Contacts of the strand formed by residues 473 - 480 (chain D) in PDB entry 1JLH
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 THR 473 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D ASP 4.4 1.2 - - - +
56D LYS* 3.1 28.7 + - - +
57D ASN* 3.4 17.2 + - - -
403D CYS* 3.2 17.7 - - + +
405D PHE* 3.8 22.7 - - + -
432D THR* 3.4 30.7 + - + +
435D LEU* 4.3 15.7 - - + -
471D ARG 3.9 9.6 + - - +
472D PRO* 1.3 81.0 - - - +
474D ASN* 1.3 63.6 + - - +
475D SER* 4.7 0.7 + - - -
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Residues in contact with ASN 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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52D VAL* 6.0 0.2 - - - -
53D ASP 3.5 4.9 - - - +
54D TYR* 3.3 14.3 - - - +
57D ASN* 2.8 32.2 + - - +
319D LEU* 3.7 23.5 + - + +
322D LEU* 3.5 11.6 - - - +
326D TYR* 6.1 1.0 - - - -
335D HIS* 5.0 3.8 - - - -
403D CYS 2.8 6.1 + - - +
404D ASP* 2.9 28.5 + - - +
405D PHE* 2.8 28.9 + - - +
473D THR* 1.3 74.4 - - - +
475D SER* 1.3 62.9 + - - +
476D ILE* 4.1 12.1 - - + -
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Residues in contact with SER 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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544C LEU* 3.8 36.6 - - - +
51D LEU 3.2 3.8 - - - +
53D ASP* 2.9 40.5 + - - +
56D LYS* 4.3 2.9 + - - -
405D PHE 3.3 4.0 - - - -
428D PHE* 4.0 12.4 - - - -
432D THR* 3.7 23.2 + - - +
473D THR* 4.7 0.3 + - - -
474D ASN* 1.3 76.8 + - - +
476D ILE* 1.3 62.8 + - - +
477D VAL* 3.9 1.3 + - - -
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Residues in contact with ILE 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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50D ILE* 4.3 14.4 - - + -
51D LEU 3.4 2.0 - - - +
52D VAL* 3.4 35.2 - - + -
319D LEU* 4.7 7.2 - - + -
404D ASP* 5.4 1.8 - - + -
405D PHE 2.7 12.7 + - - +
406D LEU* 3.2 25.3 - - + -
407D ILE 3.1 23.9 + - - -
474D ASN* 4.6 11.4 - - + -
475D SER* 1.3 81.0 - - - +
477D VAL* 1.3 62.1 + - - +
478D PHE* 3.7 17.2 - - + -
489D LEU* 4.2 15.7 - - + -
492D MET* 4.3 11.0 - - + -
493D TYR* 4.5 8.7 - - - +
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Residues in contact with VAL 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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544C LEU* 3.6 30.7 - - + -
547C PHE* 3.5 20.1 - - + -
548C ILE* 4.3 11.7 - - + -
50D ILE* 3.5 1.4 - - - -
51D LEU* 2.7 40.6 + - + +
407D ILE* 3.4 15.3 - - + +
409D VAL* 3.5 27.6 - - + -
428D PHE* 3.9 22.4 - - + -
476D ILE* 1.3 80.1 - - - +
478D PHE* 1.3 61.5 + - - +
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Residues in contact with PHE 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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547C PHE* 4.7 0.7 - - - -
49D HIS 3.2 11.0 - - - +
50D ILE* 4.4 4.0 - - + -
344D LEU* 4.6 9.4 - - + -
406D LEU* 4.1 11.7 - - + -
407D ILE 3.2 24.2 + - - -
408D PRO* 3.1 35.2 - - + +
409D VAL* 2.7 35.4 + - - -
476D ILE* 3.7 17.0 - - + -
477D VAL* 1.3 78.2 - - - +
479D THR* 1.3 58.1 + - - +
480D LYS 4.2 4.0 - - - -
481D LEU* 3.8 20.2 - - + -
485D MET* 3.8 30.5 - - + -
489D LEU* 3.6 32.8 - - + -
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Residues in contact with THR 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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547C PHE* 5.0 0.8 - - - -
551C GLN* 2.8 35.8 + - - +
554C ALA* 4.1 2.9 - - + -
556C VAL* 4.0 20.2 - - + -
48D GLY* 3.6 8.5 - - - -
49D HIS 2.8 27.7 + - - -
409D VAL* 3.3 9.0 + - - +
410D GLN* 2.7 54.4 + - - +
478D PHE* 1.3 71.9 - - - +
480D LYS* 1.3 62.6 + - + +
485D MET* 4.8 0.6 - - - +
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Residues in contact with LYS 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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555C ARG* 5.2 7.9 - - - +
556C VAL* 5.1 15.2 - - + +
47D HIS 5.7 0.7 - - - +
173D TYR* 4.3 6.2 + - - -
408D PRO* 4.1 4.9 - - - -
410D GLN* 3.7 39.2 - - + +
411D THR 4.7 10.9 + - - -
412D GLN* 3.4 33.2 + - - +
478D PHE* 3.4 3.7 + - - -
479D THR* 1.3 85.8 - - + +
481D LEU* 1.3 63.1 + - - +
482D THR* 3.0 26.6 + - + +
485D MET* 3.2 20.9 - - - +
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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