Contacts of the strand formed by residues 494 - 499 (chain A) in PDB entry 2XNF
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 PHE 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LEU* 4.3 15.9 - - + -
453A ILE* 3.5 19.5 - - - +
454A PRO* 3.7 23.8 - - + -
455A GLN* 4.2 4.9 - - - +
489A ILE* 3.1 52.5 + - + +
490A MET* 3.3 27.6 - - - +
492A ASN* 4.2 20.0 - - + -
493A GLY* 1.3 82.2 - - - +
495A ALA* 1.3 60.8 + - - +
514A LEU* 5.0 1.0 - - - +
515A TYR 5.2 1.0 + - - -
544A LEU* 5.1 8.3 - - + -
550A HIS* 5.3 7.9 - + - -
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Residues in contact with ALA 495 (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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451A GLN 3.2 1.0 - - - +
452A LEU* 3.2 5.0 - - - -
453A ILE* 2.7 46.2 + - + +
455A GLN* 4.3 6.3 - - + -
458A LEU* 4.1 6.5 - - + -
493A GLY 4.1 0.2 - - - -
494A PHE* 1.3 75.6 - - - +
496A GLY* 1.3 61.1 + - - +
497A CYS 3.6 1.1 + - - -
512A MET* 3.5 14.8 - - - -
513A LEU 3.5 4.5 - - - -
514A LEU* 3.5 26.2 - - + -
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Residues in contact with GLY 496 (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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450A MET* 4.1 9.6 - - - -
451A GLN 3.3 6.3 - - - -
452A LEU* 3.9 12.8 - - - -
490A MET* 3.7 3.6 - - - +
495A ALA* 1.3 72.3 - - - +
497A CYS* 1.3 64.1 + - - -
498A VAL* 3.3 4.1 + - - +
512A MET* 3.9 1.3 - - - -
513A LEU* 2.7 50.7 + - - +
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Residues in contact with CYS 497 (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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449A ILE 3.5 2.1 - - - +
450A MET* 3.1 2.1 - - - -
451A GLN* 2.8 38.9 + - + +
453A ILE* 4.1 12.1 - - + -
495A ALA 3.6 1.8 + - - -
496A GLY* 1.3 71.8 - - - +
498A VAL* 1.3 62.9 + - - +
499A HIS* 3.4 31.8 + - + -
510A VAL* 5.3 0.7 - - - -
511A LEU 3.7 4.9 - - - -
512A MET* 3.9 12.5 - - + -
533A PHE* 3.7 17.7 - - - -
537A ILE* 3.5 29.2 - - + -
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Residues in contact with VAL 498 (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 LEU* 5.1 2.7 - - + -
448A LEU* 3.6 41.3 - - + -
449A ILE 3.3 6.3 - - - +
450A MET* 3.9 14.1 - - + +
473A PHE* 4.8 2.9 - - + -
496A GLY 3.6 13.5 - - - +
497A CYS* 1.3 72.6 - - - +
499A HIS* 1.3 66.5 + - - +
500A PHE* 4.2 3.0 + - + -
510A VAL* 3.7 6.6 - - - +
511A LEU* 2.7 64.3 + - + +
513A LEU* 4.2 18.6 - - + -
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Residues in contact with HIS 499 (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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448A LEU* 4.0 2.1 - - - -
449A ILE* 2.7 47.6 + - + +
451A GLN* 5.7 3.4 + - + +
497A CYS* 3.4 35.8 + - + -
498A VAL* 1.3 76.2 - - - +
500A PHE* 1.3 66.1 + - - +
501A PRO* 3.7 0.9 - - - +
507A GLU* 4.6 8.3 - - - -
510A VAL* 3.8 10.3 - - + -
534A VAL* 3.6 42.1 - - + +
537A ILE* 4.1 13.0 - - + +
541A ILE* 5.1 7.4 - - + -
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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