Contacts of the strand formed by residues 423 - 426 (chain A) in PDB entry 4NPJ
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 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ILE 3.7 0.7 - - - +
419A ARG* 3.4 5.4 - - - +
420A VAL* 2.9 42.0 + - + +
421A GLY* 5.4 0.4 - - - -
422A ASN* 1.3 81.7 - - + +
424A ILE* 1.3 60.3 + - - +
425A PHE* 4.2 19.0 - - + -
443A GLU 4.2 3.3 - - - +
444A ALA* 3.4 12.2 - - - +
445A LEU* 2.8 56.9 + - - +
447A TYR* 5.7 2.8 - - - -
591A PHE* 4.9 3.6 - - - -
574B LYS* 6.0 9.6 - - - +
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Residues in contact with ILE 424 (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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417A ILE* 3.9 17.3 - - + -
418A ILE 3.4 4.7 - - - +
419A ARG* 3.3 62.1 - - + +
422A ASN 3.5 4.7 + - - +
423A GLN* 1.3 72.7 - - - +
425A PHE* 1.3 81.7 + - - +
801A CL 4.1 0.4 - - + -
574B LYS* 5.5 7.2 - - - +
576B ARG* 3.2 33.3 + - - +
583B VAL* 4.3 6.7 - - + +
584B TRP 3.6 21.5 - - - +
585B GLU* 3.5 11.2 - - + +
586B GLU* 6.0 0.4 - - + -
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Residues in contact with PHE 425 (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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389A ILE* 4.8 4.3 - - + -
417A ILE* 3.5 5.5 - - - -
418A ILE* 2.9 55.4 + - + +
420A VAL* 5.1 2.2 - - + -
423A GLN* 4.2 24.9 - - + -
424A ILE* 1.3 85.4 - - - +
426A GLN* 1.3 59.1 + - - +
442A TYR* 3.7 50.7 - + + -
443A GLU 3.3 28.5 - - - -
444A ALA* 4.1 16.6 - - + -
576B ARG* 4.6 1.3 - - - +
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Residues in contact with GLN 426 (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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415A TYR* 4.1 16.1 - - + -
416A GLY 3.6 3.1 - - - -
417A ILE* 3.7 17.7 - - + -
425A PHE* 1.3 75.3 - - - +
427A SER* 1.3 72.4 + - - +
429A VAL* 5.9 2.6 - - - +
440A GLU* 4.4 2.4 - - - +
442A TYR* 4.1 8.6 + - - -
530A ASN* 4.6 10.2 + - - -
576B ARG* 3.3 30.2 - - - +
577B TYR 5.7 1.6 - - - +
579B THR* 4.0 15.4 + - - +
581B GLU* 3.0 24.9 + - - +
582B PRO* 3.5 3.7 - - - +
583B VAL* 2.9 34.4 + - - +
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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