Contacts of the helix formed by residues 319 - 331 (chain A) in PDB entry 1N1E
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 MET 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.9 22.4 - - + -
240A GLU* 3.3 49.4 - - + +
244A LEU* 4.1 22.4 - - + -
308A LEU* 4.0 17.9 - - + -
312A ALA* 3.7 24.2 - - + -
317A VAL* 3.6 15.3 + - + +
318A LYS* 1.3 78.8 - - - +
320A PRO* 1.3 61.7 - - - +
322A CYS* 3.3 14.5 + - + -
323A HIS* 2.8 30.3 + - - +
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Residues in contact with PRO 320 (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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240A GLU* 3.3 15.9 - - + +
318A LYS* 3.6 12.6 - - + +
319A MET* 1.3 88.7 - - - +
321A LEU* 1.3 60.6 + - + +
323A HIS* 3.6 6.6 - - + +
324A GLN* 3.2 27.7 + - - +
342A LEU* 3.9 14.9 - - + +
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Residues in contact with LEU 321 (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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213A LEU* 3.8 12.6 - - + -
233A LEU* 3.9 34.8 - - + +
236A ARG* 4.0 13.2 - - + -
237A GLY* 3.6 30.1 - - - +
240A GLU* 2.8 25.6 + - - +
320A PRO* 1.3 69.8 - - + +
322A CYS* 1.3 65.7 + - - +
324A GLN* 3.2 5.2 + - - +
325A ILE* 2.9 33.3 + - + +
342A LEU* 3.5 32.5 - - + -
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Residues in contact with CYS 322 (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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209A VAL* 3.8 28.9 - - - -
212A VAL* 4.0 21.3 - - + +
213A LEU* 3.9 14.1 - - - -
240A GLU* 3.1 20.3 + - - +
305A ALA* 5.6 0.2 - - - +
308A LEU* 4.0 12.8 - - + -
309A MET* 6.5 0.2 - - - -
319A MET* 3.3 18.4 + - + +
321A LEU* 1.3 78.2 - - - +
323A HIS* 1.3 55.7 + - - +
325A ILE* 3.8 7.4 - - - +
326A TYR* 2.9 30.3 + - - +
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Residues in contact with HIS 323 (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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309A MET* 4.8 21.3 - - + +
319A MET* 2.8 20.0 + - - +
320A PRO* 3.6 7.9 - - + +
322A CYS* 1.3 77.6 - - - +
324A GLN* 1.3 82.3 + - - +
326A TYR* 3.2 15.4 + + - +
327A GLU* 3.0 54.8 + - + +
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Residues in contact with GLN 324 (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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320A PRO 3.2 11.7 + - - +
321A LEU* 3.2 7.6 + - - +
323A HIS* 1.3 99.0 + - - +
325A ILE* 1.3 63.2 + - + +
327A GLU* 3.2 6.3 + - - +
328A ILE* 3.1 29.4 + - + +
333A LYS* 2.7 38.9 + - - +
338A ALA* 3.4 24.4 - - + +
341A ASP* 4.1 10.4 - - - +
342A LEU* 3.9 28.5 - - + +
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Residues in contact with ILE 325 (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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212A VAL* 3.5 38.8 - - + +
213A LEU* 4.0 15.3 - - + +
215A ILE* 3.9 24.5 - - + -
216A GLY* 3.7 24.5 - - - -
219A VAL* 6.1 0.7 - - + -
233A LEU* 5.6 0.4 - - + -
305A ALA* 5.4 1.3 - - + -
321A LEU* 2.9 34.0 + - + +
322A CYS* 3.8 7.6 - - - +
324A GLN* 1.3 77.3 - - + +
326A TYR* 1.3 64.0 + - - +
328A ILE* 3.2 13.8 + - + +
329A VAL* 3.0 27.6 + - + +
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Residues in contact with TYR 326 (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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305A ALA* 3.8 32.9 - - + +
306A ASP* 3.6 28.0 + - - -
309A MET* 4.3 37.8 - - + +
322A CYS 2.9 18.5 + - - +
323A HIS* 3.4 12.1 - + - +
325A ILE* 1.3 76.5 - - - +
327A GLU* 1.3 77.3 + - + +
329A VAL* 4.6 0.9 - - - +
330A TYR* 2.9 60.8 + + + +
331A LYS* 4.0 23.8 + - + +
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Residues in contact with GLU 327 (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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323A HIS* 3.0 42.7 + - + +
324A GLN* 3.2 9.8 + - - +
326A TYR* 1.3 89.9 - - + +
328A ILE* 1.3 57.2 + - - +
331A LYS* 2.9 52.6 + - + +
333A LYS* 3.2 46.1 + - + +
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Residues in contact with ILE 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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215A ILE* 6.2 0.7 - - + -
219A VAL* 4.3 23.1 - - + -
282A LEU* 4.0 37.4 - - + +
288A ILE* 5.4 1.0 - - - +
324A GLN* 3.1 17.5 + - + +
325A ILE* 3.2 15.7 + - + +
327A GLU* 1.3 76.7 - - - +
329A VAL* 1.3 65.0 + - + +
332A LYS* 3.9 12.5 + - - +
333A LYS* 3.7 24.0 + - + +
335A PRO* 4.1 20.0 - - + -
338A ALA* 3.8 24.9 - - + -
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Residues in contact with VAL 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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215A ILE* 4.2 21.3 - - + -
282A LEU* 3.9 25.1 - - + -
288A ILE* 3.5 36.3 - - + +
302A VAL* 4.0 25.6 - - + +
305A ALA* 5.2 2.9 - - + -
325A ILE* 3.0 23.8 + - + +
326A TYR* 4.0 1.1 - - - +
328A ILE* 1.3 80.5 - - + +
330A TYR* 1.3 84.2 + - + +
332A LYS* 5.1 1.6 + - - +
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Residues in contact with TYR 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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129A ARG* 3.0 33.9 + - - -
302A VAL* 2.6 33.8 + - + +
303A ALA* 3.4 5.2 + - - -
305A ALA* 4.0 3.6 - - + -
306A ASP* 3.7 29.6 - - + -
326A TYR* 2.9 47.3 + + + +
329A VAL* 1.3 94.6 - - + +
331A LYS* 1.3 65.2 + - + +
332A LYS* 3.6 9.8 + - - +
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Residues in contact with LYS 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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309A MET* 6.3 0.6 - - - +
326A TYR* 4.0 29.3 + - + +
327A GLU* 2.9 40.1 + - + +
330A TYR* 1.3 84.0 - - + +
332A LYS* 1.3 66.0 + - - +
333A LYS* 2.9 13.5 + - + +
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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