Contacts of the helix formed by residues 344 - 351 (chain A) in PDB entry 1NHX
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 ASN 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A THR* 3.7 6.5 + - - +
292A ASN* 2.8 41.0 + - - +
295A MET* 3.3 25.3 - - - +
339A THR* 4.4 7.4 - - + +
340A SER 2.9 14.6 + - - +
343A THR* 1.3 82.6 + - - +
345A PRO* 1.3 70.9 - - - +
346A ASN 3.2 3.1 + - - -
347A ALA* 2.9 40.1 + - + +
348A ILE* 3.2 16.8 + - - +
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Residues in contact with PRO 345 (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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295A MET 5.5 0.9 - - - +
297A ASN* 3.8 36.1 - - + +
341A VAL* 3.3 39.2 - - + +
342A LYS 4.1 4.3 - - - +
343A THR 4.0 3.1 - - - -
344A ASN* 1.3 85.8 - - - +
346A ASN* 1.3 66.2 + - - +
348A ILE* 3.4 4.3 + - + +
349A LYS* 3.2 37.0 + - + +
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Residues in contact with ASN 346 (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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295A MET* 3.1 36.8 + - + +
296A MET 4.4 0.4 + - - -
297A ASN* 4.2 20.0 - - - +
344A ASN* 3.2 2.1 + - - +
345A PRO* 1.3 80.7 - - - +
347A ALA* 1.3 58.5 + - - +
349A LYS* 3.4 9.2 + - - +
350A THR* 2.6 34.5 + - - -
413A CYS* 4.5 1.6 - - - -
414A PRO* 3.4 28.3 - - + +
415A ILE* 3.5 31.8 - - + +
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Residues in contact with ALA 347 (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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291A THR* 5.2 0.2 - - + -
295A MET* 3.6 13.6 - - + -
339A THR* 4.2 12.3 - - + -
344A ASN* 2.9 38.8 + - + +
346A ASN* 1.3 76.3 - - - +
348A ILE* 1.3 64.3 + - - +
350A THR* 3.2 7.6 + - - -
351A ILE* 3.2 28.8 + - - +
406A PHE* 4.4 18.4 - - + -
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Residues in contact with ILE 348 (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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339A THR* 3.9 31.0 - - + +
340A SER* 3.5 27.4 - - - -
341A VAL* 3.8 18.6 - - + +
344A ASN 3.2 8.0 + - - +
345A PRO* 3.7 9.6 - - + +
346A ASN 3.3 0.2 - - - -
347A ALA* 1.3 76.8 - - - +
349A LYS* 1.3 63.7 + - + +
351A ILE* 3.3 15.3 - - + +
352A GLN* 2.8 30.8 + - - +
370A TRP* 4.4 2.0 - - + -
373A ILE* 5.3 2.0 - - + -
375A GLU* 5.2 1.8 - - - +
706A EDO 3.8 33.4 - - - +
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Residues in contact with LYS 349 (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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345A PRO* 3.2 25.2 + - - +
346A ASN* 3.9 11.1 + - - +
347A ALA 3.3 0.2 - - - -
348A ILE* 1.3 76.8 - - + +
350A THR* 1.3 67.0 - - - +
351A ILE 3.3 0.3 + - - -
352A GLN* 3.4 22.0 + - + +
353A LYS* 5.0 1.2 + - - +
412A GLN 4.8 1.9 - - - +
414A PRO* 4.0 26.5 - - + -
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Residues in contact with THR 350 (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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295A MET* 4.7 1.3 - - - -
332A PHE* 4.3 5.4 - - + -
346A ASN 2.6 22.3 + - - -
347A ALA* 3.5 11.7 - - - -
349A LYS* 1.3 78.7 - - - +
351A ILE* 1.3 57.8 + - - +
352A GLN 3.3 3.3 + - - -
353A LYS* 4.0 1.0 + - - +
408A THR* 3.5 17.2 + - + +
409A PRO 3.6 24.5 - - - +
412A GLN* 2.8 40.5 + - + +
413A CYS* 3.3 35.2 - - + +
414A PRO* 4.2 0.4 - - - +
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Residues in contact with ILE 351 (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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72A TYR* 5.3 1.2 - - - -
75A CYS* 3.8 7.8 - - - -
339A THR* 5.1 2.0 - - + -
347A ALA 3.2 19.9 + - - +
348A ILE* 3.3 19.5 - - + +
350A THR* 1.3 74.2 - - - +
352A GLN* 1.3 64.0 + - - +
353A LYS 3.1 3.2 + - - -
355A THR* 3.5 9.6 + - + +
357A PHE* 3.8 25.8 - - + -
370A TRP* 3.8 19.7 - - + -
406A PHE* 3.6 40.6 - - + -
408A THR* 3.8 16.2 - - + +
706A EDO 3.6 27.5 + - - -
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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