Contacts of the helix formed by residues 327 - 342 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A SER* 2.7 22.7 + - - -
326A PRO* 1.3 93.5 - - + +
328A ARG* 1.3 63.8 + - - +
329A GLU* 4.0 7.1 + - - +
330A LEU* 3.3 22.9 + - - +
331A ALA 3.1 6.9 + - - -
375A THR* 3.5 9.7 - - - +
547A SER 5.1 2.0 - - - +
548A VAL* 3.5 33.2 + - + +
551A ARG* 4.9 7.4 + - + +
553A LEU* 5.1 1.7 - - - +
4E U 3.8 15.9 - - - +
5E U 3.4 8.7 - - - -
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A THR* 1.3 69.7 - - - +
329A GLU* 1.3 66.5 + - - +
331A ALA* 3.0 14.6 + - - +
332A ILE* 3.0 19.0 + - - +
353A TYR* 3.8 20.5 - - + -
354A GLY* 3.4 20.6 + - - -
355A GLY* 3.6 17.0 - - - +
375A THR* 3.8 16.2 - - + -
525A GLN* 2.7 47.4 + - - +
528A ARG* 3.8 16.4 - - - +
5E U 3.0 26.4 + - - +
6E U 2.7 35.2 + - - +
7E U 4.2 5.7 + - - -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 3.5 3.8 - - - +
328A ARG* 1.3 74.1 + - - +
330A LEU* 1.3 60.9 + - - +
332A ILE* 2.7 30.1 - - + +
333A GLN* 3.0 10.2 + - - +
519A ILE* 3.8 15.2 - - + +
525A GLN* 3.1 16.2 + - - +
528A ARG* 2.6 56.6 + - - +
529A GLU* 5.2 4.0 - - + -
532A LEU* 3.5 33.0 - - + -
548A VAL* 4.0 10.3 - - - +
553A LEU* 4.0 14.6 - - + +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A SER* 3.3 19.1 - - - +
326A PRO* 4.0 7.6 - - + -
327A THR* 3.3 14.8 + - - +
328A ARG 3.1 0.8 - - - -
329A GLU* 1.3 76.9 - - - +
331A ALA* 1.3 68.1 + - - +
333A GLN* 3.2 27.0 + - - +
334A ILE* 3.0 41.9 + - + +
399A ASP* 4.2 10.8 - - - +
400A GLU* 3.6 31.0 - - + -
551A ARG 3.9 10.8 - - - +
552A GLY* 3.7 18.6 - - - +
553A LEU* 3.9 8.7 - - + +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 3.4 12.9 + - - -
327A THR 3.1 12.6 + - - +
328A ARG* 3.0 13.4 + - - +
330A LEU* 1.3 78.4 - - - +
332A ILE* 1.3 59.2 + - - +
334A ILE* 3.1 0.6 + - - -
335A PHE* 2.8 24.4 + - - +
351A ILE* 3.6 13.7 - - + -
353A TYR* 5.0 2.9 - - + -
373A ILE* 3.2 27.4 - - + +
374A ALA 4.7 5.4 - - - -
375A THR* 4.3 8.5 - - + +
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ARG 3.0 14.0 + - - +
329A GLU* 2.7 42.2 - - + +
331A ALA* 1.3 76.4 - - - +
333A GLN* 1.3 64.8 + - + +
335A PHE* 3.1 8.7 - - + +
336A ASN* 2.9 32.5 + - - +
351A ILE* 3.4 21.1 - - + -
353A TYR* 3.9 24.5 - - + +
529A GLU* 5.0 13.2 - - + +
532A LEU* 5.3 5.6 - - + -
536A LYS* 5.9 5.2 - - - +
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Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 5.2 5.5 + - - +
329A GLU 3.0 18.6 + - - +
330A LEU* 3.6 15.9 - - - +
331A ALA 3.2 0.4 - - - -
332A ILE* 1.3 79.8 - - + +
334A ILE* 1.3 65.9 + - - +
336A ASN* 3.2 7.9 + - - +
337A GLU* 3.1 31.4 + - + +
536A LYS* 6.3 0.9 - - - +
552A GLY 2.8 24.6 + - - -
553A LEU* 3.4 9.6 - - + +
554A ASP* 2.6 42.8 + - - +
555A ILE* 4.6 1.7 - - - +
2901A ANP 4.4 5.5 + - - -
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 4.4 21.8 - - + +
299A PHE* 4.7 4.5 - - + -
300A LEU* 4.3 4.3 - - + +
323A ILE* 4.2 25.8 - - + -
325A SER* 4.5 8.5 - - - -
330A LEU* 3.0 34.5 + - + +
331A ALA* 3.5 6.5 - - - +
333A GLN* 1.3 77.9 - - + +
335A PHE* 1.3 65.7 + - - +
337A GLU* 3.2 7.5 + - - +
338A ALA* 2.9 22.3 + - - +
373A ILE* 3.8 20.0 - - + -
399A ASP* 3.4 36.6 - - + +
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 4.0 20.4 - - + -
331A ALA 2.8 13.7 + - - +
332A ILE* 3.1 20.6 - - + +
334A ILE* 1.3 78.1 - - - +
336A ASN* 1.3 66.5 + - - +
338A ALA* 3.3 6.5 - - - +
339A ARG* 3.1 52.4 + - - +
349A ILE* 3.8 9.4 - - + -
350A GLY* 3.3 40.8 - - - -
351A ILE* 3.5 33.2 - - + -
373A ILE* 4.0 10.1 - - + -
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 4.2 11.9 - - - +
214A ILE* 4.8 3.5 - - - +
217A SER* 5.0 11.8 + - - +
332A ILE* 2.9 24.9 + - - +
333A GLN* 3.7 6.8 - - - +
335A PHE* 1.3 84.2 - - - +
337A GLU* 1.3 63.3 + - - +
338A ALA 3.2 0.4 - - - -
339A ARG* 3.3 24.9 + - - +
340A LYS* 2.9 27.0 + - - +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.1 30.9 + - - +
218A GLY* 5.8 0.7 - - - -
265A TYR* 4.0 9.4 + - - -
296A THR* 4.6 13.3 - - + +
300A LEU* 4.1 12.1 - - + -
333A GLN* 3.1 26.4 + - + +
334A ILE* 3.2 8.0 + - - +
336A ASN* 1.3 75.8 - - - +
338A ALA* 1.3 59.0 + - - +
340A LYS* 2.8 34.7 + - - +
341A PHE* 2.9 43.8 + - + -
554A ASP* 6.0 1.6 - - - -
2901A ANP 4.1 8.8 + - - -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.8 26.2 - - + +
304A LEU* 4.0 5.0 - - + +
334A ILE 2.9 13.4 + - - +
335A PHE* 3.3 11.7 - - - +
337A GLU* 1.3 77.1 - - - +
339A ARG* 1.3 57.4 + - - +
341A PHE* 3.2 3.3 + - - +
342A ALA* 2.9 33.7 + - - +
349A ILE* 4.0 24.9 - - + -
371A VAL* 5.3 1.6 - - + -
373A ILE* 4.7 4.9 - - + -
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Residues in contact with ARG 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 3.3 32.2 + - - +
208A SER 3.3 17.1 + - - -
209A ASN* 3.0 26.9 + - - -
214A ILE* 3.6 25.4 - - + +
335A PHE* 3.1 38.6 + - - +
336A ASN* 3.6 20.9 - - - +
337A GLU 3.3 0.2 - - - -
338A ALA* 1.3 79.2 - - - +
340A LYS* 1.3 57.3 + - - +
342A ALA* 3.6 2.8 - - - +
343A PHE* 3.0 29.6 + - - +
349A ILE* 4.2 22.6 - - + +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.5 31.8 - - - +
215A PHE* 3.7 20.2 - - + -
217A SER 3.2 17.9 + - - +
218A GLY* 4.8 0.8 - - - -
259A ASN* 3.4 9.7 - - - +
263A SER* 3.5 30.7 + - - +
265A TYR* 3.9 11.3 + - - -
336A ASN 2.9 14.1 + - - +
337A GLU* 2.8 44.0 + - - +
339A ARG* 1.3 77.9 - - - +
341A PHE* 1.3 73.5 + - - +
343A PHE* 3.3 17.5 - - - +
2901A ANP 4.3 3.8 + - - -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 3.7 17.9 - - + +
259A ASN* 2.7 26.2 + - + +
260A VAL* 4.6 10.1 - - + -
263A SER* 3.9 22.4 - - - -
265A TYR* 3.7 30.7 - + - -
296A THR* 5.2 1.1 - - - -
297A ALA* 3.8 29.6 - - + -
300A LEU* 3.9 21.3 - - + -
301A LEU* 3.5 26.0 - - + -
304A LEU* 3.4 19.7 - - + -
337A GLU* 2.9 39.8 + - + +
340A LYS* 1.3 80.2 - - - +
342A ALA* 1.3 55.4 + - - +
343A PHE 3.3 0.7 - - - -
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 5.0 4.7 - - - -
259A ASN* 3.9 0.4 - - - +
304A LEU* 4.1 20.6 - - + -
338A ALA 2.9 17.1 + - - +
339A ARG* 3.6 4.5 - - - +
341A PHE* 1.3 74.5 - - - +
343A PHE* 1.3 64.9 + - - +
344A GLU 3.3 2.3 + - - -
345A SER* 3.4 21.0 + - - +
347A LEU* 4.3 25.0 - - + +
349A ILE* 4.4 9.6 - - + -
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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