Contacts of the helix formed by residues 149 - 163 (chain B) in PDB entry 1UI5
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 ASP 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 3.3 41.5 + - + +
187A ILE* 4.7 2.6 - - + +
147B ASP 3.7 2.2 + - - +
148B ILE* 1.3 68.9 - - - +
150B VAL* 1.3 63.3 + - - +
151B ASP* 3.5 10.5 + - - +
152B SER* 2.9 36.7 + - - -
153B VAL* 3.1 23.7 + - - +
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Residues in contact with VAL 150 (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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132B THR* 3.7 29.9 - - + +
135B LEU* 4.1 10.9 - - + +
136B LEU* 3.6 35.4 - - + -
148B ILE* 3.4 32.6 + - + +
149B ASP* 1.3 69.9 + - - +
151B ASP* 1.3 68.1 + - - +
153B VAL* 3.1 6.1 + - - +
154B ALA* 2.8 31.0 + - - +
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Residues in contact with ASP 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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128B ARG* 3.5 38.3 + - - +
132B THR* 3.7 13.3 - - - +
149B ASP* 3.3 9.7 + - - +
150B VAL* 1.3 86.7 - - - +
152B SER* 1.3 62.8 + - - +
154B ALA* 3.2 4.3 + - - +
155B HIS* 2.9 24.0 + - - +
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Residues in contact with SER 152 (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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180A ARG* 4.1 11.6 + - - +
183A GLU* 3.2 30.6 - - - +
184A MSE 4.0 6.6 + - - +
187A ILE* 3.7 18.4 - - - -
149B ASP* 2.9 22.3 + - - -
151B ASP* 1.3 75.0 - - - +
153B VAL* 1.3 62.3 + - - +
155B HIS* 3.3 6.2 + - - +
156B THR* 3.0 28.2 + - - -
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Residues in contact with VAL 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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187A ILE* 4.1 12.3 - - + -
135B LEU* 3.7 29.6 - - + -
148B ILE* 4.5 9.4 - - + -
149B ASP 3.1 18.9 + - - +
150B VAL* 3.1 8.3 + - - +
152B SER* 1.3 76.4 - - - +
154B ALA* 1.3 62.8 + - - +
156B THR* 3.3 7.9 - - - -
157B LEU* 3.1 26.6 + - + +
185B TRP* 5.8 0.9 - - + -
188B LEU* 4.0 22.7 - - + -
192B MSE 3.4 29.2 - - + -
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Residues in contact with ALA 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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124B PHE* 5.2 1.3 - - + -
127B TRP 5.1 0.4 - - - +
128B ARG* 4.2 26.7 - - + -
131B ALA* 4.0 28.2 - - + +
132B THR* 4.3 3.4 - - + +
135B LEU* 4.4 1.3 - - + +
150B VAL 2.8 20.3 + - - +
151B ASP 3.5 4.7 - - - +
153B VAL* 1.3 75.4 - - - +
155B HIS* 1.3 62.1 + - - +
157B LEU* 3.3 6.9 + - - +
158B VAL* 3.2 28.0 + - + +
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Residues in contact with HIS 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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159A CYS 4.3 0.2 - - - -
160A SER* 3.4 37.7 - - - -
163A GLY 4.1 7.7 + - - -
164A THR* 3.7 23.4 - - + +
167A VAL* 4.2 13.2 - - + +
180A ARG* 3.6 17.2 + - - -
124B PHE* 3.7 32.3 - + + -
151B ASP 2.9 15.7 + - - +
152B SER* 3.7 7.9 - - - +
153B VAL 3.2 0.2 - - - -
154B ALA* 1.3 76.1 - - - +
156B THR* 1.3 57.4 + - - +
158B VAL* 3.2 3.2 + - + +
159B CYS* 2.9 46.1 + - - +
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Residues in contact with THR 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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156A THR* 3.7 6.7 - - - +
160A SER* 4.3 15.4 + - - -
184A MSE 4.8 10.4 - - - +
187A ILE* 4.6 12.7 - - + +
188A LEU* 5.8 1.4 - - - +
152B SER 3.0 19.5 + - - -
153B VAL* 3.3 8.7 - - - +
155B HIS* 1.3 76.2 - - - +
157B LEU* 1.3 56.9 + - - +
159B CYS 3.4 0.5 + - - -
160B SER* 3.0 27.4 + - - -
184B MSE 3.2 38.7 - - + -
188B LEU* 4.0 18.4 - - + -
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Residues in contact with LEU 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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86B LEU* 4.5 12.8 - - + -
90B THR* 4.4 15.0 - - + -
131B ALA* 5.3 3.8 - - + -
135B LEU* 5.1 1.3 - - + -
153B VAL* 3.1 25.5 + - + +
154B ALA* 3.7 10.5 - - - +
155B HIS 3.2 0.2 - - - -
156B THR* 1.3 75.9 - - - +
158B VAL* 1.3 66.7 + - + +
160B SER* 2.7 21.1 + - - -
161B VAL* 3.3 13.1 + - - +
181B LEU* 4.0 11.5 - - + +
184B MSE 4.7 5.2 - - + -
185B TRP* 3.5 52.0 - - + +
188B LEU* 3.6 19.5 - - + -
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Residues in contact with VAL 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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167A VAL* 4.0 29.2 - - + -
107B LEU* 5.2 0.4 - - + -
124B PHE* 4.0 18.2 - - + -
127B TRP* 4.1 39.3 - - + -
128B ARG 5.8 0.2 - - - +
154B ALA* 3.2 14.2 + - + +
155B HIS* 3.6 6.5 - - + +
157B LEU* 1.3 76.2 - - + +
159B CYS* 1.3 60.1 + - - +
161B VAL* 3.1 22.2 + - - +
162B VAL* 3.2 21.1 + - + +
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Residues in contact with CYS 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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156A THR* 3.7 12.0 + - + +
159A CYS* 2.0 64.2 - - + -
160A SER* 3.3 18.8 - - - +
167A VAL* 4.6 2.2 - - - -
155B HIS* 2.9 30.3 + - - +
156B THR 3.9 3.1 - - - +
158B VAL* 1.3 73.9 - - - +
160B SER* 1.3 61.9 + - - +
161B VAL 3.3 0.2 - - - -
162B VAL* 4.1 0.9 - - - -
163B GLY* 3.1 27.0 + - - -
180B ARG* 5.2 0.2 + - - -
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Residues in contact with SER 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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156A THR* 3.3 20.8 + - - -
156B THR 3.0 8.8 + - - -
157B LEU* 2.7 25.1 + - - -
159B CYS* 1.3 78.7 - - - +
161B VAL* 1.3 61.8 + - - +
177B GLU 4.5 0.2 - - - +
180B ARG* 3.1 41.1 + - - +
181B LEU* 3.6 17.3 - - - +
184B MSE 3.5 23.7 - - - +
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Residues in contact with VAL 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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90B THR* 4.8 6.5 - - - +
93B MSE 4.9 4.3 - - + -
94B ALA* 4.0 18.8 - - + +
97B CYS* 3.8 31.2 - - + -
157B LEU 3.4 15.3 - - - +
158B VAL* 3.1 9.7 + - - +
160B SER* 1.3 78.3 - - - +
162B VAL* 1.3 59.8 + - + +
177B GLU* 3.2 24.1 - - + +
180B ARG* 3.1 19.1 + - - -
181B LEU* 4.1 28.0 - - + -
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Residues in contact with VAL 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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159A CYS* 4.0 14.1 - - - -
167A VAL* 5.4 0.4 - - + -
97B CYS* 5.3 5.2 - - + -
104B ARG* 3.9 28.5 - - + +
107B LEU* 3.9 20.4 - - + -
127B TRP* 6.1 0.7 - - + -
158B VAL* 3.4 22.4 - - + +
159B CYS* 4.1 0.4 - - - -
161B VAL* 1.3 83.4 - - + +
163B GLY* 1.3 61.1 + - - +
165B ARG* 3.0 33.4 + - - +
166B VAL* 3.8 32.8 - - + +
177B GLU* 5.7 0.2 - - - -
180B ARG* 3.7 5.9 + - - -
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Residues in contact with GLY 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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155A HIS* 3.8 30.3 - - - -
159A CYS* 3.6 7.1 - - - +
159B CYS 3.1 20.1 + - - -
160B SER 4.2 0.2 + - - -
161B VAL 3.7 1.2 - - - -
162B VAL* 1.3 78.8 - - - +
164B THR* 1.3 62.1 + - - -
166B VAL* 3.1 21.1 - - - +
180B ARG* 4.3 4.5 - - - -
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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