Contacts of the strand formed by residues 83 - 88 (chain A) in PDB entry 2Z53
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 LYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.5 9.3 - - - -
80A TYR* 3.0 38.9 + - - +
81A ASN* 3.1 29.0 - - + +
82A GLY* 1.3 77.9 - - - +
84A CYS* 1.3 63.5 + - - +
85A ARG* 3.5 1.1 + - + -
110A SER* 3.6 17.9 - - - +
111A ARG* 4.3 13.9 - - - +
112A GLU* 3.8 31.6 + - + +
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Residues in contact with CYS 84 (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 SER* 4.3 2.2 - - - -
78A ASP 3.8 4.5 - - - -
79A LEU* 4.8 1.7 - - - +
83A LYS* 1.3 70.7 - - - +
85A ARG* 1.3 60.6 + - - +
104A LEU 3.4 13.2 - - - -
105A CYS* 2.1 50.8 - - + -
107A ASN* 5.7 1.3 - - + +
110A SER 3.0 14.5 + - - +
111A ARG* 3.1 5.4 - - + +
112A GLU 2.9 23.1 + - - -
502A EDO 4.0 22.4 - - - -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.1 25.1 - - - -
78A ASP* 2.7 53.9 + - - +
80A TYR* 3.6 35.7 - - + +
83A LYS 3.5 1.3 + - - +
84A CYS* 1.3 71.8 - - - +
86A TYR* 1.3 60.3 + - - +
87A HIS* 3.5 18.1 + - - +
105A CYS* 4.2 1.6 - - - -
112A GLU* 3.2 24.0 - - + +
114A LYS* 3.5 30.0 - - + +
151A ILE* 3.4 8.7 + - - +
154A VAL 2.8 23.4 + - - +
155A SER* 3.0 31.5 + - - +
157A PHE* 3.9 6.3 - - - -
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Residues in contact with TYR 86 (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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76A TYR 3.8 3.1 - - - -
77A SER* 4.5 0.7 - - - +
85A ARG* 1.3 74.1 - - - +
87A HIS* 1.3 59.7 + - - +
88A ILE* 3.9 24.7 + - + -
101A GLU* 3.3 38.8 + - + -
104A LEU* 4.3 16.4 - - + -
105A CYS* 3.9 27.6 - - + -
111A ARG* 3.9 18.0 + - + +
112A GLU* 2.9 32.7 + - - -
113A LYS* 3.6 34.3 + - + +
114A LYS 2.9 26.4 + - - -
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Residues in contact with HIS 87 (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 GLY* 3.0 5.9 - - - -
76A TYR* 2.8 90.3 + + + +
78A ASP* 2.7 23.4 + - - -
85A ARG* 3.5 28.2 + - + +
86A TYR* 1.3 72.2 - - - +
88A ILE* 1.3 62.5 + - - +
104A LEU* 5.6 0.2 - - - -
114A LYS* 3.0 47.9 + - + +
115A ALA 5.1 0.2 + - - -
116A ILE* 3.5 11.2 - - + +
151A ILE* 5.2 0.2 - - + -
157A PHE* 3.9 5.4 - + - -
162A GLU* 4.2 3.4 + - - -
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Residues in contact with ILE 88 (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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74A MET 3.7 12.6 - - - +
75A GLY* 4.2 0.2 - - - -
86A TYR* 3.9 31.0 + - + -
87A HIS* 1.3 76.5 - - - +
89A PHE* 1.3 77.7 + - - +
90A ASN* 3.7 0.5 + - - -
92A ILE* 4.1 9.9 - - + -
97A SER* 3.5 45.1 - - - +
100A VAL* 3.5 24.9 - - + -
101A GLU* 4.0 2.2 - - + +
113A LYS* 6.5 0.2 - - + -
115A ALA* 4.0 8.2 - - + +
116A ILE* 3.0 25.7 + - - +
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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