Contacts of the strand formed by residues 152 - 172 (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 ILE 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B PHE* 5.1 10.5 - - + +
147B GLU 3.5 0.5 - - - +
148B GLN* 4.2 3.1 - - - -
149B ASP 3.1 47.4 + - - +
150B PHE* 3.1 15.9 - - + +
151B GLY* 1.4 82.8 - - - +
153B GLU* 1.3 62.0 + - - +
154B ILE* 3.5 27.3 + - + +
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Residues in contact with GLU 153 (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 3.9 4.7 - - - +
107B VAL* 3.7 20.6 - - + +
111B ARG* 3.3 31.3 + - - +
146B GLU* 4.4 17.0 - - - +
147B GLU 3.5 5.6 - - - -
148B GLN* 3.4 34.4 + - + +
151B GLY 4.3 0.6 + - - +
152B ILE* 1.3 71.6 - - - +
154B ILE* 1.3 69.1 + - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLN* 4.5 10.8 - - - +
101B LEU 3.6 8.5 - - - +
102B PHE* 3.4 55.4 - - + +
107B VAL* 4.7 0.9 - - - -
145B ARG 3.8 0.9 - - - +
146B GLU* 3.4 3.5 - - - +
147B GLU* 2.8 44.6 + - + +
149B ASP* 4.4 13.9 - - + +
152B ILE* 3.6 33.7 - - + +
153B GLU* 1.3 85.8 - - - +
155B VAL* 1.3 67.6 + - - +
156B LYS* 4.2 10.1 - - + -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU 4.0 0.3 - - - +
100B GLN* 3.7 0.3 - - - -
101B LEU* 2.8 61.9 + - + +
107B VAL* 3.9 28.7 - - + +
110B VAL* 4.1 27.8 - - + -
111B ARG* 6.3 1.3 - - + -
144B TYR* 4.7 4.3 - - + -
145B ARG 3.4 13.0 - - - +
146B GLU* 4.0 20.0 - - + -
154B ILE* 1.3 75.6 - - - +
156B LYS* 1.3 69.6 + - - +
157B VAL* 4.2 3.8 - - + -
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Residues in contact with LYS 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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60B LEU* 2.8 37.3 + - + +
61B GLY* 4.9 1.2 - - - -
64B MET* 3.6 20.4 - - + -
99B LEU 3.3 7.6 - - - +
100B GLN* 3.5 37.7 - - + +
144B TYR* 3.2 4.2 - - - +
145B ARG* 2.9 36.8 + - + +
147B GLU* 3.0 38.9 + - + +
149B ASP* 5.1 0.8 + - - -
154B ILE* 4.8 8.1 - - + -
155B VAL* 1.3 74.2 - - - +
157B VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 5.2 0.7 - - - +
64B MET* 4.3 3.1 - - - +
98B PRO* 3.4 3.6 - - - +
99B LEU* 2.8 58.4 + - + +
101B LEU* 5.2 2.0 - - + -
110B VAL* 3.9 33.4 - - + -
120B PHE* 4.8 1.1 - - + -
141B ILE* 3.8 27.8 - - + -
143B ALA 3.5 3.8 - - - -
144B TYR* 4.2 11.9 - - + +
155B VAL* 4.1 7.6 + - + +
156B LYS* 1.3 79.9 - - - +
158B LYS* 1.3 71.2 + - - +
159B ALA* 4.2 4.5 - - + +
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Residues in contact with LYS 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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55B THR 5.1 1.2 + - - -
56B SER* 3.2 27.2 + - - +
57B HIS* 4.0 24.0 + - + -
60B LEU* 4.4 8.5 - - + -
64B MET* 4.0 21.7 - - + +
96B THR* 4.8 2.0 - - + -
97B LEU 3.7 3.6 - - - -
98B PRO* 4.8 7.2 - - + -
141B ILE* 3.6 2.3 - - - -
142B TYR* 3.0 56.2 + - + +
143B ALA* 2.9 29.0 + - + +
157B VAL* 1.3 77.5 - - - +
159B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 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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96B THR* 3.4 4.5 - - - -
97B LEU* 2.8 41.9 + - + +
120B PHE* 3.7 36.6 - - + -
139B ALA* 4.1 8.7 - - + -
140B GLU 3.4 11.9 - - - +
141B ILE* 4.2 2.0 - - - +
142B TYR* 3.5 7.0 - - - -
157B VAL* 4.1 3.6 - - + -
158B LYS* 1.3 73.7 - - - +
160B ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 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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91B LEU* 4.5 1.6 - - - -
94B GLY* 3.7 23.1 - - - +
95B GLN 3.3 12.6 - - - +
96B THR* 4.8 5.6 - - - +
139B ALA* 3.3 3.6 - - - -
140B GLU* 2.8 36.6 + - + +
142B TYR* 3.9 20.0 - - + -
159B ALA* 1.3 75.1 - - - +
161B GLY* 1.3 74.7 + - - +
162B ARG* 3.2 45.9 + - - +
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Residues in contact with GLY 161 (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* 3.7 16.6 - - - +
92B ILE 3.8 13.5 - - - -
93B PRO* 3.6 3.4 - - - -
94B GLY* 2.7 26.5 + - - -
95B GLN 3.0 12.9 + - - -
137B THR* 4.2 0.9 - - - -
138B THR 3.3 9.9 - - - -
160B ILE* 1.3 76.2 - - - +
162B ARG* 1.3 64.7 + - - +
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Residues in contact with ARG 162 (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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70B ARG* 3.5 28.8 - - - +
71B THR 4.5 3.8 - - - +
72B LEU* 4.2 19.8 - - + +
93B PRO* 3.3 21.1 - - - +
94B GLY* 5.7 0.6 - - - -
119B THR* 6.1 1.6 - - + -
137B THR* 4.1 1.0 - - - +
138B THR* 2.9 20.4 + - - +
139B ALA 4.9 0.2 - - - -
140B GLU* 3.0 41.5 + - + +
160B ILE* 3.2 57.4 - - - +
161B GLY* 1.3 75.0 + - - -
163B GLN* 1.3 69.0 + - + +
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Residues in contact with GLN 163 (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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71B THR 4.6 1.4 - - - +
72B LEU* 3.7 26.5 - - + +
73B HIS* 2.8 59.0 + - - +
75B ASP* 4.5 6.1 + - - -
93B PRO* 4.7 0.4 - - - -
137B THR* 3.3 5.4 - - - -
138B THR* 2.8 45.1 + - - +
162B ARG* 1.3 78.5 - - + +
164B ARG* 1.3 67.1 + - - +
165B PHE* 4.1 0.2 - - - -
184B ILE* 3.5 25.3 - - + +
185B LEU 5.8 0.7 - - - +
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Residues in contact with ARG 164 (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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93B PRO* 3.8 19.9 - - + +
136B GLY 3.5 7.9 - - - +
137B THR* 4.4 1.8 - - - +
163B GLN* 1.3 73.2 - - - +
165B PHE* 1.3 64.0 + - - +
184B ILE* 3.8 5.5 - - - +
185B LEU* 3.0 59.8 + - + +
186B PRO 2.9 31.3 + - - -
187B GLU* 3.9 4.4 + - - -
282B TYR* 2.9 29.2 + - - +
299B LEU* 3.1 43.5 + - + +
300B LYS 3.9 5.3 + - - -
301B ILE 3.4 18.1 + - - -
302B GLY* 3.3 16.0 - - - -
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Residues in contact with PHE 165 (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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81B ILE* 5.0 0.2 - - + -
121B ALA* 3.7 28.9 - - + -
122B VAL 4.2 2.7 - - - -
123B LEU* 4.0 9.4 - - + -
135B PHE* 3.4 13.3 - - - +
136B GLY* 2.8 52.8 + - - +
137B THR 3.4 24.9 - - - -
138B THR* 3.6 23.6 - - + -
163B GLN 4.1 0.4 - - - -
164B ARG* 1.3 75.3 - - - +
166B LYS* 1.3 57.8 + - - +
167B VAL* 3.7 18.4 - - + -
182B VAL* 3.3 45.3 - - + -
183B GLN 3.3 10.1 - - - +
184B ILE* 4.4 2.5 - - + -
185B LEU* 3.8 8.0 - - - +
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Residues in contact with LYS 166 (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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134B GLN* 2.9 31.6 + - - +
135B PHE* 3.7 26.7 - - + -
165B PHE* 1.3 74.5 - - - +
167B VAL* 1.3 88.9 + - - +
168B LEU* 3.5 10.8 + - + -
182B VAL* 3.4 2.9 - - - -
183B GLN* 2.9 45.7 + - + +
185B LEU* 4.1 15.7 - - + -
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Residues in contact with VAL 167 (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* 4.0 9.9 - - + -
133B ALA 3.8 17.3 - - - +
134B GLN* 2.9 26.7 + - - +
135B PHE 3.7 8.3 - - - +
165B PHE* 3.7 25.1 - - + -
166B LYS* 1.3 95.7 + - - +
168B LEU* 1.3 62.9 + - - +
169B GLU* 3.9 10.3 - - - +
170B LEU* 3.7 34.3 - - + -
180B ALA* 5.1 1.6 - - + -
181B LYS 3.9 3.6 - - - +
182B VAL* 4.5 2.2 - - + -
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Residues in contact with LEU 168 (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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78B CYS* 4.0 13.9 - - + -
166B LYS* 4.0 15.3 - - + +
167B VAL* 1.3 78.2 - - - +
169B GLU* 1.3 62.5 + - - +
181B LYS* 2.8 39.2 + - + +
182B VAL 3.9 19.3 - - - +
183B GLN* 3.9 36.6 - - + +
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Residues in contact with GLU 169 (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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167B VAL* 3.7 2.9 - - - +
168B LEU* 1.3 79.1 - - - +
170B LEU* 1.3 71.4 + - - +
171B ARG* 3.0 45.1 + - + +
180B ALA* 3.6 3.3 - - - -
181B LYS* 2.8 56.3 + - + +
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Residues in contact with LEU 170 (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* 4.9 2.0 - - + -
123B LEU* 3.9 29.2 - - + -
131B ARG 4.2 17.5 - - - +
132B GLU* 5.7 0.2 - - - -
133B ALA* 4.7 11.4 - - + +
167B VAL* 3.7 23.8 - - + -
169B GLU* 1.3 75.1 - - - +
171B ARG* 1.3 64.1 + - - +
172B THR 4.3 0.4 + - - -
178B GLN* 4.2 16.8 - - - +
179B GLN 3.7 3.1 - - - +
180B ALA* 3.7 29.4 - - + +
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Residues in contact with ARG 171 (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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169B GLU* 3.0 38.8 + - + +
170B LEU* 1.3 75.9 - - - +
172B THR* 1.3 63.1 + - - +
173B GLN* 3.8 3.6 + - + +
177B ILE 4.5 0.2 - - - +
178B GLN* 3.4 4.3 + - - -
179B GLN* 2.9 41.2 + - + +
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Residues in contact with THR 172 (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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170B LEU 4.3 0.4 - - - -
171B ARG* 1.3 74.4 - - - +
173B GLN* 1.3 64.3 + - - +
176B GLY* 3.8 22.5 + - - -
178B GLN* 3.6 20.5 + - - +
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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