Contacts of the helix formed by residues 361 - 367 (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 LYS 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A TRP* 5.9 0.6 - - - -
328A THR* 5.5 6.1 - - - -
332A GLU* 5.5 4.9 - - - -
357A LEU 2.6 17.6 + - - +
358A LEU* 3.1 40.7 - - - +
359A GLU 4.9 1.3 - - - +
360A MET* 1.3 71.0 - - - +
362A CYS* 1.3 74.8 + - - +
364A PRO* 2.9 14.7 - - - +
365A ASN* 3.1 29.1 + - - +
371A MET* 3.9 18.4 - - + -
535A GLU* 4.0 37.5 + - - +
601A SER* 3.9 16.7 + - - +
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Residues in contact with CYS 362 (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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331A PHE 4.7 1.3 - - - +
332A GLU* 3.8 37.0 - - + +
335A ALA* 3.6 15.7 - - + -
359A GLU 5.1 0.6 + - - -
360A MET 3.0 2.2 + - - -
361A LYS* 1.3 90.9 - - - +
363A CYS* 1.3 58.7 + - - +
365A ASN* 3.8 9.4 - - - -
366A LEU* 2.7 50.2 + - + +
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Residues in contact with CYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A LEU* 3.9 21.1 - - - -
331A PHE* 3.5 29.6 - - - -
334A LEU* 4.5 1.6 - - - -
335A ALA* 3.6 12.3 - - - +
345A ILE* 3.4 35.6 - - + +
347A ILE* 4.6 2.2 - - + -
360A MET* 3.1 11.5 + - - +
362A CYS* 1.3 78.6 - - - +
364A PRO* 1.3 68.3 - - + +
367A THR* 2.6 30.5 + - - +
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Residues in contact with PRO 364 (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 ILE 3.3 18.6 - - - +
347A ILE* 3.8 15.3 - - + -
360A MET 3.3 6.7 - - - +
361A LYS 2.9 20.9 - - - +
363A CYS* 1.3 91.5 - - + +
365A ASN* 1.3 54.6 + - - +
367A THR* 2.3 26.2 - - - +
369A GLY 3.1 29.6 - - - +
370A TYR 3.5 14.4 - - - +
371A MET* 4.1 21.1 - - + -
605A HIS* 4.4 1.1 - - + -
609A ARG* 3.4 4.4 + - - -
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Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A LYS* 3.1 43.0 + - - +
362A CYS* 3.0 11.3 + - - +
364A PRO* 1.3 78.3 - - - +
366A LEU* 1.3 61.1 + - + +
367A THR 3.3 1.2 - - - +
371A MET* 4.5 0.9 - - - +
421A GLY 4.4 1.7 - - - +
422A PRO* 3.2 28.9 - - - +
423A CYS 4.0 0.2 + - - -
535A GLU* 4.5 13.9 + - - -
601A SER 5.3 0.6 + - - -
605A HIS* 2.6 45.4 + - - +
609A ARG* 4.2 4.6 + - - +
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Residues in contact with LEU 366 (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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332A GLU* 5.0 2.5 - - + +
335A ALA* 3.9 14.8 - - + -
336A ASN* 3.9 22.9 - - - +
339A ALA* 4.6 6.4 - - + +
362A CYS* 2.7 47.0 + - + +
365A ASN* 1.3 72.7 - - + +
367A THR* 1.3 63.0 + - + +
423A CYS* 3.5 32.9 + - - +
424A VAL* 3.5 31.8 - - + +
440A THR* 5.4 4.9 - - - +
447A LYS 4.8 1.4 - - - +
448A ILE* 5.6 0.2 - - - -
449A CYS* 5.3 1.7 + - - -
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Residues in contact with THR 367 (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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335A ALA 4.1 6.3 - - - +
339A ALA* 4.0 22.0 - - + +
343A HIS 3.4 26.9 - - - +
344A VAL* 3.9 2.5 - - - -
345A ILE* 3.2 21.3 + - + +
363A CYS 2.6 24.2 + - - +
364A PRO* 2.3 25.8 - - - +
365A ASN 3.3 4.7 - - - +
366A LEU* 1.3 80.9 - - + +
368A GLY* 1.3 55.7 + - - +
369A GLY 3.0 11.5 + - - -
422A PRO* 3.9 4.1 - - - +
449A CYS* 4.1 11.0 - - - +
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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