA 3.1 7.6 + - - -
375D THR* 3.6 8.9 - - - +
548D VAL* 3.2 31.5 + - - +
551D ARG* 5.3 4.0 - - - +
553D LEU* 5.1 3.6 - - + -
4H U 3.4 16.5 + - - -
5H U 3.6 4.6 + - - -
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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
----------------------------------------------------------
327D THR* 1.3 72.5 - - - +
329D GLU* 1.3 59.3 + - - +
331D ALA* 3.0 5.5 + - - +
332D ILE* 3.0 32.2 + - - +
353D TYR* 3.8 21.6 - - + -
354D GLY* 3.4 31.3 + - - -
355D GLY* 3.8 6.3 - - - +
375D THR* 3.7 11.4 - - + +
525D GLN* 2.7 51.9 + - - +
528D ARG* 3.9 17.9 - - - +
5H U 2.9 31.1 + - - +
6H U 2.8 35.5 + - - +
7H U 4.4 5.1 + - - -
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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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327D THR* 3.8 9.5 - - + +
328D ARG* 1.3 72.7 - - - +
330D LEU* 1.3 60.9 + - - +
331D ALA 3.3 0.2 - - - -
332D ILE* 3.5 14.5 + - + +
333D GLN* 3.1 20.8 + - - +
519D ILE* 3.8 12.0 - - + +
525D GLN* 3.1 18.2 + - - +
528D ARG* 2.5 56.0 + - - +
529D GLU* 4.9 4.7 - - + -
532D LEU* 3.7 32.3 - - + +
548D VAL* 4.1 6.2 - - - +
553D LEU* 4.1 11.6 - - + +
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Residues in contact with LEU 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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325D SER* 3.6 13.7 - - - +
326D PRO* 4.2 7.6 - - + -
327D THR* 3.1 21.0 - - + +
329D GLU* 1.3 74.8 - - - +
331D ALA* 1.3 67.0 + - - +
333D GLN* 3.2 26.8 + - - +
334D ILE* 3.0 39.0 + - + +
399D ASP* 4.1 8.1 - - - +
400D GLU* 3.7 28.7 - - + +
551D ARG 3.7 16.8 - - - +
552D GLY* 3.9 15.9 - - - +
553D LEU* 4.0 8.7 - - + +
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D SER* 3.5 12.9 + - - -
327D THR 3.1 13.1 + - - +
328D ARG* 3.0 10.9 + - - +
330D LEU* 1.3 78.9 - - - +
332D ILE* 1.3 57.2 + - - +
334D ILE* 3.3 0.7 + - - -
335D PHE* 2.9 30.0 + - - +
351D ILE* 3.7 13.5 - - + -
353D TYR* 5.1 2.7 - - + -
373D ILE* 3.4 23.8 - - + +
374D ALA* 4.7 5.8 - - - -
375D THR* 4.1 11.9 - - + -
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Residues in contact with ILE 332 (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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328D ARG 3.0 18.8 + - - +
329D GLU* 3.7 15.5 - - + +
331D ALA* 1.3 77.2 - - - +
333D GLN* 1.3 61.3 + - - +
335D PHE* 3.1 8.5 - - + +
336D ASN* 3.0 34.3 + - - +
351D ILE* 3.5 9.0 - - + -
353D TYR* 3.4 45.1 - - + +
525D GLN* 4.5 1.1 - - - +
529D GLU* 3.7 24.9 - - + +
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Residues in contact with GLN 333 (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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296D THR* 5.2 5.6 + - + +
329D GLU 3.1 14.1 + - - +
330D LEU* 3.2 20.0 + - - +
332D ILE* 1.3 75.5 - - - +
334D ILE* 1.3 69.1 + - + +
336D ASN* 3.1 7.8 + - - +
337D GLU* 3.1 32.2 + - + +
536D LYS* 5.8 3.8 + - - +
552D GLY 2.8 26.2 + - - -
553D LEU* 3.5 9.3 - - + +
554D ASP* 2.8 39.7 + - - +
555D ILE* 5.4 1.0 - - - +
2904D ANP 4.4 6.3 + - - -
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Residues in contact with ILE 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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296D THR* 4.3 22.7 - - + +
299D PHE* 4.5 6.3 - - + -
300D LEU* 4.2 8.9 - - + +
323D ILE* 4.3 14.8 - - + -
325D SER* 4.5 9.9 - - - -
330D LEU* 3.0 32.5 + - + +
331D ALA 3.8 2.9 - - - +
333D GLN* 1.3 76.9 - - + +
335D PHE* 1.3 63.6 + - - +
337D GLU* 3.2 7.2 + - - +
338D ALA* 3.0 23.3 + - - +
373D ILE* 4.1 23.3 - - + -
399D ASP* 3.2 36.1 - - + +
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Residues in contact with PHE 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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207D PRO* 3.9 21.3 - - + -
331D ALA 2.9 13.5 + - - +
332D ILE* 3.1 15.0 - - + +
334D ILE* 1.3 78.2 - - - +
336D ASN* 1.3 67.9 + - - +
338D ALA* 3.4 4.4 - - - +
339D ARG* 3.1 58.5 + - - +
349D ILE* 3.2 35.7 - - + -
350D GLY* 3.5 23.1 - - - -
351D ILE* 3.6 31.6 - - + -
373D ILE* 3.9 10.9 - - + +
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Residues in contact with ASN 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PRO* 3.8 17.8 - - - +
214D ILE* 4.8 3.5 - - - +
217D SER* 5.1 6.1 + - - +
332D ILE* 3.0 32.1 + - - +
333D GLN* 3.1 8.6 + - - +
335D PHE* 1.3 80.2 - - - +
337D GLU* 1.3 69.7 + - - +
338D ALA 3.1 1.6 - - - -
339D ARG* 3.5 24.8 + - - +
340D LYS* 3.1 21.1 + - - +
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Residues in contact with GLU 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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217D SER* 2.8 31.9 + - - -
218D GLY* 5.4 1.6 + - - -
265D TYR* 4.1 2.9 + - - -
296D THR* 4.4 14.6 - - + -
300D LEU* 4.0 13.0 - - + -
333D GLN* 3.1 27.8 + - + +
334D ILE* 3.8 6.1 - - - +
336D ASN* 1.3 78.3 - - - +
338D ALA* 1.3 57.7 + - - +
340D LYS* 2.8 31.5 + - - +
341D PHE* 2.9 42.1 + - + -
554D ASP* 6.1 0.4 - - - -
2904D ANP 4.0 13.3 + - - -
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Residues in contact with ALA 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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300D LEU* 3.8 21.7 - - + +
304D LEU* 3.9 8.6 - - + +
334D ILE 3.0 13.3 + - - +
335D PHE* 3.4 11.9 - - - +
337D GLU* 1.3 72.2 - - - +
339D ARG* 1.3 51.4 + - - +
340D LYS 2.9 4.0 - - - -
341D PHE* 3.1 2.4 + - - -
342D ALA* 2.8 39.8 + - - +
349D ILE* 3.6 26.5 - - + -
371D VAL* 5.6 1.6 - - + -
373D ILE* 5.1 4.7 - - + -
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Residues in contact with ARG 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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207D PRO* 3.4 23.1 + - - +
208D SER 3.5 23.0 + - - -
209D ASN* 3.0 25.7 + - - +
214D ILE* 3.8 21.5 - - + +
335D PHE* 3.1 49.7 + - + +
336D ASN* 3.7 18.8 - - - +
337D GLU 3.4 0.2 - - - -
338D ALA* 1.3 76.0 - - - +
340D LYS* 1.3 60.5 + - - +
342D ALA* 3.8 2.8 - - - +
343D PHE* 3.2 22.9 + - - +
349D ILE* 4.3 17.3 + - + +
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Residues in contact with LYS 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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214D ILE* 3.8 27.8 - - - +
215D PHE* 3.8 20.7 - - + -
217D SER* 4.2 18.0 + - - +
218D GLY* 5.1 0.6 - - - -
259D ASN* 3.4 8.9 - - - +
263D SER* 3.2 31.6 + - - +
265D TYR* 3.4 17.0 + - - -
336D ASN 3.1 14.3 + - - +
337D GLU* 2.8 39.7 + - - +
338D ALA 2.9 0.4 - - - -
339D ARG* 1.3 79.0 - - - +
341D PHE* 1.3 78.9 + - - +
343D PHE* 3.3 18.4 + - - +
2904D ANP 4.0 5.3 + - - -
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Residues in contact with PHE 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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256D ILE* 3.3 19.1 - - + +
259D ASN* 3.0 20.0 + - + +
260D VAL* 4.4 15.5 - - + -
263D SER* 3.7 23.3 - - - -
265D TYR* 3.3 39.5 - + - -
296D THR* 5.7 0.7 - - + -
297D ALA* 3.8 22.9 - - + -
300D LEU* 4.0 17.9 - - + -
301D LEU* 3.6 27.8 - - + -
304D LEU* 3.7 17.5 - - + -
337D GLU* 2.9 32.8 + - + +
338D ALA 3.1 0.2 + - - -
340D LYS* 1.3 83.4 - - - +
342D ALA* 1.3 56.7 + - - +
343D PHE 3.3 1.3 - - - -
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Residues in contact with ALA 342 (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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256D ILE* 4.8 2.0 - - - -
259D ASN* 4.1 0.9 - - - +
304D LEU* 3.9 13.2 - - + -
338D ALA 2.8 16.4 + - - +
339D ARG* 3.8 4.3 - - - +
341D PHE* 1.3 77.8 - - - +
343D PHE* 1.3 63.5 + - - +
344D GLU 3.3 0.5 + - - -
345D SER* 2.8 37.6 + - - +
347D LEU* 4.4 12.6 - - + +
349D ILE* 4.2 20.2 - - + -
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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
------------------------------------------------------------
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