Contacts of the strand formed by residues 419 - 426 (chain A) in PDB entry 1ATH
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER* 4.5 9.4 - - - +
55A ASN* 4.3 15.7 - - + +
56A SER* 5.2 1.1 - - - -
81A LEU* 4.0 29.8 - - + -
126A LEU* 4.1 14.6 - - + +
130A LEU* 4.9 4.3 - - + +
413A ARG* 3.5 2.6 - - - +
414A GLU* 2.8 37.9 + - - +
417A LEU* 3.2 28.4 + - - +
418A ASN* 1.3 75.8 - - - +
420A ILE* 1.3 66.2 + - - +
421A ILE* 3.3 3.2 + - - +
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Residues in contact with ILE 420 (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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55A ASN* 6.3 0.4 - - - +
56A SER* 4.0 26.4 + - - +
59A ALA* 4.4 14.8 - - + -
60A THR* 5.4 1.3 - - - +
80A PRO* 4.9 4.2 - - + +
81A LEU* 3.7 22.2 + - - +
304A LEU* 4.3 16.8 - - + -
411A PHE* 4.2 29.6 - - + -
412A ILE 3.8 4.5 - - - +
413A ARG* 4.5 11.4 - - + +
418A ASN 6.0 0.4 - - - -
419A THR* 1.3 74.3 - - - +
421A ILE* 1.3 58.8 + - - +
422A PHE 3.2 25.6 - - - +
423A MET* 3.7 23.8 - - + -
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Residues in contact with ILE 421 (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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79A SER* 3.2 30.7 + - - -
80A PRO* 4.8 0.7 - - - -
81A LEU* 4.3 8.8 + - + -
130A LEU* 4.9 4.3 - - + -
140A LEU* 4.1 28.5 - - + -
219A ILE* 3.9 25.1 - - + -
279A ILE* 4.2 10.5 - - + -
412A ILE* 2.6 27.4 + - + +
414A GLU* 3.8 28.9 - - + +
419A THR* 3.9 10.3 - - - +
420A ILE* 1.3 76.8 - - - +
422A PHE* 1.3 80.0 + - + +
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Residues in contact with PHE 422 (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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77A PHE* 3.3 37.0 - + + -
78A LEU 3.4 4.0 - - - -
79A SER* 3.6 28.0 - - - +
80A PRO* 4.4 0.7 - - - -
219A ILE* 3.5 37.2 - - + -
221A PHE* 3.6 30.3 - + + -
371A ALA* 4.8 7.4 - - + -
372A PHE 5.6 4.0 - - - -
373A LEU* 6.0 1.3 - - + -
411A PHE* 3.8 2.0 - - - -
412A ILE* 3.1 46.8 + - + +
420A ILE* 3.2 14.7 - - - +
421A ILE* 1.3 95.1 - - + +
423A MET* 1.3 61.6 + - - +
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Residues in contact with MET 423 (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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59A ALA* 3.6 25.4 - - + +
60A THR* 5.1 2.9 - - - -
63A TYR* 3.7 32.5 - - + -
77A PHE* 3.2 8.8 - - - -
78A LEU* 2.8 46.8 + - + +
80A PRO* 3.6 24.2 - - + -
299A LEU* 5.7 2.0 - - - -
410A VAL 3.7 12.3 - - - +
411A PHE* 4.0 26.2 - - + +
420A ILE* 3.7 18.6 - - + -
422A PHE* 1.3 73.4 - - - +
424A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 424 (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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63A TYR* 4.0 10.2 + - - -
76A ILE 2.9 16.4 - - - -
77A PHE* 4.1 6.5 - - - -
409A LEU* 3.4 11.1 - - - +
410A VAL* 3.0 34.7 + - - +
411A PHE* 5.6 0.2 - - - -
423A MET* 1.3 77.7 - - - +
425A ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 425 (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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63A TYR* 3.1 20.2 + - - +
67A ALA* 3.6 22.0 + - - +
70A LYS* 4.6 3.4 + - - +
71A ASN 3.7 11.9 + - - -
72A ASP* 3.4 24.2 + - - +
74A ASP* 2.8 37.2 + - - +
75A ASN* 3.2 10.6 - - - +
76A ILE* 3.0 52.8 + - + +
292A LEU* 3.6 28.5 - - + +
296A GLU* 3.0 30.6 + - - +
325A ILE* 4.7 1.2 - - - +
408A PHE 3.4 5.6 - - - +
409A LEU* 4.1 1.8 - - + -
410A VAL* 4.7 0.8 - - - +
424A GLY* 1.3 71.6 - - - +
426A VAL* 1.3 61.4 + - - +
427A ALA* 3.3 13.8 + - + +
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Residues in contact with VAL 426 (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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75A ASN* 3.5 7.4 - - - +
239A PHE* 4.1 1.2 - - - -
323A PHE* 3.8 31.6 - - + -
325A ILE* 3.8 25.4 - - + -
407A PRO* 3.2 24.6 - - - +
408A PHE* 3.0 34.2 + - + +
410A VAL* 3.9 13.2 - - + +
425A ARG* 1.3 69.1 - - - +
427A ALA* 1.3 59.2 + - - +
428A ASN 4.7 0.2 - - - -
429A PRO* 3.9 34.3 - - + -
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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