Contacts of the strand formed by residues 425 - 429 (chain A) in PDB entry 1Z6T
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 PHE 425 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 5.9 6.3 - - + -
322A LEU* 4.1 11.2 - - + -
419A VAL* 4.3 5.6 - - + -
422A SER* 4.1 19.5 - - - -
424A LEU* 1.3 82.9 - - - +
426A CYS* 1.3 60.5 + - - +
435A TYR* 3.2 9.9 - - - +
436A TYR* 2.8 72.7 + + + +
437A LEU* 4.3 0.9 - - - -
438A HIS* 3.9 16.2 - + + -
441A GLN* 3.2 28.0 - - - -
900A ADP 2.9 34.1 - - - -
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Residues in contact with CYS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.6 24.9 - - + +
121A GLN* 4.4 1.0 - - - +
419A VAL* 4.1 9.2 - - + +
425A PHE* 1.3 77.1 - - - +
427A ASP* 1.3 69.0 + - - +
428A ARG* 3.0 47.1 + - - -
433A PHE* 4.1 9.9 - - - -
434A ARG 3.3 8.1 - - - -
435A TYR* 3.5 31.9 - - + -
436A TYR* 4.3 0.2 - - - -
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Residues in contact with ASP 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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118A GLY 4.7 6.6 - - - +
120A PRO* 3.8 25.2 - - - +
121A GLN* 3.9 6.2 + - - +
394A LYS* 2.6 34.1 + - + +
426A CYS* 1.3 74.4 - - - +
428A ARG* 1.3 62.3 + - - +
429A ASN 4.1 0.2 + - - -
432A SER 3.8 3.6 - - - +
433A PHE* 3.8 1.0 - - - -
434A ARG* 2.9 50.7 + - + +
436A TYR* 2.9 28.9 + - + -
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Residues in contact with ARG 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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24A TYR* 3.5 31.5 - - + +
28A HIS* 4.2 8.3 - - - -
77A HIS* 4.9 0.2 + - - -
78A GLU* 3.0 52.3 + - - +
115A CYS* 4.1 5.4 - - - -
121A GLN* 3.0 55.9 + - - +
122A ARG 5.5 2.6 + - - -
419A VAL* 5.7 2.2 - - - +
426A CYS* 3.0 39.0 + - - +
427A ASP* 1.3 73.6 - - - +
429A ASN* 1.3 60.6 + - - +
430A GLY 3.8 1.1 - - - +
432A SER 3.7 3.6 - - - -
433A PHE* 3.6 33.9 - - + -
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Residues in contact with ASN 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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78A GLU 3.8 0.2 - - - -
79A GLY* 3.9 9.0 + - - -
115A CYS* 3.3 40.6 + - - +
116A GLU* 4.7 2.2 - - - +
118A GLY* 6.2 2.2 - - - -
427A ASP 4.1 1.0 + - - -
428A ARG* 1.3 72.5 - - - +
430A GLY* 1.3 62.9 + - - +
431A LYS* 3.1 4.0 + - - +
432A SER* 3.1 27.5 + - - +
434A ARG* 5.6 8.0 - - - +
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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