Contacts of the strand formed by residues 422 - 429 (chain A) in PDB entry 5FZ9
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 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ILE* 4.6 15.2 - - + +
88A GLN 3.3 11.9 - - - -
89A ARG* 4.3 20.2 - - + -
389A PHE* 4.5 7.3 - - - -
420A ASP* 3.6 11.5 + - + +
421A VAL* 1.3 82.0 - - - +
423A VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 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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87A ILE* 3.6 4.4 - - - +
88A GLN* 2.8 44.1 + - + +
90A LEU* 4.0 24.2 - - + -
389A PHE* 3.9 20.2 - - + -
421A VAL* 4.4 1.1 - - + -
422A THR* 1.3 79.6 - - - +
424A GLU* 1.3 64.8 + - - +
491A MET* 3.9 16.4 - - + -
492A CYS 3.7 18.8 - - - +
493A PHE* 4.4 0.4 - - + -
494A SER* 3.8 28.3 - - - +
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Residues in contact with GLU 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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85A PRO* 3.8 10.6 - - + +
86A ARG 3.1 13.5 - - - +
87A ILE* 4.3 15.3 - - + +
375A ARG* 3.4 38.1 + - - -
377A TYR* 2.7 33.7 + - - -
382A PHE* 3.5 14.1 - - + -
385A MET* 3.7 10.8 - - + +
423A VAL* 1.3 79.2 - - - +
425A TYR* 1.3 66.3 + - - +
491A MET* 3.2 30.6 - - - +
494A SER* 4.1 1.6 - - - -
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Residues in contact with TYR 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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83A PHE* 4.3 6.3 - - - -
85A PRO* 3.5 4.7 - - - +
86A ARG* 2.9 73.8 + - + +
87A ILE 4.7 2.3 + - - -
88A GLN* 3.9 36.1 - - + -
98A ARG 5.6 0.2 + - - -
382A PHE* 3.9 6.2 - - - -
424A GLU* 1.3 79.2 - - - +
426A GLY* 1.3 65.0 + - - +
427A ALA* 4.1 2.2 - - + -
489A VAL 3.5 14.6 - - - +
490A GLY* 4.9 0.2 - - - -
494A SER* 4.0 15.5 - - - +
495A SER 5.8 0.4 - - - -
1757A DMS 3.1 25.9 - - + +
1768A NUK 3.4 42.8 - - + +
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Residues in contact with GLY 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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83A PHE* 3.7 20.7 - - - -
84A THR 5.1 2.0 - - - -
425A TYR* 1.3 81.0 - - - +
427A ALA* 1.3 62.0 + - - +
488A TYR* 3.3 6.8 - - - +
489A VAL 3.0 31.0 + - - +
1761A EDO 3.0 17.6 + - - -
1768A NUK 4.9 0.5 - - - -
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Residues in contact with ALA 427 (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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84A THR 5.6 0.4 + - - -
86A ARG* 3.2 31.4 + - - +
425A TYR* 4.1 17.5 - - + -
426A GLY* 1.3 74.8 - - - +
428A ASP* 1.3 74.2 + - - +
486A TRP* 4.3 8.5 - - + -
487A LEU 3.4 6.5 - - - -
488A TYR* 3.7 23.8 - - + -
1761A EDO 3.4 2.2 + - - -
1768A NUK 4.1 8.3 - - + -
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Residues in contact with ASP 428 (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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83A PHE* 5.2 0.7 - - - +
84A THR* 4.6 14.0 + - - +
86A ARG* 3.6 16.1 + - - -
100A LYS 5.7 1.9 - - - -
427A ALA* 1.3 81.3 + - - +
429A ILE* 1.3 69.9 + - - +
486A TRP* 3.8 16.0 - - - -
487A LEU* 2.8 34.2 + - - +
1761A EDO 3.4 26.4 + - - +
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Residues in contact with ILE 429 (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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428A ASP* 1.3 85.6 + - - +
430A ALA* 1.3 72.8 + - - +
431A SER* 3.4 7.7 + - - -
434A PHE 4.3 2.1 - - - +
480A CYS* 4.4 25.4 - - + +
481A GLY* 4.8 1.3 - - - -
484A LEU* 4.2 24.2 - - + -
485A PRO 3.4 10.1 - - - +
486A TRP* 3.4 43.8 - - + +
487A LEU* 4.6 1.9 - - - +
1761A EDO 5.1 0.9 + - - -
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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