Contacts of the strand formed by residues 144 - 160 (chain B) in PDB entry 5O67
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 ARG 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ASP* 5.1 4.3 - - - +
121B ALA 3.3 18.6 - - - +
122B ARG* 4.9 0.9 - - + -
142B LEU* 3.8 1.6 - - - +
143B ASP* 1.3 83.7 - - + +
145B ILE* 1.3 69.4 + - - +
146B LYS* 4.1 12.1 - - + +
180B GLN* 3.2 35.5 + - + +
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Residues in contact with ILE 145 (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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119B TYR* 4.1 2.9 - - - +
120B ASP* 3.8 3.3 + - - -
121B ALA* 3.3 37.9 + - + +
142B LEU* 3.8 24.9 - - + -
144B ARG* 1.3 82.5 - - - +
146B LYS* 1.3 68.0 + - - +
147B ALA* 5.1 2.8 - - + +
177B SER* 5.1 3.1 - - - -
178B THR 3.3 10.1 - - - +
179B TYR* 3.9 35.7 - - + +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A SER* 4.2 17.6 + - - +
361A ASP* 3.3 39.3 + - - +
392A ASP* 5.7 3.4 - - - -
118B ARG* 3.8 26.5 - - - +
119B TYR 3.5 6.7 - - - +
120B ASP* 3.8 23.1 - - - +
144B ARG* 5.5 8.7 - - + -
145B ILE* 1.3 76.0 - - - +
147B ALA* 1.3 62.9 + - - +
177B SER* 3.4 4.9 - - - -
178B THR* 2.9 55.0 + - + +
180B GLN* 6.0 5.2 - - - -
194B GLU* 6.2 1.6 - - - -
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 3.7 1.4 - - - +
118B ARG* 3.7 4.3 - - - +
119B TYR* 3.1 46.1 + - + +
145B ILE* 5.1 4.0 - - + +
146B LYS* 1.3 77.2 - - - +
148B ASP* 1.3 69.8 + - - +
149B ASN* 4.0 12.8 - - - +
175B ARG* 5.9 2.2 - - - +
176B GLU 3.4 6.5 - - - -
177B SER* 3.7 13.9 - - - +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.0 30.0 + - + -
117B ALA 3.9 2.2 - - - -
118B ARG* 2.7 32.2 + - - -
147B ALA* 1.3 72.5 - - - +
149B ASN* 1.3 64.5 + - - +
150B TRP* 4.2 7.3 - - + +
174B TYR 4.0 0.5 - - - +
175B ARG* 3.5 2.8 - - - -
176B GLU* 3.0 48.4 + - + +
502B LDA 3.7 22.3 - - + +
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR 3.5 1.2 - - - +
116B TYR* 3.4 6.6 - - - -
117B ALA* 2.9 45.9 + - + +
119B TYR* 4.1 18.2 + - + -
147B ALA* 4.0 14.6 - - - +
148B ASP* 1.3 85.4 + - - +
150B TRP* 1.3 64.4 + - - +
151B THR* 5.0 4.0 + - - +
174B TYR 3.7 3.6 - - - -
175B ARG* 3.5 37.0 + - + +
176B GLU 5.1 0.4 + - - -
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Residues in contact with TRP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 4.1 28.7 - - + -
115B THR 3.3 12.8 - - - -
116B TYR* 3.5 41.3 - + + -
148B ASP* 4.7 4.2 - - + +
149B ASN* 1.3 80.0 - - - +
151B THR* 1.3 67.5 + - - +
173B VAL* 3.9 1.2 - - - +
174B TYR* 3.0 60.5 + + + +
502B LDA 3.7 57.9 + - + +
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Residues in contact with THR 151 (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 GLY 3.5 1.2 - - - +
114B ILE* 3.1 10.4 - - - +
115B THR* 2.9 44.9 + - - +
149B ASN* 5.0 4.7 - - - +
150B TRP* 1.3 81.0 + - - +
152B LEU* 1.3 66.3 + - - +
153B ASP* 3.6 21.0 - - - +
171B PRO* 4.2 14.6 - - + -
172B VAL 3.4 11.0 - - - +
173B VAL* 4.3 12.0 - - + +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 4.2 20.0 - - + -
113B GLY 3.2 13.5 - - - +
114B ILE* 4.0 16.1 - - + +
151B THR* 1.3 75.6 - - - +
153B ASP* 1.3 60.1 + - - +
154B LEU* 4.3 18.8 - - + -
170B VAL 3.8 0.9 - - - +
171B PRO* 3.4 2.4 - - - +
172B VAL* 2.8 57.0 + - + +
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 3.5 7.4 - - - +
113B GLY* 2.7 42.9 + - - +
115B THR* 4.7 8.8 + - - -
151B THR* 3.6 18.6 - - - +
152B LEU* 1.3 74.6 - - - +
154B LEU* 1.3 65.1 + - - +
155B THR* 4.1 6.7 - - - +
169B ASN* 2.8 31.9 + - - +
170B VAL 3.7 2.2 - - - -
171B PRO* 4.2 6.7 - - - +
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Residues in contact with LEU 154 (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 PHE* 4.3 18.4 - - + -
111B GLU 3.9 2.2 - - - -
112B THR* 4.3 14.8 - - + +
152B LEU* 4.3 22.2 - - + -
153B ASP* 1.3 80.3 - - - +
155B THR* 1.3 59.8 + - - +
168B VAL* 4.0 0.5 - - - +
169B ASN* 3.3 1.7 + - - -
170B VAL* 2.8 49.6 + - + +
172B VAL* 4.3 19.7 - - + -
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Residues in contact with THR 155 (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 PHE* 3.0 22.5 - - - -
111B GLU* 3.0 50.5 + - - +
153B ASP* 4.2 6.1 - - - +
154B LEU* 1.3 76.9 + - - +
156B GLY* 1.3 58.3 + - - +
157B ARG* 4.4 11.2 + - - +
167B ASP* 3.1 29.4 - - - +
168B VAL 3.3 9.4 - - - +
169B ASN* 3.6 22.9 + - + +
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Residues in contact with GLY 156 (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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108B PHE* 4.7 10.1 - - - -
109B SER 3.7 6.5 - - - -
110B PHE* 4.2 7.6 - - - -
155B THR* 1.3 74.2 - - - +
157B ARG* 1.3 62.0 + - - +
167B ASP* 3.3 2.5 - - - +
168B VAL* 2.8 37.5 + - - +
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Residues in contact with ARG 157 (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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101B GLY* 5.0 10.6 + - - -
103B ALA* 4.4 12.1 - - - +
107B LYS 3.9 0.9 - - - +
108B PHE* 3.3 8.7 - - - -
109B SER* 2.9 57.0 + - - +
111B GLU* 2.8 42.9 + - + +
155B THR* 4.8 7.4 - - - +
156B GLY* 1.3 77.0 - - - +
158B TYR* 1.3 61.4 + - - +
159B ASN* 4.2 1.1 - - - +
165B GLN* 3.6 34.3 + - - +
166B PHE 3.2 12.1 - - - +
167B ASP* 3.8 25.3 + - + +
405B TYR* 5.9 0.2 - - - -
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Residues in contact with TYR 158 (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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107B LYS* 3.2 47.8 - - + +
108B PHE* 4.0 21.8 - + + -
157B ARG* 1.3 73.5 - - - +
159B ASN* 1.3 69.6 + - - +
160B LEU* 3.9 26.2 - - + +
165B GLN* 3.4 5.5 - - - -
166B PHE* 2.8 56.5 + + + +
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Residues in contact with ASN 159 (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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102B PHE* 3.5 13.8 - - - -
103B ALA* 2.9 36.9 + - + +
104B GLY* 4.1 3.5 - - - +
106B GLY 3.9 10.4 - - - +
107B LYS* 2.7 34.5 + - - +
157B ARG* 4.2 1.2 - - - +
158B TYR* 1.3 82.6 - - - +
160B LEU* 1.3 70.3 + - - +
161B ASP 4.1 0.9 + - - -
162B ASN* 3.5 26.2 + - - -
164B TRP 3.6 6.0 - - - +
165B GLN* 3.1 30.1 + - + +
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Residues in contact with LEU 160 (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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158B TYR* 3.9 28.3 - - + +
159B ASN* 1.3 73.4 + - - +
161B ASP* 1.3 76.8 + - - +
162B ASN 3.2 1.1 - - - -
163B ARG* 2.8 27.4 + - + +
164B TRP* 2.8 48.5 + - + +
166B PHE* 4.8 10.3 - - + -
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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