Contacts of the strand formed by residues 464 - 470 (chain D) in PDB entry 3D8F
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 464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D LEU* 4.4 5.9 - - - +
398D ILE* 3.9 24.7 - - + +
402D SER* 3.3 24.3 + - - -
455D VAL* 3.4 20.2 - - - +
462D GLU* 2.7 33.4 + - - +
463D ARG* 1.3 79.7 + - - +
465D PHE* 1.3 58.7 + - - +
481D VAL* 4.6 4.9 - - + -
482D PHE 3.4 9.9 - - - +
483D ARG* 3.8 22.9 + - - +
488D ALA* 3.1 16.2 - - - +
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Residues in contact with PHE 465 (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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424D LEU* 4.5 6.3 - - + -
431D LEU* 4.4 7.9 - - + -
453D TRP* 3.7 14.8 - + + -
454D GLY 3.8 8.1 - - - -
464D ASP* 1.3 75.0 - - - +
466D ALA* 1.3 80.9 + - - +
467D TYR* 3.8 24.2 - + + -
481D VAL* 3.4 3.1 - - - -
482D PHE* 2.9 50.1 + + + +
484D CYS* 3.8 22.1 - - - -
488D ALA* 4.1 11.7 - - + -
491D ILE* 3.8 32.5 - - + -
492D ALA* 4.0 11.7 - - + -
495D LEU* 3.7 23.3 - - + -
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Residues in contact with ALA 466 (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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394D VAL* 3.8 16.2 - - + -
398D ILE* 3.7 31.4 - - + +
453D TRP* 3.0 27.6 - - - +
454D GLY 3.1 11.8 + - - +
464D ASP 4.2 0.2 + - - -
465D PHE* 1.3 80.6 - - - +
467D TYR* 1.3 61.5 + - - +
479D CYS* 4.0 8.7 - - - -
480D HIS 3.3 11.0 - - - +
481D VAL* 4.3 2.5 - - + -
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Residues in contact with TYR 467 (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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416D TRP* 4.3 1.9 - - - -
431D LEU* 4.0 16.2 - - + -
433D LEU* 4.3 4.0 - - - +
443D HIS* 4.0 23.9 + - - -
445D GLN* 3.8 25.6 + - + +
450D ILE* 3.8 28.0 - - + -
452D VAL 3.3 6.7 - - - +
453D TRP* 4.1 1.1 - - + +
465D PHE* 3.8 19.7 - + + -
466D ALA* 1.3 76.6 - - - +
468D VAL* 1.3 69.7 + - - +
469D ALA* 3.9 12.6 - - + -
478D LYS 4.0 0.5 - - - +
479D CYS* 3.6 0.6 - - - -
480D HIS* 3.1 52.4 + + + -
482D PHE* 3.3 40.2 - + - -
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Residues in contact with VAL 468 (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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380D MET* 3.7 16.8 - - + -
385D LEU* 4.0 18.2 - - + -
394D VAL* 4.6 8.1 - - + -
450D ILE* 3.4 6.1 - - - +
451D ARG* 2.7 49.4 + - + -
452D VAL* 2.8 30.9 + - + +
467D TYR* 1.3 76.9 - - - +
469D ALA* 1.3 60.4 + - - +
477D LEU* 5.1 5.2 - - + -
478D LYS 3.3 12.8 - - - +
479D CYS* 3.6 27.1 - - + -
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Residues in contact with ALA 469 (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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445D GLN* 3.2 35.4 - - + +
449D SER 4.1 9.9 - - - +
450D ILE* 4.7 0.2 - - - -
451D ARG* 4.8 2.5 - - - +
467D TYR* 3.9 15.8 + - + -
468D VAL* 1.3 75.9 - - - +
470D ARG* 1.3 63.0 + - - +
471D ASP 3.5 2.3 + - - -
477D LEU* 4.5 4.0 - - - -
478D LYS* 3.0 34.0 + - - +
480D HIS* 4.6 6.2 + - + +
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Residues in contact with ARG 470 (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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382D GLU* 4.7 7.5 + - - +
445D GLN* 4.9 3.6 - - - +
449D SER 4.9 2.6 + - - -
451D ARG* 5.3 3.2 - - + +
469D ALA* 1.3 75.3 - - - +
471D ASP* 1.3 75.2 + - - +
472D LYS* 3.2 5.8 + - - +
475D GLN* 2.6 65.9 + - - +
476D MET* 3.6 12.7 - - - +
477D LEU* 3.8 37.9 - - + +
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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