Contacts of the strand formed by residues 107 - 115 (chain C) in PDB entry 4JZJ
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 ALA 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C TRP* 3.4 10.4 + - - -
106C GLY* 1.3 76.0 - - - -
108C GLU* 1.3 59.5 + - - +
110C LEU* 5.8 0.9 - - + -
124C TRP* 3.4 33.2 - - + -
125C ALA 3.4 6.7 - - - -
136C TYR* 3.7 10.0 - - + -
183C VAL* 4.0 21.5 + - + +
193C PRO 4.4 1.4 + - - -
195C THR* 2.7 31.2 + - - +
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Residues in contact with GLU 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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104C TRP* 3.5 22.7 - - + +
106C GLY 4.2 2.5 - - - +
107C ALA* 1.3 81.2 - - - +
109C ASN* 1.3 83.0 + - - +
110C LEU* 3.3 3.2 + - - +
124C TRP* 3.5 1.6 - - - -
125C ALA* 2.8 36.3 + - + +
126C VAL 4.9 2.0 - - - +
127C GLY* 4.3 3.8 - - - -
128C PRO* 3.2 32.9 - - - +
195C THR* 4.9 2.5 - - - -
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU* 1.3 95.0 + - - +
110C LEU* 1.3 64.1 + - - +
111C THR* 3.3 17.4 + - + +
123C SER* 3.5 8.8 + - - +
124C TRP* 3.8 3.3 - - - -
125C ALA* 4.2 11.9 - - + +
195C THR* 5.9 0.6 - - - +
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Residues in contact with LEU 110 (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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107C ALA* 5.8 0.2 - - + -
108C GLU 3.3 2.4 - - - +
109C ASN* 1.3 74.1 - - - +
111C THR* 1.3 63.0 + - - +
112C CYS* 4.2 7.2 - - - -
122C CYS* 4.2 18.6 - - + -
123C SER 3.4 13.5 - - - +
124C TRP* 4.2 9.0 - - + -
181C ILE* 4.4 9.9 - - + +
183C VAL* 3.6 26.2 - - + -
195C THR* 4.1 28.8 - - + +
196C ASP* 4.0 27.4 - - - -
197C LYS* 3.3 40.0 + - + +
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Residues in contact with THR 111 (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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109C ASN* 3.5 16.8 - - + +
110C LEU* 1.3 81.5 - - - +
112C CYS* 1.3 66.4 + - - +
113C TRP* 3.5 10.2 - - - -
122C CYS* 3.2 3.1 - - - +
123C SER* 2.9 47.4 + - - +
197C LYS* 4.6 6.7 - - - +
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Residues in contact with CYS 112 (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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110C LEU* 4.2 6.7 - - - -
111C THR* 1.3 77.7 - - - +
113C TRP* 1.3 67.6 + - - +
120C LEU* 4.2 10.8 - - + -
121C SER 3.3 4.0 - - - +
122C CYS* 2.1 46.7 - - - -
181C ILE* 3.8 23.1 - - + -
197C LYS* 4.9 8.8 - - - +
199C VAL* 4.4 17.7 - - + -
204C ILE* 3.6 18.8 - - + +
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Residues in contact with TRP 113 (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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111C THR* 3.5 24.2 - - - -
112C CYS* 1.3 82.0 - - - +
114C ILE* 1.3 61.4 + - - +
115C HIS* 3.5 25.5 + + + +
119C PHE 3.7 0.2 - - - +
120C LEU* 3.5 5.9 - - - +
121C SER* 2.9 62.9 + - - -
122C CYS 3.9 13.9 - - - -
123C SER* 3.6 20.4 - - - -
204C ILE* 3.3 18.1 - - - +
206C ILE* 3.3 31.3 - - + +
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Residues in contact with ILE 114 (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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113C TRP* 1.3 72.1 - - - +
115C HIS* 1.3 61.5 + - - +
116C ASP 4.8 0.4 - - - +
117C VAL 3.9 21.3 - - - +
119C PHE 3.2 6.5 - - - +
120C LEU* 3.8 24.9 - - + -
169C ILE* 4.0 14.4 - - + -
201C PHE* 3.6 36.6 - - + +
204C ILE* 3.2 22.1 + - + +
205C GLU* 3.3 22.3 - - + +
206C ILE* 2.7 31.4 + - - +
231C PHE* 4.0 14.1 - - + -
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Residues in contact with HIS 115 (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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113C TRP* 3.5 33.6 + + + +
114C ILE* 1.3 75.3 - - - +
116C ASP* 1.3 102.1 + - - +
118C ASP 3.8 0.2 + - - -
119C PHE* 2.9 53.9 + + + +
121C SER* 3.2 25.9 + - - -
165C ARG* 4.1 8.1 - - - -
206C ILE* 3.9 16.6 - - + -
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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