Contacts of the strand formed by residues 448 - 453 (chain D) in PDB entry 6NYY
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 VAL 448 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D PHE* 3.8 40.2 - - + -
327D LEU* 4.8 8.1 - - + -
340D ILE* 3.7 29.4 - - + -
341D PRO 4.3 7.0 - - - +
342D LYS 4.4 3.6 - - - -
343D GLY* 4.6 4.7 - - - -
402D CYS 3.1 10.0 + - - +
403D ILE* 3.3 29.1 - - + -
404D LEU* 2.6 35.2 + - - +
446D ASN 5.1 0.4 - - - -
447D VAL* 1.3 72.4 - - - +
449D ILE* 1.3 58.0 + - - +
450D LEU* 3.8 7.4 - - + -
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Residues in contact with ILE 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LYS* 3.5 18.8 + - + +
343D GLY* 3.2 17.6 - - - -
344D ALA 3.2 3.8 + - - -
393D PHE* 3.6 26.2 - - + -
404D LEU* 3.5 26.9 - - + -
406D ILE* 4.4 10.8 - - + -
437D GLU 5.3 0.4 - - - +
438D MET* 3.6 42.2 - - + +
447D VAL* 3.8 21.1 - - + +
448D VAL* 1.3 77.4 - - - +
450D LEU* 1.3 60.9 + - - +
469D PHE* 3.4 10.5 - - + -
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Residues in contact with LEU 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ILE* 4.8 13.5 - - + -
323D PHE* 3.7 31.0 - - + -
344D ALA* 3.4 18.4 - - + +
346D LEU* 5.5 6.7 - - + -
358D ALA* 4.9 6.7 - - + -
361D THR* 4.2 25.1 - - + +
369D PHE* 4.7 6.3 - - + -
403D ILE* 3.9 19.7 - - + -
404D LEU 2.6 17.0 + - - +
405D PHE* 3.8 16.6 - - + -
406D ILE* 3.0 23.6 + - - +
448D VAL* 3.8 9.2 - - + -
449D ILE* 1.3 75.9 - - - +
451D ALA* 1.3 64.9 + - - +
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Residues in contact with ALA 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ALA 3.0 5.3 + - - +
345D ILE* 3.3 21.6 - - + -
346D LEU* 2.8 34.0 + - - +
405D PHE* 4.0 8.3 - - - -
406D ILE* 3.3 19.3 - - + +
409D ILE* 3.7 21.3 - - + -
450D LEU* 1.3 78.9 - - - +
452D GLY* 1.3 52.9 + - - +
469D PHE* 3.8 9.2 - - + -
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Residues in contact with GLY 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D ILE* 4.6 0.7 - - - -
346D LEU* 3.3 15.9 - - - -
354D LYS* 5.4 4.9 - - - -
405D PHE* 3.9 13.5 - - - -
406D ILE 3.3 5.3 + - - -
407D ASP* 4.6 4.0 - - - -
408D GLN* 3.0 27.5 + - - -
409D ILE* 3.4 4.2 + - - +
451D ALA* 1.3 76.0 - - - +
453D THR* 1.3 65.2 + - - -
801D ANP 6.1 0.2 - - - -
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Residues in contact with THR 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D ILE* 4.1 13.0 - - + -
346D LEU 2.8 13.7 + - - +
347D THR* 3.5 30.7 - - + -
354D LYS* 2.5 29.5 + - - +
408D GLN* 4.9 6.3 - - - +
409D ILE* 3.9 15.3 - - - +
410D ASP* 2.7 30.3 + - - -
452D GLY* 1.3 75.7 - - - -
454D ASN* 1.3 61.8 + - - +
455D ARG 3.2 7.3 + - - +
456D PRO 4.5 2.0 - - - -
459D LEU* 4.2 11.9 - - + -
801D ANP 5.2 0.4 + - - -
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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