Contacts of the strand formed by residues 473 - 480 (chain D) in PDB entry 5U03
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 TYR 473 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454D ARG* 3.5 50.2 + - + -
455D THR 3.3 14.8 - - - +
456D LEU* 3.6 17.9 - - + -
457D PHE* 4.0 5.2 - - - -
471D ALA* 3.2 21.2 - - + +
472D ASP* 1.3 87.6 - - + +
474D LEU* 1.4 70.4 + - - +
475D GLU* 3.9 12.1 - - + -
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Residues in contact with LEU 474 (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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454D ARG* 3.5 3.1 - - - +
455D THR* 2.8 64.0 + - + +
457D PHE* 3.7 28.3 - - + -
468D TYR* 3.4 50.0 - - + +
471D ALA* 5.6 0.4 - - + -
473D TYR* 1.4 78.0 - - - +
475D GLU* 1.4 63.7 + - - +
476D GLU* 3.6 17.5 - - + +
511D ILE* 4.4 3.8 - - + -
525D TYR* 4.0 13.5 - - + +
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Residues in contact with GLU 475 (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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452D LYS* 3.4 36.2 + - + +
453D ARG 3.2 8.3 - - - +
454D ARG* 2.8 51.9 + - + +
473D TYR* 4.0 9.8 - - + -
474D LEU* 1.4 79.2 - - - +
476D GLU* 1.3 66.8 + - - +
530D LEU* 3.7 12.6 - - - +
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Residues in contact with GLU 476 (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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452D LYS* 3.2 6.6 - - - -
453D ARG 3.0 28.4 + - - -
455D THR* 5.2 1.8 + - - +
468D TYR* 2.8 30.3 + - - -
474D LEU* 3.6 18.2 + - + +
475D GLU* 1.3 80.3 - - - +
477D ARG* 1.3 61.3 + - - +
478D HIS* 3.2 5.9 - - - +
525D TYR* 3.4 42.0 - - + -
527D PRO* 3.3 26.6 - - - +
530D LEU* 3.5 18.0 - - - +
537D SER* 5.7 0.5 - - - -
538D PRO* 5.4 0.9 - - - +
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Residues in contact with ARG 477 (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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59D PHE* 4.2 8.8 - - - -
60D VAL* 2.9 52.8 + - + +
61D LEU* 3.5 7.6 + - - +
62D ASP* 2.8 40.0 + - - +
75D GLU* 4.4 0.6 + - - -
81D ARG* 3.5 9.7 - - - +
451D GLY 3.8 1.6 - - - -
452D LYS* 3.6 26.2 - - - +
476D GLU* 1.3 78.2 + - - +
478D HIS* 1.4 58.9 + - - +
525D TYR* 3.1 8.5 - - - +
526D HIS* 2.7 45.8 + - + +
529D PHE* 3.6 21.5 - - + +
530D LEU* 3.6 32.6 - - - +
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Residues in contact with HIS 478 (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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60D VAL* 4.4 4.9 - - - +
449D ARG* 3.0 37.5 + - + +
450D LEU* 3.1 5.5 - - - +
451D GLY 2.7 35.1 + - - +
453D ARG* 3.5 33.9 + - + +
454D ARG 5.0 0.2 - - - -
455D THR* 3.5 18.0 + - - -
476D GLU* 3.2 20.0 + - - +
477D ARG* 1.4 79.3 - - - +
479D ARG* 1.4 65.6 + - - +
480D HIS* 3.4 17.4 - + + -
510D GLU* 3.3 27.8 - - + -
525D TYR* 4.0 5.2 - - + +
526D HIS* 4.0 1.3 - - - -
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Residues in contact with ARG 479 (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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48D GLY* 2.9 32.2 + - - -
50D PHE 5.2 2.0 + - - -
58D VAL* 4.4 22.6 - - - +
60D VAL* 4.7 12.6 - - + +
66D GLU* 3.0 26.7 + - - +
373D PHE* 4.9 19.5 - - + -
399D CYS* 4.5 3.5 - - - -
448D MET* 3.9 20.1 - - - +
449D ARG 3.1 6.1 - - - -
450D LEU* 3.4 20.6 - - + +
478D HIS* 1.4 75.7 - - - +
480D HIS* 1.4 71.9 + - - +
526D HIS* 3.1 30.5 + - + +
529D PHE* 5.6 4.0 - - - -
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Residues in contact with HIS 480 (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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399D CYS* 4.0 15.3 - - - -
403D GLN* 5.0 2.0 - - - +
448D MET* 3.4 11.6 - - - +
449D ARG* 2.8 43.5 + - - +
478D HIS* 3.4 35.7 + + + -
479D ARG* 1.4 82.7 + - - +
481D ARG* 1.4 60.2 + - - +
482D PHE 4.8 0.4 - - - +
483D GLU* 3.3 25.8 - - - +
510D GLU* 2.9 28.6 + - - -
524D GLN* 3.5 45.0 + - + +
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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