Contacts of the helix formed by residues 330 - 342 (chain A) in PDB entry 1D0N
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 ALA 330 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 3.8 20.9 - - - +
280A ALA* 4.8 7.6 - - + -
326A GLU 3.5 15.7 + - - +
327A GLU* 3.5 8.7 + - + +
328A ARG 3.0 1.6 - - - -
329A LYS* 1.3 79.0 - - - +
331A ALA* 1.3 53.1 + - - +
332A LEU 3.3 3.4 - - - -
333A LYS* 3.1 11.3 + - + +
334A THR* 2.8 43.9 + - - +
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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
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118A GLN* 5.3 2.0 - - - +
304A CYS* 6.1 1.1 - - - -
317A VAL* 4.2 21.5 - - + +
319A LYS* 4.1 18.6 - - + -
327A GLU 3.5 7.6 + - - +
328A ARG 3.2 16.3 + - - +
329A LYS 3.5 1.2 - - - -
330A ALA* 1.3 77.5 - - - +
332A LEU* 1.3 59.7 + - + +
334A THR* 3.3 7.9 + - - -
335A ALA* 3.0 29.1 + - - +
352A VAL* 4.5 12.3 - - + -
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Residues in contact with LEU 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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87A TYR* 3.3 43.1 + - + +
102A ALA* 3.9 19.7 - - + +
105A THR* 4.3 9.9 - - + -
106A VAL* 3.8 29.3 - - + +
118A GLN* 4.6 16.2 - - + +
120A ARG* 5.6 2.0 - - + +
329A LYS 5.3 1.0 + - - +
330A ALA 3.3 0.8 - - - -
331A ALA* 1.3 76.1 - - + +
333A LYS* 1.3 66.1 + - - +
335A ALA* 3.3 6.9 + - - +
336A SER* 3.3 22.4 + - - -
350A VAL* 5.1 7.0 - - + -
352A VAL* 3.6 25.8 - - + -
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Residues in contact with LYS 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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280A ALA* 2.8 47.2 + - + +
281A GLY* 5.0 0.8 - - - -
330A ALA* 3.1 15.7 + - + +
332A LEU* 1.3 76.1 - - - +
334A THR* 1.3 66.4 + - - +
336A SER* 2.9 18.4 + - - -
337A ASP* 3.0 34.0 + - - +
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Residues in contact with THR 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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276A VAL* 3.8 24.0 - - + -
278A ASN* 3.5 37.9 + - - +
280A ALA* 5.4 0.7 - - - +
283A MET* 3.7 7.0 - - - +
306A ILE* 4.5 8.7 - - + -
317A VAL* 5.7 4.0 - - + -
327A GLU* 4.7 3.8 + - - +
330A ALA* 2.8 31.0 + - - +
331A ALA* 3.4 9.7 - - - -
333A LYS* 1.3 76.6 - - - +
335A ALA* 1.3 61.7 + - - +
337A ASP* 3.4 4.6 + - - +
338A PHE* 3.0 21.8 + - - +
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 5.0 1.1 - - - -
315A ILE* 3.9 7.6 - - + +
317A VAL* 3.7 23.8 - - + +
331A ALA 3.0 13.8 + - - +
332A LEU* 3.6 10.1 - - - +
333A LYS 3.2 0.2 - - - -
334A THR* 1.3 77.5 - - - +
336A SER* 1.3 55.8 + - - +
338A PHE* 3.3 7.6 + - - +
339A ILE* 3.0 34.3 + - - +
350A VAL* 3.8 24.0 - - + -
352A VAL* 5.5 0.2 - - + -
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Residues in contact with SER 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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87A TYR* 5.6 0.7 + - - -
120A ARG* 5.1 13.2 + - - -
332A LEU 3.3 11.5 + - - -
333A LYS* 2.9 14.1 + - - -
335A ALA* 1.3 76.9 - - - +
337A ASP* 1.3 69.3 + - - +
338A PHE 3.1 0.2 - - - -
339A ILE* 3.0 12.0 + - - +
340A SER* 3.0 26.5 + - - -
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Residues in contact with ASP 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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278A ASN* 4.5 5.4 + - - -
280A ALA 2.7 28.8 - - - +
281A GLY* 4.8 1.6 - - - +
283A MET* 3.5 25.7 - - + +
333A LYS* 3.0 31.1 + - - +
334A THR* 3.8 2.0 - - - +
336A SER* 1.3 78.8 - - - +
338A PHE* 1.3 57.3 + - - +
340A SER* 3.5 7.0 - - - -
341A LYS* 2.9 31.7 + - - +
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Residues in contact with PHE 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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274A TYR* 3.9 19.7 - + - -
283A MET* 3.6 9.8 - - + +
285A VAL* 4.2 27.4 - - + -
306A ILE* 3.7 45.3 - - + -
308A ASP* 3.6 30.1 - - - -
315A ILE* 4.1 15.9 - - + -
334A THR 3.0 13.5 + - - +
335A ALA 3.4 8.5 - - - +
336A SER 3.1 0.2 - - - -
337A ASP* 1.3 77.8 - - - +
339A ILE* 1.3 60.1 + - - +
341A LYS* 3.9 1.5 - - + -
342A MET* 3.0 63.9 + - + +
344A TYR* 4.0 7.2 - + - -
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Residues in contact with ILE 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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120A ARG* 4.4 8.7 - - - +
315A ILE* 3.9 11.9 - - + -
335A ALA 3.0 20.1 + - - +
336A SER* 3.0 11.4 + - - +
338A PHE* 1.3 76.5 - - - +
340A SER* 1.3 60.2 + - - +
342A MET* 4.5 0.2 - - - -
343A ASP 3.2 1.4 + - - -
344A TYR* 2.9 68.7 + - + +
345A PRO 3.8 9.2 - - - +
346A LYS* 4.9 5.4 - - - +
348A THR* 3.7 26.9 - - + +
350A VAL* 3.9 24.2 - - + -
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 3.0 15.0 + - - -
337A ASP* 3.5 10.8 - - - -
338A PHE 3.1 0.2 - - - -
339A ILE* 1.3 75.6 - - - +
341A LYS* 1.3 56.4 + - - +
342A MET 2.9 3.6 - - - -
343A ASP* 2.6 27.1 + - - +
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Residues in contact with LYS 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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283A MET* 2.7 57.4 + - + +
285A VAL* 4.3 11.8 - - + +
337A ASP 2.9 18.4 + - - +
338A PHE* 4.2 2.7 - - + +
340A SER* 1.3 72.3 - - - +
342A MET* 1.3 67.0 + - + +
343A ASP* 3.3 1.1 + - - +
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Residues in contact with MET 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 4.0 18.6 - - - +
285A VAL* 6.4 0.2 - - - -
308A ASP* 3.8 10.1 - - - +
338A PHE* 3.0 51.7 + - + +
340A SER 2.9 1.2 - - - -
341A LYS* 1.3 87.7 - - + +
343A ASP* 1.3 72.6 + - - +
344A TYR* 3.4 45.2 + - + +
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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