Contacts of the strand formed by residues 491 - 494 (chain A) in PDB entry 5N4D
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 ALA 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A ALA 4.1 0.2 + - - -
490A ALA* 1.3 75.5 - - - +
492A ILE* 1.3 69.1 + - - +
521A ILE* 3.3 24.9 - - + -
523A ALA* 5.2 1.1 - - + -
560A LEU* 4.0 18.8 - - + -
566A ALA* 4.0 17.3 - - + -
570A LYS 2.9 9.0 + - - +
571A VAL* 4.3 7.0 - - + -
572A ALA* 2.8 27.2 + - - +
722A LEU* 4.5 0.5 - - - +
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Residues in contact with ILE 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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490A ALA* 5.2 0.7 - - + -
491A ALA* 1.3 80.5 - - - +
493A GLN* 1.3 63.8 + - - +
494A TYR* 5.2 0.7 - - + -
514A PHE* 3.3 38.1 - - + -
515A LEU* 5.8 1.6 - - + -
520A ALA* 4.7 2.9 - - + -
521A ILE 2.9 12.2 + - - +
522A PHE* 3.4 24.9 - - + -
523A ALA 2.9 23.7 + - - -
572A ALA* 3.5 7.9 - - + +
574A ASN* 4.8 7.6 - - + -
715A TRP* 3.5 41.3 - - + -
718A ILE* 4.0 18.8 - - + -
722A LEU* 5.0 3.8 - - + -
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Residues in contact with GLN 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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475A MET* 5.2 0.2 - - - -
491A ALA 3.9 0.2 - - - -
492A ILE* 1.3 73.9 - - - +
494A TYR* 1.3 60.3 + - - +
523A ALA* 3.3 17.5 - - + +
525A PRO* 4.0 6.5 - - + -
553A PHE* 3.0 59.6 + - + -
556A ALA* 3.7 9.0 - - - +
557A ALA* 3.3 32.1 + - - +
560A LEU* 3.5 12.6 - - + +
571A VAL* 3.8 7.7 - - + +
572A ALA 2.7 15.5 + - - +
573A ILE* 3.2 13.2 - - + +
574A ASN 3.0 23.5 + - - +
595A PHE* 4.8 0.2 - - - -
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Residues in contact with TYR 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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492A ILE* 5.2 0.7 - - + -
493A GLN* 1.3 73.5 - - - +
495A GLY* 1.3 66.8 + - - +
496A TYR* 5.4 2.5 - + + -
506A PHE* 5.1 5.2 - + - -
511A ILE* 6.1 1.6 - - + -
522A PHE* 3.7 34.1 - + + -
523A ALA 3.0 8.4 + - - +
524A VAL* 4.0 8.7 - - + +
525A PRO* 3.5 21.3 - - - +
553A PHE* 3.8 3.1 - - - -
574A ASN* 3.3 39.0 - - + -
575A GLY* 4.2 5.2 - - - -
576A ALA* 4.6 7.3 + - - +
715A TRP* 5.7 1.8 - + - -
9C TRP* 3.2 64.7 + + - -
10C THR* 4.8 5.6 - - + -
13C HIS* 3.3 32.9 + + - -
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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