Contacts of the strand formed by residues 153 - 164 (chain D) in PDB entry 3ZJX
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 THR 153 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 3.4 22.4 - - - +
115D ALA 3.2 3.6 - - - +
116D THR* 2.7 28.0 + - - +
151D THR 4.7 1.7 + - - -
152D ASN* 1.3 75.3 - - - +
154D ASN* 1.3 67.2 + - - +
155D THR* 4.3 7.7 + - + +
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Residues in contact with ASN 154 (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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114D THR* 3.4 1.6 - - - -
115D ALA 2.8 38.7 + - - +
144D THR* 3.5 15.5 - - + +
145D SER* 3.2 40.0 + - - +
146D TYR* 4.6 4.8 - - - +
147D SER* 4.7 4.4 - - - +
152D ASN* 4.4 17.3 + - - +
153D THR* 1.3 77.6 - - - +
155D THR* 1.3 63.8 + - - +
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D VAL 3.2 7.6 - - - -
114D THR* 4.1 19.5 - - - +
144D THR* 3.8 5.8 - - - +
153D THR* 4.3 8.5 + - + +
154D ASN* 1.3 79.8 - - - +
156D ASN* 1.3 68.4 + - - +
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Residues in contact with ASN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D THR* 3.5 2.1 - - - -
113D VAL* 3.0 39.4 + - + +
142D LEU* 4.3 8.0 - - + +
143D THR* 2.9 38.5 + - - +
144D THR* 4.2 1.6 - - + -
155D THR* 1.3 80.1 - - - +
157D SER* 1.3 79.2 + - - +
158D LYS* 5.1 8.9 - - - +
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Residues in contact with SER 157 (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 THR* 3.8 17.9 - - - +
111D ASP 3.1 13.0 - - - -
112D THR* 3.9 7.9 - - - +
142D LEU* 4.4 2.2 - - - -
156D ASN* 1.3 87.1 + - - +
158D LYS* 1.3 70.9 - - - +
159D GLU 5.6 0.2 + - - -
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Residues in contact with LYS 158 (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 THR* 3.4 3.1 - - - -
111D ASP* 2.8 41.4 + - + +
140D VAL* 3.3 27.6 - - + +
141D SER* 3.0 30.1 + - - +
142D LEU* 3.8 15.9 - - + -
156D ASN* 5.1 8.5 - - - +
157D SER* 1.3 80.3 - - - +
159D GLU* 1.3 61.8 + - - +
160D ILE* 3.3 16.5 - - + +
281D ASN* 5.3 8.1 - - - +
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Residues in contact with GLU 159 (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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108D LYS* 3.4 35.0 + - + +
109D ASN 3.5 8.7 + - - +
110D THR* 4.2 16.8 + - + +
158D LYS* 1.3 72.3 - - - +
160D ILE* 1.3 68.6 + - - +
161D THR* 4.8 5.5 - - + +
281D ASN* 3.6 33.3 + - - +
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Residues in contact with ILE 160 (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 CYS 3.9 0.9 - - - +
108D LYS* 3.3 3.5 - - - +
109D ASN* 2.6 48.9 + - + +
111D ASP* 3.2 33.0 - - + +
140D VAL* 4.6 20.9 - - + -
158D LYS* 3.3 32.8 - - + +
159D GLU* 1.3 77.1 - - - +
161D THR* 1.3 70.4 + - - +
162D ALA* 4.6 4.0 - - + +
281D ASN* 3.4 9.6 - - - +
283D VAL* 3.9 26.5 - - + -
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Residues in contact with THR 161 (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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106D THR* 5.9 2.9 - - - -
107D CYS 3.4 5.6 - - - -
108D LYS* 3.8 34.8 - - + +
159D GLU* 4.8 8.1 - - + +
160D ILE* 1.3 78.0 - - - +
162D ALA* 1.3 62.4 + - - +
163D ASN* 3.8 6.5 + - - -
281D ASN* 2.8 13.7 + - + +
282D ILE* 3.3 27.0 - - + +
283D VAL 2.9 24.8 + - - +
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Residues in contact with ALA 162 (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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105D PHE 3.8 0.2 - - - +
106D THR* 3.0 30.1 - - - -
107D CYS* 2.6 35.1 + - - +
160D ILE* 4.1 4.4 - - + +
161D THR* 1.3 72.8 - - - +
163D ASN* 1.3 60.7 + - - +
164D VAL* 3.9 5.3 - - + +
183D LEU* 6.4 0.7 - - + -
252D LEU* 5.7 0.9 - - + -
283D VAL* 3.4 7.6 - - + +
285D TYR* 3.5 28.0 - - + +
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Residues in contact with ASN 163 (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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105D PHE 3.8 3.8 - - - +
106D THR* 3.3 22.6 - - + +
161D THR* 3.8 6.8 + - - -
162D ALA* 1.3 71.8 - - - +
164D VAL* 1.3 62.8 + - - +
165D PRO* 3.8 2.5 - - - +
282D ILE* 3.6 29.7 - - - +
283D VAL 2.9 12.0 + - - +
284D LYS* 3.6 9.7 - - + +
285D TYR* 3.0 26.0 + - - -
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Residues in contact with VAL 164 (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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104D SER* 3.3 3.3 - - - -
105D PHE* 2.8 84.8 + - + +
107D CYS* 5.2 0.7 - - - -
162D ALA* 4.3 11.7 - - + +
163D ASN* 1.3 75.0 - - - +
165D PRO* 1.3 76.5 - - + +
167D GLN* 3.9 11.9 - - + +
252D LEU* 3.6 26.0 - - + -
254D VAL* 6.4 0.2 - - + -
269D ILE* 4.4 3.6 - - + -
285D TYR* 4.0 15.5 - - + -
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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