Contacts of the strand formed by residues 119 - 125 (chain D) 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 PHE 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D ILE* 3.2 8.1 - - - +
115D HIS* 3.0 61.4 + + + +
116D ASP* 4.2 16.4 - - + -
117D VAL 3.6 0.4 - - - -
118D ASP* 1.3 96.9 - - + +
120D LEU* 1.3 59.8 + - - +
165D ARG* 4.3 13.9 - - + -
166D PHE 3.4 14.6 - - - +
167D ASP* 3.6 31.9 - - + -
168D ASP 4.5 2.9 - - - -
169D ILE* 3.6 3.9 - - - +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D CYS* 4.3 5.2 - - + -
113D TRP 3.4 20.6 - - - +
114D ILE* 3.7 15.0 - - + -
119D PHE* 1.3 73.0 - - - +
121D SER* 1.3 74.5 + - - +
122D CYS* 4.7 3.8 - - - -
140D LEU* 3.6 31.4 - - + -
165D ARG* 3.2 1.7 - - - -
166D PHE* 2.6 50.8 + - + -
169D ILE* 3.5 14.0 - - + +
181D ILE* 4.4 12.1 - - + -
199D VAL* 5.5 1.3 - - + -
201D PHE* 4.3 17.0 - - + -
204D ILE* 3.9 11.9 - - + -
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D CYS* 3.2 3.5 - - - +
113D TRP* 3.0 48.3 + - - -
115D HIS* 3.3 25.5 + - - -
119D PHE 4.1 0.4 - - - -
120D LEU* 1.3 73.2 - - - +
122D CYS* 1.3 66.3 + - - +
164D CYS 3.1 8.4 + - - -
165D ARG* 3.5 20.4 - - - +
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Residues in contact with CYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.3 2.2 - - + -
111D THR 3.3 6.5 - - - -
112D CYS* 2.1 39.9 - - - -
113D TRP* 4.2 3.8 - - - -
120D LEU* 4.7 11.4 - - - -
121D SER* 1.3 76.7 - - - +
123D SER* 1.3 66.5 + - - +
124D TRP* 4.0 4.3 - - + -
138D LEU* 3.9 32.8 - - + -
163D GLY* 3.3 3.3 - - - -
164D CYS* 2.9 31.9 + - + +
166D PHE* 5.6 1.1 - - - -
181D ILE* 4.3 6.1 - - - -
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ASN 3.3 2.6 + - - +
110D LEU* 3.5 2.6 - - - +
111D THR* 3.0 31.7 + - - -
113D TRP* 3.2 26.9 - - - -
122D CYS* 1.3 78.8 - - - +
124D TRP* 1.3 68.5 + - - +
154D LYS* 6.4 0.9 - - - -
162D ILE 3.2 12.8 - - - -
163D GLY* 4.7 1.1 - - - -
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Residues in contact with TRP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ALA* 3.8 26.2 - - + -
108D GLU 3.3 15.7 - - - +
109D ASN* 4.0 3.8 - - - -
110D LEU* 4.0 17.5 - - + -
122D CYS* 4.0 3.8 - - + -
123D SER* 1.3 86.1 - - - +
125D ALA* 1.3 70.0 + - - +
136D TYR* 3.7 15.7 - + + +
138D LEU* 3.6 34.8 - - + -
153D TYR* 4.5 5.8 - + - -
161D ARG* 2.7 37.4 + - + -
162D ILE* 3.0 26.8 + - + +
163D GLY* 3.4 40.2 - - - -
164D CYS* 3.9 3.1 - - + -
183D VAL* 4.2 15.0 - - + -
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ALA* 3.5 6.1 - - - -
108D GLU* 2.8 44.1 + - + +
109D ASN* 4.9 9.4 - - + +
124D TRP* 1.3 79.6 - - - +
126D VAL* 1.3 66.7 + - - +
127D GLY 3.5 0.5 + - - -
162D ILE* 4.8 2.5 - - - -
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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