Contacts of the strand formed by residues 474 - 481 (chain A) in PDB entry 1JIQ
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 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP 4.4 1.4 - - - +
57A LYS* 2.9 31.2 + - - +
58A ASN* 3.4 15.0 - - - +
404A CYS* 3.2 15.5 - - + +
406A PHE* 3.9 13.7 - - + -
433A THR* 3.4 30.7 + - + +
436A LEU* 3.7 30.3 - - + -
472A ARG 4.1 5.7 + - - +
473A PRO* 1.3 80.1 - - - +
475A ASN* 1.3 65.0 + - - +
476A SER* 4.3 0.7 + - - -
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Residues in contact with ASN 475 (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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53A VAL* 5.8 0.7 - - + -
54A ASP 3.6 3.6 + - - +
55A TYR* 3.3 20.8 - - - +
58A ASN* 2.8 32.2 + - - -
320A LEU* 3.7 20.8 - - + +
323A LEU* 3.9 10.8 - - - +
336A HIS* 5.1 2.1 - - - -
404A CYS 2.8 6.3 + - - +
405A ASP* 2.8 29.8 - - + +
406A PHE* 2.8 28.8 + - - +
474A THR* 1.3 75.1 - - - +
476A SER* 1.3 61.8 + - - +
477A ILE* 4.7 10.5 - - + -
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Residues in contact with SER 476 (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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52A LEU 3.5 2.3 - - - +
54A ASP* 2.8 39.6 + - - +
57A LYS* 5.0 1.8 - - - -
406A PHE* 3.3 4.0 - - - +
429A PHE* 3.9 15.3 - - - -
433A THR* 3.6 30.8 + - - +
474A THR* 4.2 1.1 + - - -
475A ASN* 1.3 70.1 + - - +
477A ILE* 1.3 61.2 + - - +
478A VAL* 4.0 1.3 - - - -
545B LEU* 3.8 32.0 - - - +
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Residues in contact with ILE 477 (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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51A ILE* 4.1 22.0 - - + -
52A LEU 3.4 2.7 - - - +
53A VAL* 4.1 16.8 - - + -
320A LEU* 4.4 17.3 - - + -
405A ASP* 4.7 7.9 - - + -
406A PHE 2.8 10.9 + - - +
407A LEU* 3.2 20.5 - - + -
408A ILE 3.1 23.4 + - - -
475A ASN* 4.7 5.4 - - + -
476A SER* 1.3 77.2 - - - +
478A VAL* 1.3 60.7 + - - +
479A PHE* 3.7 13.4 - - + -
490A LEU* 4.3 7.4 - - + -
493A MET* 4.1 17.9 - - + -
494A TYR* 3.5 25.6 - - + +
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Residues in contact with VAL 478 (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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51A ILE* 3.4 2.1 - - - +
52A LEU* 2.7 39.3 + - + +
408A ILE* 3.4 13.7 - - + +
410A VAL* 3.5 27.8 - - + -
429A PHE* 3.8 29.4 - - + -
476A SER 4.7 0.2 - - - -
477A ILE* 1.3 77.2 - - - +
479A PHE* 1.3 62.8 + - - +
545B LEU* 3.8 24.5 - - + -
548B PHE* 3.6 20.9 - - + -
549B ILE* 4.3 11.9 - - + -
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Residues in contact with PHE 479 (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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50A HIS 3.1 11.4 - - - +
51A ILE* 4.3 4.0 - - + -
345A LEU* 4.5 11.4 - - + -
407A LEU* 4.0 13.5 - - + -
408A ILE* 3.1 24.1 + - - -
409A PRO* 3.1 31.5 - - + +
410A VAL* 2.7 32.5 + - - -
477A ILE* 3.7 17.3 - - + -
478A VAL* 1.3 78.0 - - - +
480A THR* 1.3 57.9 + - - +
481A LYS 3.3 5.2 - - - -
482A LEU* 3.9 13.7 - - + -
486A MET* 3.8 30.3 - - + -
490A LEU* 3.7 38.1 - - + -
548B PHE* 4.8 1.1 - - - -
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Residues in contact with THR 480 (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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49A GLY* 3.6 9.4 - - - -
50A HIS* 2.8 28.3 + - - +
410A VAL* 3.3 10.3 + - - +
411A GLN* 2.8 52.6 + - - +
479A PHE* 1.3 71.8 - - - +
481A LYS* 1.3 61.5 + - - +
486A MET* 4.6 1.0 - - - +
548B PHE* 5.1 0.8 - - - -
552B GLN* 2.5 37.1 + - - +
555B ALA* 4.1 5.8 - - + -
557B VAL* 3.9 16.8 - - + -
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Residues in contact with LYS 481 (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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48A HIS 5.6 0.9 - - - +
49A GLY* 5.7 0.2 - - - -
174A TYR* 4.2 6.1 - - - -
409A PRO* 4.1 8.7 - - - -
411A GLN* 3.8 30.7 + - + +
412A THR 4.6 12.1 + - - -
413A GLN* 3.8 29.6 + - - +
479A PHE* 3.3 3.6 + - - -
480A THR* 1.3 82.9 - - - +
482A LEU* 1.3 63.7 + - - +
483A THR* 3.1 23.5 + - + +
486A MET* 3.3 20.7 - - - +
557B VAL* 4.0 21.5 - - + -
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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