Contacts of the helix formed by residues 144 - 161 (chain A) in PDB entry 1UXI
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 ALA 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.9 12.3 - - + -
123A ASP* 5.6 0.9 - - - +
142A GLY 3.7 4.3 + - - +
143A GLN* 1.3 86.0 + - - +
145A GLY* 1.3 64.1 + - - +
146A VAL 3.3 1.7 - - - +
147A LEU* 3.1 4.9 + - - +
148A ASP* 2.9 34.4 + - - +
173A GLY 5.9 1.8 - - - +
175A HIS* 3.6 38.3 + - + +
236A MET* 5.0 0.4 - - - -
249A PRO 5.1 0.8 + - - -
251A ALA* 5.3 2.9 - - + +
266A GLY* 6.3 2.2 - - - -
1310A NAD 4.2 2.0 - - - -
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Residues in contact with GLY 145 (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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144A ALA* 1.3 78.6 - - - +
146A VAL* 1.3 52.6 + - - +
148A ASP* 3.2 7.0 + - - +
149A ALA* 2.7 37.9 + - - +
171A LEU* 4.6 7.5 - - - +
249A PRO* 3.3 35.2 + - - +
250A VAL* 4.8 2.0 - - - +
251A ALA 5.4 0.2 - - - +
266A GLY* 6.0 3.9 - - - -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 3.8 8.7 - - - +
144A ALA 3.3 0.6 - - - +
145A GLY* 1.3 73.9 - - - +
147A LEU* 1.3 59.0 + - - +
149A ALA* 3.8 3.5 - - - +
150A ALA* 2.9 30.2 + - - +
153A ARG* 5.4 4.3 + - - +
232A ALA* 3.7 22.0 - - + +
235A GLN* 3.2 26.7 - - - +
236A MET* 4.4 11.7 - - + -
248A MET* 3.7 37.0 - - + -
249A PRO* 3.3 15.4 + - + +
52B ILE* 4.1 8.3 - - + -
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Residues in contact with LEU 147 (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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143A GLN* 3.1 22.5 - - - +
144A ALA 3.5 2.0 - - - +
146A VAL* 1.3 77.4 - - - +
148A ASP* 1.3 64.4 + - - +
150A ALA* 3.0 6.6 + - + +
151A ARG* 3.0 40.1 + - + +
175A HIS* 4.1 2.5 - - + -
228A ALA* 3.4 33.9 - - + -
229A PRO* 3.7 25.1 - - + -
232A ALA* 4.0 8.3 - - + -
1310A NAD 3.1 26.9 - - - +
1311A FUM 3.4 20.2 - - - +
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Residues in contact with ASP 148 (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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144A ALA* 2.9 25.1 + - - +
145A GLY* 3.7 2.9 + - - +
147A LEU* 1.3 72.2 - - - +
149A ALA* 1.3 63.6 + - - +
151A ARG* 3.3 16.0 + - - +
152A TYR 3.2 16.1 + - - -
171A LEU* 3.6 23.5 - - + +
175A HIS* 2.7 37.4 + - - -
179A MET* 3.1 36.8 - - - +
209A THR* 3.4 13.9 - - - +
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Residues in contact with ALA 149 (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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145A GLY 2.7 21.7 + - - +
146A VAL* 4.0 4.0 - - - +
148A ASP* 1.3 69.8 - - - +
150A ALA* 1.3 58.5 + - - +
151A ARG 3.4 0.2 - - - -
152A TYR* 3.5 8.7 - - - +
153A ARG* 2.8 42.9 + - - +
169A ALA 3.4 25.6 - - - +
171A LEU* 4.0 16.3 - - + +
249A PRO* 4.6 7.6 - - + -
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL 2.9 19.1 + - - +
147A LEU* 3.0 9.1 + - + +
149A ALA* 1.3 76.2 - - - +
151A ARG* 1.3 63.9 + - - +
153A ARG* 3.4 9.1 + - - +
154A THR* 2.9 30.2 + - - -
48B GLU 3.6 12.6 - - - +
51B PRO* 3.7 6.8 - - + +
52B ILE* 3.5 32.5 - - + -
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Residues in contact with ARG 151 (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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88A ARG* 4.6 0.8 - - - +
147A LEU* 3.0 42.0 + - + +
148A ASP* 3.3 17.8 + - - +
150A ALA* 1.3 75.7 - - - +
152A TYR* 1.3 58.1 + - - +
154A THR* 3.2 7.5 + - - -
155A PHE* 3.0 47.7 + - + -
209A THR* 4.7 7.3 + - + -
212A GLY* 3.7 25.6 + - - -
213A GLY* 3.5 21.0 - - - +
216A ILE* 3.8 3.2 - - - +
225A ALA* 3.5 29.3 - - - +
228A ALA* 5.6 0.2 - - - +
1311A FUM 2.8 30.5 + - - +
45B ASP* 5.4 0.2 + - - -
48B GLU* 2.7 36.3 + - + +
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Residues in contact with TYR 152 (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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148A ASP 3.2 10.5 + - - +
149A ALA* 3.5 11.0 - - + +
151A ARG* 1.3 76.9 - - - +
153A ARG* 1.3 64.0 + - - +
155A PHE* 3.2 4.4 + - - +
156A ILE* 3.0 45.8 + - + +
169A ALA* 3.2 36.8 - - + -
170A MET 4.8 7.4 - - - -
171A LEU* 5.0 1.6 - - + -
181A PRO* 4.3 19.5 - - + -
182A LEU 4.8 2.5 - - - -
183A PRO* 3.2 24.9 - - + +
186A SER* 3.1 21.4 + - - -
202A LEU* 4.1 6.8 - - + +
205A ILE* 3.8 18.2 - - + -
206A VAL* 4.4 10.1 - - + -
209A THR* 3.3 30.9 + - + +
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Residues in contact with ARG 153 (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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146A VAL* 5.4 3.8 + - - +
149A ALA* 2.8 38.1 + - - +
150A ALA* 3.4 9.4 + - - +
152A TYR* 1.3 71.6 - - - +
154A THR* 1.3 57.2 + - - +
156A ILE* 3.3 4.3 + - - +
157A ALA* 2.9 30.3 + - - +
164A VAL* 4.5 4.4 + - - -
165A LYS 5.9 0.8 + - - -
167A VAL* 2.7 45.2 + - + +
168A GLN* 4.0 7.6 - - - +
169A ALA* 3.7 27.8 - - + +
235A GLN* 5.6 4.6 + - - +
51B PRO* 3.3 46.2 + - + +
52B ILE* 4.5 7.7 - - - +
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Residues in contact with THR 154 (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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150A ALA 2.9 19.3 + - - -
151A ARG* 3.4 9.6 - - - -
153A ARG* 1.3 77.2 - - - +
155A PHE* 1.3 66.6 + - + +
156A ILE 3.1 0.2 + - - -
157A ALA* 3.2 6.7 + - - +
158A MET* 2.9 38.2 + - - +
164A VAL* 4.7 1.8 - - + -
44B LEU* 5.7 1.1 - - + -
47B TYR* 3.6 34.1 - - + -
48B GLU* 3.5 21.8 - - + -
50B SER* 5.1 0.2 - - - +
51B PRO* 3.1 24.8 - - - +
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Residues in contact with PHE 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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151A ARG* 3.0 29.0 + - + +
152A TYR* 3.2 4.2 + - - +
154A THR* 1.3 77.8 - - + +
156A ILE* 1.3 56.5 + - - +
158A MET* 3.6 11.6 - - - +
159A GLU* 3.0 29.1 + - - +
205A ILE* 3.7 21.4 - - + +
208A ARG* 3.2 68.2 - - + +
209A THR* 3.7 34.1 - - - -
212A GLY* 5.1 0.4 - - - -
215A GLU* 4.1 4.5 - - - -
44B LEU* 4.6 4.9 - - + -
48B GLU* 3.5 27.8 - - + -
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Residues in contact with ILE 156 (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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152A TYR* 3.0 60.8 + - + +
153A ARG 3.5 7.2 - - - +
154A THR 3.1 0.2 - - - -
155A PHE* 1.3 74.7 - - - +
157A ALA* 1.3 55.9 + - - +
159A GLU* 3.0 2.9 + - - +
160A ALA* 2.7 34.0 + - - +
167A VAL* 3.7 24.2 - - + -
169A ALA* 4.8 0.2 - - + -
186A SER* 4.3 1.3 - - - +
188A ILE* 4.0 20.0 - - + -
193A VAL* 4.0 22.7 - - + -
197A ILE* 4.1 20.8 - - + +
202A LEU* 5.0 0.9 - - + -
205A ILE* 4.3 7.0 - - + -
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Residues in contact with ALA 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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153A ARG 2.9 16.9 + - - +
154A THR 3.7 2.0 - - - +
156A ILE* 1.3 75.3 - - - +
158A MET* 1.3 57.9 + - + +
161A GLY* 2.8 27.5 + - - -
162A VAL* 3.2 36.8 + - - +
164A VAL* 3.6 32.5 - - + +
167A VAL* 4.0 6.3 - - + -
47B TYR* 6.4 0.2 - - + -
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Residues in contact with MET 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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154A THR* 2.9 37.0 + - + +
155A PHE* 3.6 20.9 - - - +
157A ALA* 1.3 79.7 - - + +
159A GLU* 1.3 61.2 + - - +
161A GLY* 3.5 8.2 + - - -
208A ARG* 4.6 13.9 - - - +
44B LEU* 5.6 6.1 - - + -
47B TYR* 4.1 32.1 - - + +
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Residues in contact with GLU 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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155A PHE 3.0 18.4 + - - +
156A ILE 3.0 4.4 + - - +
158A MET* 1.3 78.8 - - - +
160A ALA* 1.3 60.8 + - - +
161A GLY 3.2 1.1 + - - -
196A PHE 5.7 0.2 - - - +
197A ILE* 3.6 32.3 - - + +
201A ARG* 3.3 42.4 + - - +
205A ILE* 3.8 12.6 - - + +
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Residues in contact with ALA 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 ILE 2.7 19.3 + - - +
159A GLU* 1.3 72.9 - - - +
161A GLY* 1.3 63.7 + - - +
162A VAL* 3.4 15.1 - - + +
188A ILE* 4.0 26.2 - - + -
196A PHE* 4.0 26.2 - - + -
197A ILE* 4.7 5.8 - - + -
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Residues in contact with GLY 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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157A ALA 2.8 9.0 + - - -
158A MET 3.5 6.0 + - - -
159A GLU 3.2 4.4 + - - -
160A ALA* 1.3 80.3 - - - +
162A VAL* 1.3 61.8 + - - +
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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