Contacts of the helix formed by residues 144 - 161 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.6 12.6 - - + -
123B ASP* 5.6 0.4 - - - +
142B GLY 3.7 2.7 + - - +
143B GLN* 1.3 88.6 - - - +
145B GLY* 1.3 64.6 + - - +
146B VAL 3.3 1.7 - - - +
147B LEU* 3.1 6.1 + - - +
148B ASP* 2.9 32.8 + - - +
175B HIS* 3.6 37.6 + - + +
236B MET* 5.1 0.6 - - - -
249B PRO 5.2 0.8 + - - -
251B ALA* 5.4 2.9 - - + +
1310B NAD 4.0 2.0 - - - -
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Residues in contact with GLY 145 (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 ALA* 1.3 76.5 - - - +
146B VAL* 1.3 61.0 + - - +
148B ASP* 3.9 8.5 - - - +
149B ALA* 2.8 34.3 + - - +
171B LEU* 4.5 7.9 - - - +
249B PRO* 3.5 33.2 + - - +
250B VAL* 4.9 2.4 - - - +
266B GLY* 6.2 3.2 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.1 7.0 - - + -
143B GLN* 3.6 8.5 - - - +
144B ALA 3.3 0.8 - - - -
145B GLY* 1.3 74.4 - - - +
147B LEU* 1.3 57.3 + - - +
149B ALA* 3.8 3.4 - - - +
150B ALA* 2.9 27.0 + - - +
153B ARG* 5.5 4.4 + - - +
232B ALA* 3.6 20.4 - - + +
235B GLN* 3.2 26.9 - - - +
236B MET* 4.2 14.4 - - + -
248B MET* 3.8 35.2 - - + -
249B PRO* 3.4 16.7 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLN* 3.0 21.6 - - - +
144B ALA 3.4 3.8 - - - +
146B VAL* 1.3 73.8 - - - +
148B ASP* 1.3 67.9 + - - +
150B ALA* 2.8 16.7 + - + +
151B ARG* 2.9 30.9 + - + +
175B HIS* 4.1 2.5 - - + -
228B ALA* 3.3 34.8 - - + -
229B PRO* 3.6 28.0 - - + -
232B ALA* 4.1 6.7 - - + -
1310B NAD 3.3 22.7 - - + +
1311B FUM 3.3 24.5 - - - +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA* 2.9 19.8 + - - +
145B GLY 3.9 0.6 + - - +
147B LEU* 1.3 73.1 - - - +
149B ALA* 1.3 58.1 + - - +
151B ARG* 3.3 19.0 + - - +
152B TYR 3.0 22.5 + - - -
171B LEU* 3.5 30.0 - - + +
174B GLY 5.1 0.3 - - - +
175B HIS* 2.6 45.4 + - - -
179B MET* 3.3 28.0 - - - +
209B THR* 3.5 10.1 - - - +
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Residues in contact with ALA 149 (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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145B GLY 2.8 22.0 + - - +
146B VAL* 4.0 4.3 - - - +
148B ASP* 1.3 71.0 - - - +
150B ALA* 1.3 60.8 + - - +
152B TYR* 3.6 3.9 - - - +
153B ARG* 2.7 42.7 + - - +
169B ALA 3.5 24.2 - - - +
171B LEU* 3.8 17.0 - - + +
249B PRO* 4.7 8.1 - - + -
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Residues in contact with ALA 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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48A GLU 3.4 19.1 - - - +
51A PRO* 3.6 8.1 - - + +
52A ILE* 3.6 25.6 - - + -
146B VAL 2.9 15.8 + - - +
147B LEU* 2.8 12.4 + - + +
149B ALA* 1.3 77.5 - - - +
151B ARG* 1.3 63.1 + - - +
153B ARG* 3.2 11.4 + - - +
154B THR* 2.8 28.1 + - - -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.0 37.1 + - + +
88B ARG* 4.4 1.2 - - - +
147B LEU* 2.9 37.1 + - + +
148B ASP* 3.5 19.2 + - - +
150B ALA* 1.3 76.7 - - - +
152B TYR* 1.3 62.9 + - - +
154B THR* 3.0 9.1 + - - -
155B PHE* 2.9 41.2 + - + -
209B THR* 4.8 8.1 + - + -
212B GLY* 3.8 18.1 - - - -
213B GLY* 3.3 24.8 - - - +
216B ILE* 4.0 3.8 - - - +
225B ALA* 3.6 18.8 - - - +
228B ALA* 5.5 0.2 - - - +
1311B FUM 2.5 43.4 + - - +
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Residues in contact with TYR 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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148B ASP 3.0 15.1 + - - +
149B ALA* 3.6 7.6 - - - +
151B ARG* 1.3 77.2 - - - +
153B ARG* 1.3 53.4 + - - +
155B PHE* 3.3 2.9 + - - +
156B ILE* 2.6 46.5 + - + +
169B ALA* 3.2 26.5 - - + -
170B MET 4.9 4.7 - - - -
171B LEU* 4.5 1.8 - - + -
181B PRO* 4.2 25.4 - - + -
182B LEU 4.9 0.4 - - - -
183B PRO* 3.5 21.8 - - + +
186B SER* 3.1 33.5 + - - -
193B VAL* 4.2 2.3 - - - +
202B LEU* 3.9 10.1 - - + +
205B ILE* 3.8 20.6 - - + -
206B VAL* 4.4 10.3 - - + -
209B THR* 3.3 30.4 + - + +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 3.6 44.7 + - + +
52A ILE* 4.5 6.7 - - - +
146B VAL* 5.5 3.6 + - - +
149B ALA* 2.7 38.1 + - - +
150B ALA* 3.7 9.0 - - - +
152B TYR* 1.3 73.2 - - - +
154B THR* 1.3 58.1 + - - +
156B ILE* 3.5 10.1 + - - +
157B ALA* 2.9 29.5 + - - +
164B VAL* 4.2 6.5 + - - +
165B LYS 5.4 2.2 + - - -
167B VAL* 2.8 40.2 + - + +
168B GLN* 3.9 5.4 - - - +
169B ALA* 3.9 30.1 - - + +
235B GLN* 5.5 5.5 + - - +
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.5 34.8 - - + +
48A GLU* 3.4 16.9 - - + -
50A SER* 4.6 1.8 - - - +
51A PRO* 3.1 23.3 - - - +
150B ALA 2.8 19.5 + - - -
151B ARG* 3.3 9.0 - - - -
153B ARG* 1.3 74.3 - - - +
155B PHE* 1.3 61.7 + - - +
157B ALA* 3.1 6.1 + - - +
158B MET* 2.8 54.7 + - + +
164B VAL* 4.5 2.0 - - + -
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Residues in contact with PHE 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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44A LEU* 4.6 2.0 - - + -
48A GLU* 3.3 28.3 - - + -
151B ARG* 2.9 22.3 + - + -
152B TYR 3.7 4.0 - - - +
154B THR* 1.3 76.9 - - - +
156B ILE* 1.3 57.1 + - - +
158B MET* 3.1 26.6 + - + +
159B GLU* 2.8 31.5 + - - +
205B ILE* 3.7 23.9 - - + +
208B ARG* 3.4 58.8 - - + -
209B THR* 3.6 32.1 - - - -
212B GLY* 5.1 2.0 - - - -
215B GLU* 4.2 3.4 - - - -
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Residues in contact with ILE 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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152B TYR* 2.6 56.9 + - + +
153B ARG* 3.9 2.7 - - - -
155B PHE* 1.3 70.8 - - - +
157B ALA* 1.3 64.9 + - - +
159B GLU* 3.8 0.2 - - - +
160B ALA* 2.8 31.6 + - + +
167B VAL* 3.5 24.0 - - + -
169B ALA* 5.8 0.2 - - + -
188B ILE* 3.2 39.0 - - + -
193B VAL* 4.1 15.5 - - + -
197B ILE* 3.9 22.8 - - + +
202B LEU* 5.7 0.9 - - + -
205B ILE* 4.4 4.7 - - + -
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Residues in contact with ALA 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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47A TYR* 5.7 0.9 - - - +
153B ARG 2.9 19.5 + - - +
154B THR 3.5 2.7 - - - +
156B ILE* 1.3 81.8 - - - +
158B MET* 1.3 58.3 + - + +
161B GLY* 2.8 26.3 + - - -
162B VAL* 3.1 28.9 + - - +
164B VAL* 3.4 35.9 - - + -
167B VAL* 4.2 4.3 - - + -
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Residues in contact with MET 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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44A LEU* 5.0 4.9 - - + -
47A TYR* 3.3 39.5 + - + +
154B THR* 2.8 28.7 + - + +
155B PHE* 3.1 48.7 - - + +
157B ALA* 1.3 80.3 - - - +
159B GLU* 1.3 64.7 + - - +
161B GLY* 3.2 9.9 + - - -
208B ARG* 4.2 10.3 - - - +
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Residues in contact with GLU 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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155B PHE 2.8 20.9 + - - +
156B ILE 3.8 2.5 - - - +
158B MET* 1.3 76.0 - - - +
160B ALA* 1.3 59.6 + - - +
161B GLY 3.5 0.2 + - - -
197B ILE* 3.8 17.3 - - + -
201B ARG* 2.9 55.8 + - + +
205B ILE* 3.7 19.9 - - + +
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Residues in contact with ALA 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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156B ILE* 2.8 35.0 + - + +
159B GLU* 1.3 73.4 - - - +
161B GLY* 1.3 62.5 + - - +
162B VAL* 4.0 18.5 - - + +
188B ILE* 4.2 7.9 - - + -
196B PHE* 4.2 23.1 - - + -
197B ILE* 4.7 4.5 - - + -
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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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157B ALA 2.8 11.7 + - - -
158B MET* 3.2 9.8 + - - -
160B ALA* 1.3 80.1 - - - +
162B VAL* 1.3 61.7 + - - +
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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