Contacts of the strand formed by residues 152 - 165 (chain B) in PDB entry 5V8V
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 GLY 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B ARG* 3.3 11.8 - - - +
149B TYR* 2.7 41.2 + - - +
150B SER 3.4 0.4 - - - -
151B THR* 1.3 82.6 + - - +
153B THR* 1.3 60.9 + - - -
181B PRO* 6.3 0.7 - - - -
184B PRO* 6.1 0.7 - - - -
185B PHE* 6.4 0.9 - - - -
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Residues in contact with THR 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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146B THR* 3.7 19.3 - - + +
147B LEU 3.3 6.0 + - - -
148B ARG* 3.7 27.2 + - - +
149B TYR* 6.0 0.9 - - - -
152B GLY* 1.3 75.0 + - - -
154B VAL* 1.3 75.7 + - - +
155B SER* 3.8 9.6 - - - +
179B GLU* 5.6 3.6 - - - +
181B PRO* 3.6 28.8 - - - +
185B PHE* 5.3 1.5 - - - -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TRP* 4.6 7.0 - - + -
145B LEU 4.1 0.2 - - - +
146B THR* 3.4 2.4 - - - -
147B LEU* 2.9 66.1 + - + +
149B TYR* 4.3 12.3 - - + -
153B THR* 1.3 75.4 - - - +
155B SER* 1.3 67.7 + - - +
177B VAL* 4.2 15.5 - - + -
179B GLU* 3.6 16.8 - - - +
180B MET* 4.4 7.9 - - + -
181B PRO* 4.6 0.7 - - + -
185B PHE* 3.5 36.8 - - + -
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Residues in contact with SER 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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144B GLU* 4.7 8.1 - - - -
145B LEU 3.3 9.0 - - - -
146B THR* 3.5 12.9 + - - -
153B THR* 3.8 9.5 - - - +
154B VAL* 1.3 79.7 + - - +
156B GLY* 1.3 51.3 + - - +
177B VAL* 3.4 7.6 - - - +
178B THR* 2.5 35.1 + - - -
179B GLU* 3.1 38.6 + - - +
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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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144B GLU* 3.1 16.1 + - - +
145B LEU* 3.0 31.2 + - - +
155B SER* 1.3 76.5 - - - +
157B PHE* 1.3 64.8 + - - +
176B GLU 3.1 15.3 - - - -
177B VAL* 4.1 1.6 - - - -
178B THR* 3.3 13.4 + - - -
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Residues in contact with PHE 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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114B SER* 3.8 12.1 - - - -
116B LYS* 4.2 22.2 - - + -
138B TYR* 5.2 4.7 - - - -
140B HIS* 6.4 0.9 - + - -
142B GLY* 3.9 21.5 - - - +
143B THR 3.0 13.7 - - - +
144B GLU* 4.7 1.6 - - + -
145B LEU* 4.3 2.8 - - - +
156B GLY* 1.3 77.9 - - - +
158B LEU* 1.3 76.6 + - - +
159B SER* 3.8 1.1 - - - -
175B GLY* 3.4 2.2 - - - -
176B GLU* 2.7 66.3 + - + -
178B THR* 3.4 25.6 - - + -
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Residues in contact with LEU 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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109B ASN* 5.7 0.9 - - - +
141B ASN* 3.8 20.0 - - - +
142B GLY 3.2 19.8 + - - -
143B THR* 2.9 29.2 + - + +
144B GLU 5.6 0.2 - - - +
145B LEU* 3.9 36.3 - - + -
157B PHE* 1.3 80.4 - - - +
159B SER* 1.3 66.7 + - - +
173B MET* 3.8 27.1 - - + -
174B PHE 3.5 11.2 - - - +
204B GLY* 5.5 2.9 - - - +
206B VAL* 3.8 27.8 - - + -
501B NAG 4.7 3.1 - - - +
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Residues in contact with SER 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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138B TYR* 3.5 17.3 + - - -
139B LYS 4.1 4.7 - - - -
141B ASN 4.7 3.4 - - - +
157B PHE* 3.8 4.0 - - - -
158B LEU* 1.3 82.0 + - - +
160B GLN* 1.3 60.2 + - - +
173B MET* 3.5 8.1 - - - +
174B PHE* 2.8 53.1 + - - +
176B GLU* 2.5 33.4 + - - +
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Residues in contact with GLN 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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137B SER 4.6 0.9 - - - -
138B TYR* 3.4 4.2 - - - -
139B LYS* 2.9 64.3 + - + +
141B ASN* 5.2 2.1 - - + +
159B SER* 1.3 74.7 - - - +
161B ASP* 1.3 67.6 + - - +
171B THR* 3.2 28.4 - - + +
172B GLN 3.6 14.1 - - - +
173B MET* 4.1 17.2 - - - +
174B PHE* 4.2 0.7 - - - -
501B NAG 5.7 5.1 + - - -
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Residues in contact with ASP 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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92B ILE* 3.9 6.3 - - + -
93B GLY* 3.1 22.4 - - - -
130B PHE* 3.8 7.7 - - + -
135B SER* 2.5 28.1 + - - -
137B SER* 3.0 27.2 - - - -
138B TYR* 3.2 9.2 + - - +
160B GLN* 1.3 77.7 - - - +
162B ILE* 1.3 79.3 + - - +
163B ILE* 3.8 3.6 + - - +
171B THR* 4.7 5.8 - - - -
172B GLN* 3.0 31.0 + - - +
174B PHE* 3.9 17.6 - - + -
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Residues in contact with ILE 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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91B GLY 3.8 0.7 - - - +
92B ILE* 3.3 4.5 - - - +
93B GLY 3.0 29.0 + - - +
94B THR* 5.2 3.1 - - - +
137B SER* 4.2 13.6 - - - +
161B ASP* 1.3 89.5 + - - +
163B ILE* 1.3 60.2 + - - +
164B THR* 4.3 1.6 - - + -
169B THR* 5.6 7.9 - - + -
170B VAL 3.4 11.9 - - - +
171B THR* 4.6 4.0 - - + +
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Residues in contact with ILE 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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90B ILE* 4.3 10.5 - - + -
91B GLY 3.3 7.0 - - - +
92B ILE* 3.7 33.2 - - + -
110B VAL* 4.2 16.2 - - + -
161B ASP 4.1 2.9 - - - +
162B ILE* 1.3 79.6 - - - +
164B THR* 1.3 65.7 + - - +
165B VAL* 3.8 21.4 + - + +
168B ILE 3.6 1.9 - - - +
169B THR* 3.3 4.2 - - - -
170B VAL* 2.9 40.4 + - + +
172B GLN* 3.6 32.1 - - + -
174B PHE* 4.4 10.1 - - + -
209B ILE* 4.2 7.9 - - + -
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Residues in contact with THR 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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89B GLU 4.6 0.2 - - - +
90B ILE* 3.4 12.0 - - - +
91B GLY* 2.7 48.7 + - - +
96B PRO* 4.6 12.5 - - + +
162B ILE* 5.9 1.6 - - + -
163B ILE* 1.3 71.2 - - - +
165B VAL* 1.3 59.8 + - - +
166B GLY 4.2 7.4 + - - +
168B ILE 3.3 4.0 - - - +
169B THR* 3.4 26.5 - - + -
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Residues in contact with VAL 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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74B SER* 4.0 4.1 + - - -
76B VAL* 3.9 19.1 - - + -
89B GLU 5.2 0.9 - - - -
90B ILE* 4.1 12.3 - - + -
103B PHE* 4.1 21.8 - - + -
163B ILE* 3.8 22.2 - - + +
164B THR* 1.3 76.6 - - - +
166B GLY* 1.3 62.7 + - - +
167B GLY 3.2 0.5 + - - -
168B ILE* 2.7 38.3 + - + +
170B VAL* 5.2 1.3 - - + -
194B VAL* 6.0 0.7 - - + -
209B ILE* 3.9 18.4 - - + -
213B ILE* 5.2 6.1 - - + -
242B ILE* 6.3 0.2 - - + -
244B LEU* 4.1 20.2 - - + +
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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