Contacts of the strand formed by residues 132 - 149 (chain B) in PDB entry 5FQD
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 GLU 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B TYR* 3.3 9.9 - - - -
126B SER* 3.1 37.5 + - - +
127B ASN* 2.8 44.8 + - + +
130B GLU* 3.2 21.6 - - + +
131B ARG* 1.3 71.5 - - - +
133B ALA* 1.3 60.3 + - - +
134B GLN* 4.3 6.2 + - - +
170B LEU* 5.7 0.2 - - - -
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Residues in contact with ALA 133 (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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123B LEU* 3.8 35.4 - - + -
124B ALA 3.5 17.7 - - - +
125B TYR* 4.1 4.7 - - + -
126B SER* 4.4 0.2 - - - -
131B ARG 4.0 1.6 + - - -
132B GLU* 1.3 75.4 - - - +
134B GLN* 1.3 68.5 + - - +
135B PHE 3.9 5.4 - - - +
167B VAL* 3.8 16.7 - - + +
170B LEU* 4.7 7.9 - - + +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ALA 4.3 1.2 + - - -
126B SER* 2.8 38.6 + - - -
132B GLU* 4.3 7.9 + - - +
133B ALA* 1.3 82.0 - - - +
135B PHE* 1.3 82.9 + - + +
166B LYS* 2.9 35.9 + - - +
167B VAL* 2.9 17.0 + - - -
296B ILE* 5.3 6.4 - - - +
300B LYS* 5.7 2.9 + - - -
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.0 1.2 - - - -
124B ALA* 3.1 28.6 + - + +
133B ALA* 3.9 3.5 - - - +
134B GLN* 1.3 97.0 - - + +
136B GLY* 1.3 58.5 + - - +
165B PHE 3.4 17.9 - - - +
166B LYS* 3.7 24.7 - - + -
167B VAL* 3.7 13.8 - - - +
185B LEU* 3.8 22.4 - - + -
296B ILE* 4.9 7.4 - - + -
299B LEU* 4.4 14.8 - - + -
300B LYS* 3.6 55.4 - - + -
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Residues in contact with GLY 136 (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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122B VAL 3.3 13.5 - - - -
124B ALA* 3.9 4.3 - - - -
135B PHE* 1.3 79.2 - - - +
137B THR* 1.3 63.1 + - - -
164B ARG* 3.5 2.4 - - - +
165B PHE* 2.8 45.9 + - - +
299B LEU* 4.0 10.8 - - - +
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Residues in contact with THR 137 (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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91B LEU* 2.7 34.1 + - + +
93B PRO* 4.0 21.8 - - + -
122B VAL* 2.9 35.4 + - - +
136B GLY* 1.3 76.7 + - - -
138B THR* 1.3 74.4 + - - +
161B GLY* 4.2 4.7 - - - -
162B ARG 4.1 5.2 - - - +
163B GLN 3.3 17.9 - - - +
164B ARG* 4.4 0.5 - - - -
165B PHE* 3.4 6.6 - - - -
299B LEU* 3.4 15.4 - - - +
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Residues in contact with THR 138 (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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73B HIS* 4.9 3.6 - - - +
81B ILE* 3.8 24.0 - - + -
91B LEU* 4.0 0.6 - - - +
119B THR* 3.7 18.7 - - + +
120B PHE 3.4 6.3 - - - +
137B THR* 1.3 75.5 - - - +
139B ALA* 1.3 59.9 + - - +
161B GLY* 3.3 6.2 - - - -
162B ARG* 2.9 31.5 + - - +
163B GLN* 2.8 44.6 + - + +
165B PHE* 3.8 17.3 - - + -
184B ILE* 4.3 13.0 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.6 22.4 - - + -
97B LEU* 5.1 0.4 - - + -
119B THR* 3.3 5.8 - - - -
120B PHE* 2.8 70.1 + - + -
122B VAL* 3.7 3.8 - - + -
138B THR* 1.3 74.7 - - - +
140B GLU* 1.3 60.1 + - - +
141B ILE 4.1 0.2 - - - -
159B ALA* 4.1 7.6 - - + -
160B ILE 3.3 4.9 - - - +
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Residues in contact with GLU 140 (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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69B GLY 4.3 0.4 - - - -
70B ARG* 3.5 9.3 - - - +
71B THR* 3.0 38.8 + - - +
117B ASP 4.2 3.0 - - - +
118B ARG* 3.3 29.7 + - - +
119B THR* 3.9 15.0 - - - +
139B ALA* 1.3 71.2 - - - +
141B ILE* 1.4 72.4 + - - +
142B TYR* 3.3 3.1 + - - +
159B ALA* 4.0 1.3 - - - -
160B ILE* 2.8 35.4 + - - +
162B ARG* 3.0 48.1 + - + +
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Residues in contact with ILE 141 (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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67B PHE* 3.8 2.5 - - + -
110B VAL* 4.5 14.4 - - + -
113B LEU* 3.8 30.3 - - + -
114B ILE* 3.5 36.3 - - + -
118B ARG* 2.9 52.9 + - + +
120B PHE* 3.6 20.6 - - + -
140B GLU* 1.4 68.4 - - - +
142B TYR* 1.3 58.9 + - - +
143B ALA 3.3 26.9 - - - +
157B VAL* 3.8 15.3 - - + -
158B LYS 3.6 8.3 - - - +
159B ALA* 4.1 1.3 - - - +
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Residues in contact with TYR 142 (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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55B THR 5.6 1.0 + - - -
57B HIS* 5.5 0.5 - - - -
66B GLU* 3.5 6.1 - - + +
67B PHE* 3.0 37.0 + - - +
70B ARG* 4.0 26.5 - - - +
96B THR* 3.0 27.0 + - + +
118B ARG* 4.6 0.7 - - - +
140B GLU 3.3 2.4 + - - +
141B ILE* 1.3 73.9 - - - +
143B ALA* 1.3 63.6 + - + +
158B LYS* 3.0 41.8 + - + +
159B ALA 3.5 30.1 - - - -
160B ILE* 3.9 22.0 - - + -
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Residues in contact with ALA 143 (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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64B MET* 3.9 17.5 - - + -
65B GLU 3.2 12.8 - - - +
66B GLU* 4.7 7.9 - - + -
67B PHE* 4.4 1.3 - - - -
141B ILE* 3.3 12.9 - - - +
142B TYR* 1.3 86.6 - - + +
144B TYR* 1.3 61.6 + - - +
157B VAL* 3.5 0.3 - - - -
158B LYS* 2.9 47.9 + - + +
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Residues in contact with TYR 144 (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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64B MET* 3.8 6.0 - - - +
65B GLU* 2.9 66.6 + - + +
67B PHE* 3.4 40.2 - + - -
114B ILE* 4.1 28.2 - - + +
143B ALA* 1.3 75.7 - - - +
145B ARG* 1.3 67.7 + - - +
146B GLU* 3.6 33.8 + - + -
155B VAL* 4.7 4.7 - - + -
156B LYS 3.2 12.8 - - - +
157B VAL* 4.2 11.2 - - + -
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Residues in contact with ARG 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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60B LEU 5.7 0.7 - - - -
62B ALA* 3.6 40.9 - - - +
63B ASP 3.7 17.3 + - - +
64B MET* 4.1 13.5 - - + -
65B GLU* 4.7 11.8 + - - +
144B TYR* 1.3 80.5 - - - +
146B GLU* 1.3 73.3 + - - +
147B GLU* 3.3 31.9 + - - +
154B ILE 3.8 0.9 - - - +
155B VAL* 3.4 3.7 - - - -
156B LYS* 2.9 41.2 + - + +
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Residues in contact with GLU 146 (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 VAL* 5.7 1.2 - - + +
111B ARG* 3.3 38.3 + - + +
144B TYR* 3.6 27.1 + - + -
145B ARG* 1.3 81.9 + - - +
147B GLU* 1.3 63.9 + - - +
153B GLU* 4.4 12.4 - - - +
154B ILE 3.4 6.3 - - - +
155B VAL* 4.0 16.8 - - + -
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Residues in contact with GLU 147 (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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60B LEU 4.3 1.7 - - - +
61B GLY* 5.6 0.3 - - - -
62B ALA 5.4 1.7 + - - -
145B ARG* 3.3 36.9 + - + +
146B GLU* 1.3 80.3 - - - +
148B GLN* 1.4 58.9 + - - +
149B ASP* 3.0 29.3 + - - +
152B ILE 3.5 1.0 - - - +
153B GLU* 3.5 6.2 - - - -
154B ILE* 2.8 42.3 + - + +
156B LYS* 3.0 42.0 + - + +
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Residues in contact with GLN 148 (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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147B GLU* 1.4 72.1 - - - +
149B ASP* 1.4 58.1 + - - +
150B PHE 3.6 3.3 + - - -
151B GLY* 3.7 31.5 + - - +
152B ILE 3.5 10.3 - - - +
153B GLU* 3.4 25.1 + - + +
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Residues in contact with ASP 149 (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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147B GLU* 3.0 31.5 - - + +
148B GLN* 1.4 69.9 - - - +
150B PHE* 1.4 88.3 + - + +
152B ILE* 3.1 32.0 + - - +
154B ILE* 4.4 15.4 - - + +
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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