Contacts of the strand formed by residues 106 - 109 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA* 3.7 17.2 - - + +
102C ARG* 3.7 3.6 - - - +
103C VAL 2.9 34.5 + - - +
104C LYS 4.0 1.6 - - - +
105C ASP* 1.4 97.5 - - - +
107C VAL* 1.3 62.5 + - - +
108C TYR* 3.8 15.3 - - + +
130C LEU* 4.8 8.3 - - + -
132C ASN* 3.8 16.4 - - - +
133C SER* 3.3 38.0 - - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLY* 4.7 1.3 - - - -
86C LEU 3.5 25.8 - - - +
87C CYS* 3.5 1.0 - - - -
88C ALA* 2.8 28.9 + - - +
94C ILE* 3.7 13.5 - - + -
100C THR* 3.3 33.2 - - + -
101C MET 3.6 3.6 - - - -
102C ARG* 3.7 17.5 - - + +
105C ASP 5.3 1.8 - - - +
106C LYS* 1.3 73.7 - - - +
108C TYR* 1.3 60.9 + - - +
346K MET* 4.1 20.6 - - + -
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C CYS* 3.9 3.4 - - - -
88C ALA* 3.6 15.2 - - + +
89C SER* 3.8 28.7 - - - -
94C ILE* 3.8 5.8 - - - -
100C THR* 3.4 4.5 + - - -
101C MET* 2.8 42.6 + - + +
103C VAL* 4.0 16.2 - - + -
106C LYS* 3.8 19.5 - - + +
107C VAL* 1.3 77.5 - - - +
109C HIS* 1.3 73.1 + - - +
110C LEU 3.3 0.2 + - - -
112C CYS* 4.4 9.9 - - + -
113C PHE* 4.3 15.3 - + + +
130C LEU* 3.5 10.7 - - - +
133C SER* 2.7 42.7 + - - -
135C ILE* 3.7 24.7 - - + -
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Residues in contact with HIS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C CYS* 3.5 9.7 - - - +
90C CYS* 3.4 12.8 - - - -
92C LYS* 3.7 9.2 - - + -
93C ARG 2.8 28.9 + - - -
94C ILE* 3.5 18.7 - - + +
98C GLU* 3.2 25.5 + - + -
99C MET 4.1 5.2 - - - -
100C THR* 4.8 0.2 - - - -
108C TYR* 1.3 74.6 - - - +
110C LEU* 1.3 57.1 + - - +
111C GLU* 4.2 4.9 - - + +
112C CYS* 2.8 31.3 + - - +
113C PHE 3.2 7.6 + - - -
202C ZN 2.1 35.7 - - - -
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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