Contacts of the strand formed by residues 445 - 451 (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 GLN 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A THR* 4.3 11.1 - - - +
406A LEU 3.0 6.5 - - - +
407A GLU* 3.1 47.1 + - + +
426A LEU* 3.1 36.3 + - + +
428A SER* 3.5 22.6 - - - +
443A THR* 2.6 25.6 + - - +
444A CYS* 1.3 82.0 - - + +
446A TRP* 1.3 62.9 + - - +
484A GLN* 5.8 2.6 - - - +
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Residues in contact with TRP 446 (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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405A THR* 3.5 4.5 - - - +
406A LEU* 2.7 62.9 + - + +
408A ILE* 3.7 24.2 - - + -
416A ILE* 3.8 31.2 - - + -
418A GLY* 4.8 2.0 - - - -
419A ALA* 3.6 16.6 - - + +
423A CYS* 3.8 33.2 - - + -
424A VAL 3.1 8.7 - - - +
426A LEU* 4.2 4.5 - - - +
440A THR* 3.1 31.0 + - + -
443A THR* 3.1 41.2 - - + +
444A CYS* 3.2 22.4 - - - -
445A GLN* 1.3 74.3 - - - +
447A LYS* 1.3 60.7 + - - +
448A ILE* 5.1 0.4 - - + -
459A ILE* 4.9 1.8 - - + -
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Residues in contact with LYS 447 (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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281A ASN* 4.8 4.8 + - - -
339A ALA 3.1 19.5 + - - -
340A THR* 2.8 27.5 + - - +
341A THR 4.3 1.2 + - - -
342A GLY* 4.0 10.7 - - - +
366A LEU 4.8 0.5 - - - +
403A GLY* 5.2 7.4 - - - -
404A GLY 3.3 8.7 - - - +
405A THR* 4.7 6.7 - - - +
423A CYS* 3.2 6.2 - - - -
424A VAL* 2.7 45.7 + - + +
426A LEU* 4.1 28.8 - - + +
446A TRP* 1.3 74.2 - - - +
448A ILE* 1.3 65.2 + - - +
449A CYS* 3.9 19.2 + - - +
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Residues in contact with ILE 448 (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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44A PRO* 5.0 5.4 - - + -
366A LEU 5.6 0.7 - - - -
368A GLY* 5.0 3.4 - - - +
403A GLY 3.9 0.2 + - - -
404A GLY* 2.7 39.5 + - - +
406A LEU* 4.4 20.9 - - + -
422A PRO* 3.6 20.9 - - + +
423A CYS* 4.1 5.6 - - + +
446A TRP 4.7 3.8 - - - +
447A LYS* 1.3 80.0 - - - +
449A CYS* 1.3 59.4 + - - +
450A GLY* 3.2 20.7 + - - +
451A LEU* 4.0 26.7 - - + +
455A THR* 4.6 5.8 - - + -
457A LEU* 3.7 30.3 - - + -
483A THR* 5.9 2.0 - - + -
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Residues in contact with CYS 449 (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 ALA* 3.4 29.4 - - - -
342A GLY* 3.4 34.2 - - - +
343A HIS 3.7 22.0 - - - +
344A VAL* 3.2 12.3 - - + +
366A LEU 5.3 0.9 + - - -
367A THR* 4.1 12.8 - - - +
368A GLY 4.5 2.4 - - - +
402A PHE* 3.2 5.5 - - - +
403A GLY* 2.7 29.1 + - - +
424A VAL* 6.0 0.9 - - - -
447A LYS* 3.9 10.0 + - - +
448A ILE* 1.3 72.7 - - - +
450A GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 450 (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* 5.3 4.3 - - - -
344A VAL* 3.4 15.7 - - - +
368A GLY* 2.9 39.7 - - - +
401A GLY 3.6 5.8 - - - -
448A ILE* 3.2 5.4 - - - +
449A CYS* 1.3 81.9 - - - +
451A LEU* 1.3 63.8 + - - +
455A THR* 4.4 2.6 + - - +
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Residues in contact with LEU 451 (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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44A PRO* 4.4 12.1 - - + -
45A LEU* 3.2 34.1 - - + -
370A TYR* 5.6 2.0 - - - -
400A MET* 3.3 5.9 - - - +
401A GLY* 2.7 58.7 + - - +
402A PHE* 4.3 0.7 - - - +
404A GLY* 5.1 1.1 - - - -
448A ILE* 4.0 29.8 - - + +
450A GLY* 1.3 76.1 - - - +
452A SER* 1.3 60.3 + - - +
455A THR* 3.3 15.5 - - - +
483A THR* 4.4 19.3 - - + -
485A TYR* 4.5 12.1 - - + -
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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