Contacts of the strand formed by residues 120 - 124 (chain A) in PDB entry 5BZR
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 ASP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A HIS* 2.7 30.9 + - + +
40A VAL 3.3 11.7 - - - +
41A GLU* 3.7 17.0 - - - +
42A LYS 4.7 0.5 + - - -
45A ARG 3.9 1.6 - - - +
46A TYR* 3.4 8.3 - - - -
48A ILE* 3.9 7.2 - - - -
82A ARG* 2.8 45.3 + - - +
83A TYR 3.0 13.3 + - - +
84A GLY* 3.2 2.9 - - - -
85A PHE* 3.1 25.6 + - - -
119A TYR* 1.3 81.8 - - - +
121A THR* 1.3 62.1 + - - +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.5 5.8 - - - -
40A VAL* 2.8 45.9 + - + +
48A ILE* 3.9 4.2 - - + +
53A ALA* 3.3 21.9 - - + +
56A LEU* 4.1 17.9 - - + -
57A CYS* 4.1 2.4 - - - -
64A LEU* 3.3 17.8 - - - +
84A GLY* 4.5 0.2 - - - -
85A PHE* 3.6 4.9 + - - +
120A ASP* 1.3 78.3 - - - +
122A TYR* 1.3 78.5 + - - +
123A CYS* 4.0 20.6 - - - -
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Residues in contact with TYR 122 (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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37A VAL* 4.5 0.7 - - + -
38A PHE 3.2 15.3 - - - +
39A HIS* 3.6 26.8 - + + -
57A CYS* 3.2 8.1 - - - -
64A LEU* 3.4 2.8 - - - +
65A PRO* 3.4 26.2 - - + +
70A MET* 3.4 20.2 - - + -
78A PHE* 3.7 20.6 - + - -
80A THR* 2.8 17.5 + - + -
82A ARG 2.7 24.0 + - - -
84A GLY* 3.4 19.3 - - - -
85A PHE 3.0 18.9 + - - +
86A ILE* 4.0 2.7 - - + -
91A VAL* 3.4 23.1 + - + -
93A PRO* 3.2 13.4 - - + +
121A THR* 1.3 87.4 + - - +
123A CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 123 (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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37A VAL* 3.2 5.5 - - - +
38A PHE* 2.9 58.0 + - + -
40A VAL* 4.2 12.8 - - - -
56A LEU 4.7 1.3 - - - -
57A CYS* 2.1 53.4 - - + -
60A PHE* 4.7 1.8 - - - -
62A SER* 4.0 3.4 - - - -
63A THR 3.4 6.3 - - - -
65A PRO* 3.7 3.4 - - - -
121A THR* 4.0 12.3 - - - -
122A TYR* 1.3 74.5 - - - +
124A PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 124 (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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35A ALA 3.4 26.2 - - - -
36A GLY* 3.3 6.3 - - - -
37A VAL* 3.9 8.1 - - + -
62A SER* 3.1 7.2 - - - -
63A THR* 2.7 46.5 + - - +
65A PRO* 4.0 14.1 - - + -
69A GLN* 3.3 44.2 - - + +
123A CYS* 1.3 74.9 - - - +
125A ASN* 1.3 68.7 + - - +
126A ALA* 3.5 33.9 + - + -
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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