Contacts of the helix formed by residues 379 - 389 (chain A) in PDB entry 2NUP
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 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A ASP* 5.5 3.8 - - + +
376A SER* 2.9 40.0 + - - +
377A PHE 3.0 2.0 + - - -
378A ASN* 1.3 80.7 - - - +
380A SER* 1.3 64.1 + - - +
381A LEU* 3.5 11.2 + - + +
382A PHE* 3.1 17.0 + - - +
383A LYS* 3.1 28.7 + - - +
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Residues in contact with SER 380 (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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379A THR* 1.3 72.0 - - - +
381A LEU* 1.3 56.1 + - - +
383A LYS* 4.5 5.8 - - - -
384A GLN* 2.7 57.2 + - - +
702A MET* 3.9 7.6 - - - -
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Residues in contact with LEU 381 (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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373A MET 4.5 16.4 - - - +
374A GLY* 4.6 11.4 - - - -
375A ASP 5.4 1.6 - - - +
379A THR* 3.6 10.5 - - - +
380A SER* 1.3 77.6 - - - +
382A PHE* 1.3 61.1 + - - +
384A GLN* 4.2 0.7 - - - +
385A THR* 2.7 36.2 + - - +
702A MET* 3.3 48.4 - - + +
703A PRO 3.9 13.7 - - - +
704A ARG* 4.3 22.2 - - + -
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Residues in contact with PHE 382 (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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147A LEU* 4.5 1.8 - - + -
150A SER* 3.4 26.0 - - - -
289A PHE* 4.2 12.8 - + - -
348A TYR* 4.0 25.6 - + + -
350A CYS* 4.0 15.5 - - - -
372A VAL* 4.4 13.9 - - + -
374A GLY* 6.1 1.1 - - - -
376A SER 3.8 10.5 - - - +
377A PHE* 3.4 49.4 - + + +
379A THR* 3.1 13.2 + - - +
381A LEU* 1.3 78.0 - - - +
383A LYS* 1.3 60.9 + - - +
385A THR* 3.0 5.2 + - - -
386A PHE* 2.7 64.0 + + + +
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Residues in contact with LYS 383 (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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146A ALA* 3.7 18.9 - - - +
149A GLU* 4.3 19.0 + - - -
150A SER* 3.9 15.7 - - - +
153A MET* 5.8 0.5 - - - +
377A PHE 3.8 7.9 - - - +
378A ASN* 3.1 32.5 + - - +
379A THR 3.1 20.9 + - - +
380A SER* 3.9 5.2 - - - +
382A PHE* 1.3 85.0 - - - +
384A GLN* 1.3 64.1 + - + +
386A PHE* 3.4 3.8 + - - +
387A GLN* 3.3 27.6 + - - +
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Residues in contact with GLN 384 (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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380A SER* 2.7 38.4 + - - +
383A LYS* 1.3 71.5 - - + +
385A THR* 1.3 64.9 + - - +
387A GLN* 3.2 29.5 + - - +
388A ARG* 3.0 41.0 + - - +
697A HIS* 3.5 16.9 - - - -
702A MET* 3.9 31.6 - - - +
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Residues in contact with THR 385 (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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372A VAL* 3.6 34.8 - - + +
381A LEU* 2.7 28.1 + - - +
382A PHE 3.6 3.1 - - - -
384A GLN* 1.3 76.1 - - - +
386A PHE* 1.3 64.1 + - - +
388A ARG* 3.3 16.5 + - - +
389A VAL* 3.7 1.6 + - - +
700A PHE* 3.5 36.4 - - + -
701A PRO* 4.2 11.8 - - + -
702A MET* 3.3 23.6 + - - +
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Residues in contact with PHE 386 (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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133A TYR* 5.0 2.7 - + - -
150A SER* 3.0 46.2 - - - -
151A MET* 4.1 2.0 - - - -
153A MET* 5.0 3.8 - - - -
154A SER* 3.7 17.9 - - - -
287A MET* 5.0 2.2 - - - -
289A PHE* 3.9 29.4 - + - -
348A TYR* 3.6 31.6 - + - -
382A PHE* 2.7 39.6 + + + +
383A LYS 3.7 4.3 - - - +
385A THR* 1.3 75.6 - - - +
387A GLN* 1.3 59.8 + - - +
389A VAL* 3.2 20.2 - - + +
390A PHE* 3.4 31.5 - + - -
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Residues in contact with GLN 387 (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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153A MET* 3.7 30.5 - - + +
157A LEU* 4.7 3.4 - - + +
383A LYS* 3.3 16.7 + - - +
384A GLN* 3.2 33.2 + - + +
386A PHE* 1.3 75.0 - - - +
388A ARG* 1.3 70.7 + - + +
389A VAL 3.1 1.6 - - - -
390A PHE* 3.1 22.1 + - - +
391A THR* 3.8 1.6 + - - -
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Residues in contact with ARG 388 (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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384A GLN* 3.0 32.3 + - - +
385A THR* 3.3 13.1 + - - +
387A GLN* 1.3 75.5 - - - +
389A VAL* 1.3 68.2 + - - +
390A PHE 2.9 2.7 - - - -
391A THR* 2.7 35.0 + - - +
697A HIS* 2.9 62.4 + - - +
698A SER 5.6 0.4 - - - -
699A ARG 4.4 4.7 + - - -
700A PHE* 4.0 25.5 + - + +
702A MET* 3.4 30.7 - - - +
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Residues in contact with VAL 389 (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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285A ARG* 4.7 4.5 - - - +
348A TYR* 3.6 31.2 - - + +
370A TYR* 3.8 26.7 + - + -
385A THR 3.7 10.3 - - - +
386A PHE* 3.2 19.3 - - + +
388A ARG* 1.3 78.8 - - - +
390A PHE* 1.3 80.4 + - + +
391A THR 3.6 3.3 + - - +
398A PHE* 5.6 0.2 - - - +
399A LYS 5.6 1.9 + - - +
400A MET* 3.3 22.6 - - + +
700A PHE* 3.9 18.8 - - + -
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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