Contacts of the strand formed by residues 489 - 494 (chain A) in PDB entry 3NGN
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 ASP 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A CYS* 4.9 7.2 - - - +
195A ASN* 4.3 6.1 - - - +
239A GLN* 4.4 2.1 - - - +
409A ALA 3.3 7.4 - - - +
410A ASP* 3.1 32.7 - - - +
478A THR* 2.5 41.1 + - + +
487A VAL* 3.9 4.9 - - - +
488A ILE* 1.3 80.2 - - - +
490A TYR* 1.3 72.0 + - - +
529A HIS* 2.6 32.2 + - - +
530A PHE 5.4 1.8 - - - +
532A LEU* 3.7 18.7 - - + +
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Residues in contact with TYR 490 (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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193A CYS* 3.8 3.2 - - - -
407A LEU 3.8 0.6 - - - +
408A CYS* 3.4 3.8 - - - -
409A ALA* 3.0 32.7 + - + +
411A LEU* 3.6 22.7 - - + -
413A SER 2.7 30.2 + - - -
414A LEU 3.3 0.9 - - - -
415A PRO* 3.1 27.3 - - + +
420A VAL* 3.6 19.3 - - + -
468A SER* 3.9 17.3 - - - -
487A VAL* 3.2 20.7 + - + -
488A ILE 3.3 20.2 - - - -
489A ASP* 1.3 88.3 - - - +
491A ILE* 1.3 66.0 + - - +
492A PHE* 3.6 32.1 - + + -
532A LEU* 3.6 5.9 - - - +
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Residues in contact with ILE 491 (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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191A VAL* 3.6 32.8 - - + +
193A CYS* 3.7 26.9 - - + +
406A VAL* 4.1 23.8 - - + -
407A LEU 3.4 4.5 - - - +
408A CYS* 4.3 3.1 - - - -
468A SER* 3.5 5.9 + - - -
469A ALA* 2.9 36.3 + - + +
470A TYR* 5.1 2.1 - - + +
490A TYR* 1.3 76.6 - - - +
492A PHE* 1.3 65.8 + - - +
493A TYR* 5.6 1.3 - - + -
532A LEU* 3.8 23.9 - - + +
534A THR* 3.9 25.1 - - + +
536A LEU* 5.1 2.7 - - + -
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Residues in contact with PHE 492 (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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406A VAL* 3.5 4.2 - - - +
407A LEU* 2.7 56.8 + - + +
409A ALA* 6.5 0.9 - - + -
411A LEU* 4.2 4.3 - - + -
420A VAL* 4.4 10.1 - - + -
423A LEU* 3.7 39.5 - - + -
424A SER* 4.0 22.9 - - - -
466A LEU* 4.1 18.3 - - + +
467A LYS* 3.1 21.8 - - - -
468A SER* 3.5 17.5 - - - -
490A TYR* 3.6 41.7 - + + -
491A ILE* 1.3 75.5 - - - +
493A TYR* 1.3 60.5 + - - +
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Residues in contact with TYR 493 (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 LEU 3.3 9.9 - - - +
406A VAL* 4.5 5.8 - - + -
466A LEU* 3.3 6.7 - - - -
467A LYS* 2.9 71.2 + - + +
468A SER 4.0 1.1 + - - -
469A ALA* 3.7 22.9 - - + -
471A GLU* 6.1 0.2 - - - +
491A ILE* 5.6 1.3 - - + -
492A PHE* 1.3 76.4 - - - +
494A SER* 1.3 66.9 + - - +
495A LYS* 4.1 9.9 - - + -
498A MET* 3.5 48.0 - - + -
499A ASN* 4.3 3.9 - - - -
500A VAL* 3.0 33.4 + - + +
536A LEU* 4.0 20.6 - - + -
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Residues in contact with SER 494 (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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403A ILE 5.5 0.4 - - - -
404A PRO* 3.6 0.2 - - - +
405A LEU* 2.8 38.5 + - - -
464A PHE* 5.7 4.3 - - - -
465A GLN 3.2 14.8 - - - -
466A LEU* 3.9 8.9 - - - +
493A TYR* 1.3 70.6 - - - +
495A LYS* 1.3 60.6 - - - +
496A THR* 3.2 1.8 - - - -
497A HIS* 3.2 24.0 + - - -
498A MET* 3.2 32.0 + - - +
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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