Contacts of the helix formed by residues 328 - 338 (chain A) in PDB entry 1N54
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 GLU 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A HIS* 3.2 13.0 + - + +
326A TRP 2.9 3.5 + - - -
327A LYS* 1.3 85.0 - - + +
329A ARG* 1.3 65.2 + - - +
330A LYS* 3.3 1.9 + - + -
331A THR* 3.4 25.7 + - - +
332A CYS 3.2 17.0 + - - -
11B SER* 2.7 33.8 + - - +
12B ASP* 2.9 5.4 + - - -
13B SER* 2.4 43.5 + - - +
14B TYR* 4.2 11.7 - - + -
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Residues in contact with ARG 329 (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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326A TRP 3.8 5.4 + - - -
327A LYS 3.9 1.0 + - - -
328A GLU* 1.3 72.7 - - - +
330A LYS* 1.3 66.4 + - - +
332A CYS* 3.5 7.9 + - - +
333A ALA* 3.3 20.8 + - - +
371A MET* 5.6 2.9 - - - +
374A THR* 3.8 22.4 - - - -
375A LEU* 4.3 18.6 - - + +
378A GLU* 3.9 31.4 + - + +
14B TYR* 3.8 33.8 + - + -
99B ARG 2.7 31.9 + - - +
100B TYR* 3.1 38.1 + - + +
102B ASN* 2.8 23.6 + - - +
103B GLY* 4.2 10.5 - - - -
104B THR* 4.8 3.1 - - - +
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Residues in contact with LYS 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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328A GLU* 3.3 1.2 - - + -
329A ARG* 1.3 83.8 - - - +
331A THR* 1.3 64.1 + - - +
333A ALA* 3.5 15.0 - - + +
334A ALA* 4.0 4.2 + - - +
378A GLU* 3.0 28.0 - - - +
381A LYS* 6.1 0.4 - - - +
382A LEU* 6.2 6.1 - - - -
14B TYR* 3.4 28.6 - - + +
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Residues in contact with THR 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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325A HIS* 4.9 12.6 - - + +
328A GLU* 3.4 29.6 + - - +
329A ARG 3.4 0.4 - - - -
330A LYS* 1.3 74.2 - - - +
332A CYS* 1.3 68.2 + - - +
333A ALA 2.9 3.6 + - - -
334A ALA* 2.9 19.0 + - + +
335A GLN* 3.1 26.3 + - + +
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Residues in contact with CYS 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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321A ILE* 4.3 3.8 - - - +
322A ILE* 4.0 21.5 - - - -
325A HIS* 2.9 34.9 + - + +
326A TRP* 5.0 0.9 - - - -
328A GLU 3.2 9.7 + - - +
329A ARG* 3.6 8.1 - - - +
331A THR* 1.3 78.8 - - - +
333A ALA* 1.3 60.4 + - - +
335A GLN* 3.5 5.3 + - - +
336A LEU* 3.1 30.1 + - - +
371A MET* 5.9 0.2 - - - -
375A LEU* 3.9 29.8 - - - -
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Residues in contact with ALA 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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329A ARG 3.3 8.5 + - - +
330A LYS* 3.5 13.7 - - + +
331A THR 2.9 0.8 + - - -
332A CYS* 1.3 79.5 - - - +
334A ALA* 1.3 53.0 + - - +
336A LEU* 3.0 5.4 + - - +
337A VAL* 2.7 37.3 + - - +
375A LEU* 4.4 6.3 - - + -
378A GLU* 4.4 18.8 - - + +
379A LEU* 4.3 17.5 - - + +
382A LEU* 3.7 18.6 - - + -
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Residues in contact with ALA 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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330A LYS 4.0 4.0 + - - +
331A THR* 2.9 12.5 + - + +
333A ALA* 1.3 75.4 - - - +
335A GLN* 1.3 59.4 + - + +
336A LEU 2.9 5.1 + - - -
337A VAL* 3.0 1.7 + - - +
338A SER* 2.5 39.1 + - - +
382A LEU* 3.7 15.2 - - + +
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Residues in contact with GLN 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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40A GLU* 5.6 11.4 - - - +
41A LYS* 5.8 4.2 - - - +
81A GLU* 6.0 1.6 - - - +
82A LYS* 4.2 21.4 + - - +
321A ILE* 3.3 30.6 - - + +
325A HIS* 3.4 33.3 + - + +
331A THR* 3.1 23.6 + - + +
332A CYS 3.9 7.0 - - - +
334A ALA* 1.3 81.0 - - + +
336A LEU* 1.3 59.6 + - - +
338A SER* 3.9 17.2 + - - +
339A TYR* 4.4 0.7 - - - -
340A PRO* 5.5 0.5 - - - +
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Residues in contact with LEU 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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318A LEU* 3.4 27.8 - - + +
321A ILE* 3.2 33.2 - - + -
322A ILE* 4.1 21.1 - - + -
332A CYS* 3.1 18.1 + - - +
333A ALA* 3.0 8.9 + - - +
334A ALA 2.9 0.2 - - - -
335A GLN* 1.3 75.5 - - - +
337A VAL* 1.3 66.2 + - - +
338A SER 3.1 2.0 + - - -
339A TYR* 3.3 18.9 + - - +
347A LEU* 3.6 6.9 - - - +
351A ILE* 3.9 38.1 - - + +
355A ILE* 5.3 1.6 - - + -
375A LEU* 4.9 6.1 - - + -
379A LEU* 4.7 10.8 - - + -
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Residues in contact with VAL 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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333A ALA 2.7 22.0 + - - +
334A ALA* 4.0 3.1 - - - +
336A LEU* 1.3 73.0 - - - +
338A SER* 1.3 58.8 + - - +
339A TYR 3.4 0.4 + - - -
347A LEU* 3.1 22.6 - - + +
348A ASN* 5.8 2.5 - - - +
351A ILE* 4.2 8.5 - - + -
379A LEU* 3.6 22.9 - - + -
382A LEU* 3.9 20.9 - - + -
383A GLN* 4.2 32.8 - - + +
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Residues in contact with SER 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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41A LYS* 6.5 0.7 - - - -
334A ALA* 2.5 28.4 + - - +
335A GLN* 3.9 12.7 + - - +
336A LEU 3.1 0.6 + - - -
337A VAL* 1.3 76.5 - - - +
339A TYR* 1.3 62.3 + - - +
340A PRO* 3.8 5.2 - - - +
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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