Contacts of the strand formed by residues 105 - 119 (chain B) 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 PHE 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B VAL* 3.9 18.6 - - + -
103B GLN* 3.6 15.0 - - + -
104B SER* 1.3 75.3 + - - +
106B THR* 1.3 75.2 + - - +
107B CYS* 5.0 2.2 - - - -
163B ASN* 3.7 0.7 - - - +
164B VAL* 2.8 74.3 + - + +
165B PRO 4.9 2.0 - - - -
181B ALA* 4.1 18.8 - - + -
252B LEU* 4.6 9.9 - - + -
254B VAL* 5.4 2.5 - - + -
1296B BOG 3.3 72.7 - - + +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 1.3 82.1 - - - +
107B CYS* 1.3 67.8 + - - +
108B LYS* 5.9 3.1 - - - +
161B THR* 5.9 3.1 - - - -
162B ALA 3.0 9.2 - - - -
163B ASN* 3.3 23.8 - - - +
1296B BOG 3.2 44.4 + - - +
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Residues in contact with CYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 3.8 36.3 - - + -
105B PHE* 5.0 4.5 - - - -
106B THR* 1.3 76.5 - - - +
108B LYS* 1.3 67.4 + - - +
160B ILE 3.9 0.3 - - - +
161B THR* 3.4 1.7 - - - -
162B ALA* 2.6 55.3 + - - +
164B VAL* 5.2 0.2 - - - -
183B LEU* 5.1 14.8 - - - -
252B LEU* 4.8 12.8 - - - -
1296B BOG 5.0 7.9 - - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 5.6 5.4 - - - +
106B THR* 5.9 3.4 - - - +
107B CYS* 1.3 83.8 - - - +
109B ASN* 1.3 63.6 + - - +
159B GLU* 3.6 29.7 + - + +
160B ILE 3.3 5.4 - - - +
161B THR* 3.8 22.0 - - + +
183B LEU* 5.4 0.9 - - - +
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 5.0 2.8 - - - +
108B LYS* 1.3 77.9 - - - +
110B THR* 1.3 69.8 + - - +
111B ASP* 3.0 28.1 + - - -
158B LYS 3.8 0.2 - - - +
159B GLU* 3.5 2.4 - - - +
160B ILE* 2.6 50.6 + - + +
183B LEU* 3.8 23.9 - - + +
185B LYS* 3.7 22.3 - - - +
247B VAL* 5.9 0.2 - - - +
249B GLY* 3.6 15.5 - - - +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN* 1.3 85.5 + - - +
111B ASP* 1.3 72.3 + - - +
112B THR* 3.8 14.7 + - + +
157B SER* 3.8 20.4 - - - +
158B LYS 3.4 9.2 - - - +
159B GLU* 4.2 17.3 + - + +
247B VAL* 4.3 9.7 - - - +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN* 3.0 12.7 + - - +
110B THR* 1.3 72.5 - - - +
112B THR* 1.3 58.9 + - - +
138B THR* 4.3 18.0 + - - +
140B VAL* 4.8 5.7 - - - +
142B LEU* 4.0 7.6 - - + +
157B SER* 3.1 6.9 - - - -
158B LYS* 2.8 39.1 + - + +
160B ILE* 3.2 23.0 - - + +
247B VAL 3.2 6.3 - - - +
248B MET* 3.8 20.6 - - + +
249B GLY 2.9 29.6 + - - -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.8 22.4 + - + +
111B ASP* 1.3 78.6 - - - +
113B VAL* 1.3 63.0 + - - +
142B LEU* 3.5 8.1 - - - +
156B ASN 3.5 7.2 - - - -
157B SER* 4.0 8.3 - - - -
245B SER 5.2 1.0 + - - -
246B ALA* 3.1 7.5 - - - +
247B VAL* 2.9 50.1 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B THR* 1.3 78.8 - - - +
114B THR* 1.3 69.3 + - - +
131B PHE* 4.9 7.2 - - + -
133B VAL* 3.7 27.6 - - + -
142B LEU* 3.7 20.6 - - + -
143B THR 4.4 2.9 - - - +
144B THR* 4.0 27.6 - - + -
154B ASN 4.5 0.4 - - - -
155B THR* 3.2 7.1 - - - -
156B ASN* 3.0 48.4 + - + +
244B TYR* 4.9 1.6 - - + -
245B SER 3.6 6.1 - - - +
246B ALA* 4.1 6.3 - - + +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 1.3 76.5 - - - +
115B ALA* 1.3 62.7 + - - +
116B THR* 4.5 2.1 + - - -
153B THR* 3.4 22.9 - - - +
154B ASN 3.4 4.0 + - - -
155B THR* 4.1 11.5 - - - +
244B TYR* 3.2 6.4 - - - +
245B SER* 3.0 48.8 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 1.3 76.7 + - - +
116B THR* 1.3 62.3 + - - +
144B THR* 3.5 27.8 - - + -
145B SER 4.3 6.9 - - - +
146B TYR* 3.6 28.0 - - + +
152B ASN 3.8 0.7 - - - +
153B THR* 3.2 2.8 - - - -
154B ASN* 2.8 38.5 + - - +
243B ASN 3.4 4.9 - - - -
244B TYR* 4.7 2.5 - - + -
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 4.5 2.1 + - - -
115B ALA* 1.3 71.4 - - - +
117B THR* 1.3 75.4 + - - +
118B THR* 3.4 10.1 + - + +
146B TYR* 3.5 4.4 - - - -
151B THR* 4.9 2.9 - - - +
152B ASN 3.3 6.1 - - - +
153B THR* 2.7 36.9 + - - +
242B GLY* 3.1 2.8 - - - -
243B ASN* 3.0 43.4 + - - +
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B THR* 1.3 80.0 - - - +
118B THR* 1.3 61.2 + - - +
119B HIS 4.0 17.9 - - - +
120B THR* 4.0 9.4 - - + +
146B TYR* 3.6 16.9 - - - -
147B SER* 2.8 29.0 + - - +
150B ASN 3.3 25.1 + - - +
151B THR* 3.5 20.0 - - - -
152B ASN 3.1 8.8 + - - -
194B LEU* 3.8 7.3 - - + +
241B LYS 3.7 12.6 - - - +
242B GLY* 4.1 1.6 - - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR* 3.4 13.9 + - + +
117B THR* 1.3 75.3 - - - +
119B HIS* 1.3 80.4 + - - +
120B THR 4.2 0.7 - - - -
151B THR* 4.3 9.9 - - - +
241B LYS* 3.0 27.2 + - - +
242B GLY* 3.3 4.4 + - - -
243B ASN* 3.8 28.0 - - - +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B THR* 4.0 3.4 - - - +
118B THR* 1.3 110.1 + - - +
120B THR* 1.3 68.5 + - - +
194B LEU* 4.9 0.5 - - - +
240B GLY* 3.2 3.5 - - - -
241B LYS* 2.9 55.5 + - + +
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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