Contacts of the strand formed by residues 473 - 480 (chain A) in PDB entry 1GZD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP 4.6 1.9 - - - +
56A LYS* 3.2 33.8 + - - +
57A ASN* 3.6 11.6 - - - +
402A PRO* 5.5 0.4 - - - -
403A CYS* 3.3 22.7 - - + +
405A PHE* 4.4 6.1 - - + -
432A THR* 3.6 26.0 + - + +
435A LEU* 3.9 30.3 - - + -
471A ARG 4.0 6.1 + - - +
472A PRO* 1.3 85.9 - - - +
474A ASN* 1.3 67.1 + - - +
475A SER* 5.3 0.3 + - - -
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Residues in contact with ASN 474 (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* 4.6 3.1 - - + -
53A ASP 3.7 4.9 - - - +
54A TYR* 3.7 16.5 - - - +
57A ASN* 2.8 32.2 + - - +
319A LEU* 3.7 19.6 - - - +
322A LEU* 3.8 11.0 - - - +
335A HIS* 5.1 2.4 - - - -
403A CYS 2.8 8.2 + - - +
404A ASP* 2.7 25.6 - - - +
405A PHE* 2.9 27.8 + - - +
473A THR* 1.3 76.5 - - - +
475A SER* 1.3 61.7 + - - +
476A ILE* 4.0 11.7 - - + -
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Residues in contact with SER 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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51A LEU 3.5 1.7 - - - +
53A ASP* 2.9 50.7 + - - +
56A LYS* 4.7 6.3 + - - -
405A PHE* 3.4 4.4 - - - +
428A PHE* 3.7 23.9 - - - -
432A THR* 4.0 20.6 + - - +
473A THR* 5.3 0.5 + - - -
474A ASN* 1.3 73.8 + - - +
476A ILE* 1.3 63.1 + - - +
477A VAL* 4.0 6.5 + - - +
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Residues in contact with ILE 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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50A ILE* 4.0 24.7 - - + -
51A LEU 3.2 3.4 - - - +
52A LEU* 3.9 21.3 - - + -
319A LEU* 5.1 4.7 - - + -
404A ASP* 4.3 9.4 - - + -
405A PHE 2.8 17.4 + - - +
406A LEU* 3.3 13.1 - - + -
407A ILE 3.2 22.7 + - - -
428A PHE* 4.5 0.2 - - - -
474A ASN* 4.0 19.3 - - + -
475A SER* 1.3 78.2 - - - +
477A VAL* 1.3 61.9 + - - +
478A PHE* 3.7 14.5 - - + -
489A LEU* 4.3 11.9 - - + -
492A MET* 4.5 9.6 - - + -
493A TYR* 4.0 20.9 - - - +
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Residues in contact with VAL 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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49A ARG 3.9 0.7 - - - +
50A ILE* 3.6 0.4 - - - -
51A LEU* 2.7 53.6 + - + +
53A ASP* 6.3 0.4 - - + -
407A ILE* 3.6 14.8 - - + +
409A VAL* 3.6 27.4 - - + -
425A LEU* 5.9 2.2 - - + -
428A PHE* 3.9 26.2 - - + -
475A SER* 4.5 6.7 - - - +
476A ILE* 1.3 79.0 - - - +
478A PHE* 1.3 60.5 + - - +
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Residues in contact with PHE 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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49A ARG 2.9 13.9 - - - +
50A ILE* 4.0 12.8 - - + -
344A LEU* 4.6 7.4 - - + -
406A LEU* 4.1 11.9 - - + -
407A ILE* 3.3 30.1 + - - -
408A PRO* 3.3 27.5 - - + +
409A VAL* 3.0 24.0 + - - +
476A ILE* 3.7 20.2 - - + -
477A VAL* 1.3 77.7 - - - +
479A THR* 1.3 66.9 + - - +
480A LYS 4.1 7.2 - - - -
481A LEU* 3.7 22.9 - - + -
485A ILE* 3.9 21.8 - - + -
489A LEU* 3.7 22.7 - - + -
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Residues in contact with THR 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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48A GLY* 3.7 12.8 - - - -
49A ARG* 2.9 39.4 + - - +
409A VAL* 3.3 9.2 + - + +
410A GLN* 2.9 51.8 + - - +
478A PHE* 1.3 73.3 - - - +
480A LYS* 1.3 65.0 + - + +
485A ILE* 5.6 2.1 - - - +
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Residues in contact with LYS 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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173A TYR* 4.8 3.6 + - - -
408A PRO* 4.1 2.7 - - - -
410A GLN* 3.6 39.7 - - + +
411A THR 4.6 9.4 - - - -
412A GLN* 3.9 28.9 + - - +
478A PHE* 3.5 5.7 - - - -
479A THR* 1.3 85.0 - - + +
481A LEU* 1.3 61.7 + - - +
482A THR* 3.3 26.7 + - + +
485A ILE* 3.6 22.5 - - - +
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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