Contacts of the helix formed by residues 149 - 163 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP 3.4 4.3 + - - +
148A ILE* 1.3 69.0 - - - +
150A VAL* 1.3 63.3 + - - +
151A ASP* 3.6 15.9 + - - +
152A SER* 3.0 31.2 + - - -
153A VAL* 3.4 15.1 + - - +
179B ARG* 3.2 27.0 - - - +
183B GLU* 2.8 28.1 + - + +
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR* 4.3 8.7 - - + +
135A LEU* 3.8 25.1 - - + +
136A LEU* 3.3 44.4 - - + -
139A VAL* 3.9 21.8 - - + -
144A VAL* 5.4 0.7 - - + -
148A ILE* 3.1 18.3 + - + +
149A ASP* 1.3 73.3 + - - +
151A ASP* 1.3 71.3 + - + +
153A VAL* 3.0 9.2 + - - +
154A ALA* 2.9 25.2 + - - +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 4.2 13.5 + - - -
132A THR* 4.5 12.8 + - + +
149A ASP* 3.3 10.0 + - - +
150A VAL* 1.3 85.5 - - + +
152A SER* 1.3 65.0 + - - +
154A ALA* 3.4 2.1 + - - +
155A HIS* 3.2 50.1 + - - -
172B GLU* 4.9 3.5 - - - +
176B ARG* 5.5 7.5 + - - -
180B ARG* 5.2 3.5 + - - +
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASP* 3.0 29.5 + - - -
150A VAL 3.2 0.8 - - - -
151A ASP* 1.3 81.4 + - - +
153A VAL* 1.3 61.9 + - - +
155A HIS* 3.5 3.8 + - - +
156A THR* 3.0 27.2 + - - -
179B ARG* 4.1 3.3 - - - +
180B ARG* 3.4 46.0 + - - +
183B GLU* 4.0 12.3 - - - -
184B MSE 5.2 1.6 - - - -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.6 19.7 - - + -
148A ILE* 4.0 14.4 - - + -
149A ASP 3.4 12.8 + - - +
150A VAL* 3.0 7.3 + - - +
152A SER* 1.3 74.9 - - - +
154A ALA* 1.3 59.9 + - - +
156A THR* 3.0 7.0 + - - -
157A LEU* 2.8 31.7 + - + +
188A LEU* 4.5 19.3 - - + -
192A MSE 4.1 18.8 - - + -
183B GLU* 4.5 4.3 - - + -
184B MSE 4.3 5.6 - - + -
187B ILE* 3.6 28.5 - - + -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.7 17.7 - - + +
131A ALA* 3.9 7.9 - - + -
132A THR* 3.3 36.3 - - - +
135A LEU* 3.8 7.6 - - + +
150A VAL 2.9 14.5 + - - +
151A ASP 3.6 4.3 - - - +
152A SER 3.4 0.2 - - - -
153A VAL* 1.3 74.8 - - - +
155A HIS* 1.3 62.7 + - - +
157A LEU* 3.4 2.3 + - - +
158A VAL* 3.0 28.8 + - - +
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Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.7 29.4 + - + +
151A ASP* 3.2 34.6 + - - -
152A SER 3.7 2.2 - - - +
153A VAL 3.2 0.2 - - - -
154A ALA* 1.3 78.8 - - - +
156A THR* 1.3 61.7 + - - +
158A VAL* 3.5 3.8 + - - +
159A CYS* 3.1 24.3 + - - +
163B GLY* 3.8 13.4 - - - -
164B THR* 3.4 39.2 + - + +
172B GLU* 3.0 43.3 - - + +
180B ARG* 3.5 29.1 - - - -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER 3.0 12.8 + - - -
153A VAL* 3.0 8.4 + - - -
155A HIS* 1.3 77.9 - - - +
157A LEU* 1.3 52.9 + - - +
159A CYS 3.4 0.5 + - - -
160A SER* 2.7 48.5 + - - +
188A LEU* 5.7 3.4 - - + -
156B THR* 3.7 25.6 - - - +
159B CYS* 3.7 9.4 - - - +
160B SER* 3.3 23.0 - - - +
180B ARG* 5.0 1.2 + - - +
184B MSE 3.8 30.1 - - + +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.9 32.8 - - + -
90A THR* 4.8 4.0 - - + -
131A ALA* 4.2 14.8 - - + -
135A LEU* 5.1 5.2 - - + -
153A VAL* 2.8 18.7 + - + +
154A ALA* 3.6 5.4 - - - +
156A THR* 1.3 74.9 - - - +
158A VAL* 1.3 60.5 + - + +
160A SER* 4.2 2.7 - - - -
161A VAL* 2.9 49.9 + - + +
184A MSE 3.3 37.2 - - + -
185A TRP* 4.0 11.9 - - + -
188A LEU* 4.0 20.6 - - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.9 39.3 - - + +
127A TRP* 3.7 22.9 - - + +
128A ARG* 3.6 29.2 - - - +
131A ALA* 4.6 5.8 - - + -
154A ALA 3.0 20.4 + - - +
155A HIS 3.9 3.4 - - - +
157A LEU* 1.3 78.1 - - + +
159A CYS* 1.3 63.2 + - - +
161A VAL* 4.2 2.9 - - - +
162A VAL* 3.3 24.9 + - - +
164B THR* 4.1 10.3 - - + -
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Residues in contact with CYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 5.3 0.7 - - - -
155A HIS 3.1 16.1 + - - +
158A VAL* 1.3 80.8 - - - +
160A SER* 1.3 62.5 + - - +
162A VAL* 3.7 11.8 + - - +
163A GLY 3.9 8.0 + - - +
166A VAL* 5.7 0.8 - - - +
167A VAL* 4.2 13.5 - - - +
155B HIS* 4.2 2.9 + - - -
159B CYS* 2.0 55.6 - - + +
162B VAL* 4.0 16.2 - - - -
163B GLY 3.6 16.8 - - - +
166B VAL* 4.3 11.7 - - + -
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Residues in contact with SER 160 (chain A).
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* 2.7 33.9 + - - +
157A LEU* 3.8 1.3 - - - -
158A VAL 3.3 0.2 - - - -
159A CYS* 1.3 68.8 - - - +
161A VAL* 1.3 61.0 + - - +
162A VAL 3.1 1.3 - - - -
163A GLY 3.0 7.4 + - - -
180A ARG* 2.3 30.0 + - - -
184A MSE 3.4 28.9 - - - +
155B HIS* 3.4 10.7 + - - -
156B THR* 4.3 11.4 + - - -
159B CYS* 3.3 16.3 - - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 3.6 33.7 - - + +
93A MSE 5.8 5.2 - - + -
94A ALA* 6.2 1.3 - - + +
157A LEU* 2.9 47.6 + - + +
158A VAL* 4.2 3.8 - - - +
160A SER* 1.3 73.9 - - - +
162A VAL* 1.3 66.9 + - + +
163A GLY* 3.1 1.2 + - - -
177A GLU* 4.9 3.6 - - - +
180A ARG* 3.8 14.4 + - - +
181A LEU* 3.8 24.5 - - + +
184A MSE 3.9 0.4 - - - -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.6 31.0 - - + +
124A PHE* 3.9 12.6 - - + -
127A TRP* 3.6 33.7 - - + -
158A VAL 3.3 17.3 + - - +
159A CYS* 4.0 7.6 - - - +
160A SER 3.0 1.2 + - - -
161A VAL* 1.3 84.0 - - + +
163A GLY* 1.3 57.1 - - - +
165A ARG* 5.8 0.9 - - - +
166A VAL* 3.2 40.2 - - + +
177A GLU* 5.2 2.7 - - - +
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Residues in contact with GLY 163 (chain A).
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 3.9 3.1 + - - +
160A SER 3.0 13.8 + - - -
161A VAL 3.1 0.2 + - - -
162A VAL* 1.3 82.4 - - - +
164A THR* 1.3 65.4 + - - -
165A ARG* 3.2 4.9 + - - -
166A VAL* 3.4 15.9 + - - +
167A VAL* 4.0 2.6 + - - +
177A GLU* 5.1 3.8 - - - -
180A ARG* 3.8 17.9 - - - -
155B HIS* 4.1 8.0 + - - -
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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