Contacts of the strand formed by residues 106 - 109 (chain A) in PDB entry 2XJZ
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 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 3.8 18.6 - - + +
102A ARG* 3.6 1.2 - - - +
103A VAL* 3.0 36.1 + - + +
104A LYS* 4.0 2.2 - - + +
105A ASP* 1.4 84.2 - - + +
107A VAL* 1.3 64.2 + - - +
108A TYR* 3.8 22.0 - - + +
130A LEU* 4.5 12.6 - - + -
132A ASN* 3.9 16.0 + - - +
133A SER* 3.5 25.5 - - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY* 6.1 0.2 - - - -
86A LEU 3.6 8.1 + - - +
87A CYS* 3.4 4.9 - - - -
88A ALA* 2.9 26.5 + - - +
94A ILE* 3.7 21.3 - - + -
100A THR* 3.9 16.6 - - + +
101A MET 3.7 4.9 - - - +
102A ARG* 3.9 25.8 - - + +
105A ASP 4.4 7.4 - - - +
106A LYS* 1.3 79.8 - - - +
108A TYR* 1.3 64.5 + - - +
346I MET* 3.8 24.7 - - + -
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS* 3.8 4.3 - - - -
88A ALA* 3.6 15.6 - - + +
89A SER* 3.9 28.5 - - - -
94A ILE* 4.1 6.1 - - - -
100A THR* 3.2 6.6 - - - -
101A MET* 2.9 47.1 + - + +
103A VAL* 4.4 13.9 - - + -
106A LYS* 3.8 20.0 - - + +
107A VAL* 1.3 75.4 - - - +
109A HIS* 1.4 72.0 + - - +
112A CYS 4.4 5.2 - - - -
113A PHE* 4.1 13.5 - + + +
130A LEU* 3.4 13.6 - - + +
133A SER* 2.7 37.6 + - - -
135A ILE* 3.4 27.9 - - + +
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Residues in contact with HIS 109 (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 CYS* 3.4 9.9 - - + +
90A CYS* 3.4 13.0 - - - -
92A LYS* 3.7 8.5 - - + -
93A ARG 2.9 27.9 + - - -
94A ILE* 3.5 19.0 - - + +
98A GLU* 3.1 26.4 + - + -
99A MET 4.2 4.9 - - - -
100A THR* 4.8 0.7 - - - +
108A TYR* 1.4 73.4 - - - +
110A LEU* 1.3 60.2 + - - +
111A GLU* 4.2 5.2 - - + +
112A CYS* 2.8 28.4 + - + +
113A PHE 3.2 7.4 + - - -
202A ZN 2.3 35.2 - - - -
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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
------------------------------------------------------------
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