Contacts of the helix formed by residues 204 - 221 (chain A) in PDB entry 1U5Q
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A HIS* 3.0 48.0 + - - -
147A MET 4.8 0.2 - - - -
148A ILE* 3.9 18.1 - - - +
177A ALA* 4.9 4.0 - - - +
203A ASP* 1.3 74.8 - - - +
205A LYS* 1.3 57.2 + - - +
206A VAL 3.1 1.6 - - - -
207A ASP* 2.9 18.0 + - - +
208A VAL 3.6 0.7 + - - -
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Residues in contact with LYS 205 (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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192A GLU* 4.3 3.4 - - - +
203A ASP* 2.9 25.5 - - + +
204A GLY* 1.3 76.3 - - - +
206A VAL* 1.3 60.3 + - - +
208A VAL* 2.8 26.3 + - - +
209A TRP 3.0 4.9 + - - -
266A PRO* 2.9 36.9 + - + +
267A GLN* 4.1 9.9 + - - +
269A ARG* 3.0 45.4 + - + +
270A PRO 4.1 11.7 - - - +
271A THR* 4.0 29.8 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.6 20.0 - - + -
150A ARG* 4.7 6.3 - - + -
190A ALA* 3.9 6.4 + - + +
192A GLU* 3.4 31.9 - - + +
193A VAL* 3.6 17.7 - - + -
202A TYR* 3.5 22.0 - - + -
203A ASP 3.2 20.9 - - - +
205A LYS* 1.3 78.4 - - - +
207A ASP* 1.3 63.1 + - - +
209A TRP* 3.4 5.1 + - - +
210A SER* 3.0 29.0 + - - +
269A ARG* 3.7 6.5 - - - +
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Residues in contact with ASP 207 (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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139A LEU* 3.7 16.8 - - + +
143A HIS* 3.0 26.5 + - + +
148A ILE* 3.5 7.5 - - - +
149A HIS* 2.8 31.9 + - - +
150A ARG* 2.7 30.4 + - - -
152A VAL* 4.0 6.1 - - + +
204A GLY 2.9 10.0 + - - +
206A VAL* 1.3 77.5 - - - +
208A VAL* 1.3 60.3 + - - +
209A TRP 3.2 0.4 - - - -
210A SER* 3.7 7.7 + - - -
211A LEU* 2.8 29.8 + - - +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.4 2.0 - - + -
139A LEU* 5.3 1.1 - - + -
143A HIS* 4.6 2.2 - - + -
204A GLY 4.3 3.1 - - - +
205A LYS* 2.8 21.0 + - - +
207A ASP* 1.3 79.0 - - - +
209A TRP* 1.3 59.9 + - - +
211A LEU* 3.2 9.3 + - - +
212A GLY 2.9 17.2 + - - -
261A CYS* 3.3 22.1 - - - +
269A ARG* 3.9 7.6 - - + -
270A PRO* 3.6 17.3 - - + +
272A SER* 3.6 39.5 - - - +
275A LEU* 3.4 26.0 - - + -
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Residues in contact with TRP 209 (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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187A TYR 5.4 0.6 + - - -
188A TRP 3.5 11.2 - - - -
189A MET 3.4 11.7 + - - -
190A ALA* 3.4 25.6 - - + -
191A PRO* 3.8 28.0 - - + -
205A LYS 3.0 5.1 + - - -
206A VAL 3.4 7.6 - - - +
208A VAL* 1.3 76.2 - - - +
210A SER* 1.3 58.7 + - - +
212A GLY* 2.7 22.7 + - - -
213A ILE* 2.9 31.6 + - + +
237A ILE* 4.3 14.1 - - + +
242A SER* 3.6 21.8 - - - -
243A PRO* 4.5 9.9 - - + -
261A CYS 3.5 12.5 + - - -
262A LEU* 3.1 53.7 - - + +
263A GLN 3.6 15.9 - - - -
264A LYS* 4.0 8.7 - - + -
269A ARG* 3.8 11.0 - - - +
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Residues in contact with SER 210 (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 ARG* 5.3 5.0 + - - -
151A ASP* 5.6 0.2 - - - -
152A VAL* 3.6 33.4 + - - +
188A TRP* 2.8 27.9 + - - +
189A MET* 4.5 3.5 - - - -
190A ALA 4.7 0.3 + - - -
206A VAL* 3.0 18.4 + - - +
207A ASP* 3.8 7.5 + - - -
209A TRP* 1.3 75.7 - - - +
211A LEU* 1.3 57.6 + - - +
213A ILE* 3.2 5.7 + - - +
214A THR* 2.9 31.3 + - - -
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Residues in contact with LEU 211 (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* 4.2 30.1 - - + +
135A ALA* 4.2 23.6 - - + -
136A LEU* 4.0 30.1 - - + -
139A LEU* 4.2 13.5 - - + -
152A VAL* 4.0 15.7 - - + +
157A ILE* 4.7 3.6 - - + -
207A ASP 2.8 18.6 + - - +
208A VAL* 3.4 7.2 - - - +
210A SER* 1.3 78.7 - - - +
212A GLY* 1.3 56.6 + - - +
214A THR* 3.1 9.4 + - + -
215A CYS* 2.8 32.0 + - - -
257A PHE* 4.3 10.3 - - + -
261A CYS* 4.8 3.6 - - - -
275A LEU* 5.4 0.7 - - + -
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Residues in contact with GLY 212 (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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208A VAL 2.9 7.5 + - - -
209A TRP 2.7 15.2 + - - -
211A LEU* 1.3 71.2 - - - +
213A ILE* 1.3 60.7 + - - -
215A CYS* 3.1 17.8 + - - +
216A ILE* 3.3 15.6 + - - +
258A VAL* 4.3 5.5 - - - +
261A CYS* 3.6 25.1 - - - +
262A LEU* 4.1 11.9 - - - -
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Residues in contact with ILE 213 (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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187A TYR 3.7 14.8 - - - +
188A TRP* 3.5 25.6 - - + +
209A TRP* 2.9 39.6 + - + +
210A SER 3.2 7.6 + - - +
212A GLY* 1.3 74.0 - - - +
214A THR* 1.3 56.5 + - - +
216A ILE* 3.1 8.5 + - + +
217A GLU* 2.9 24.9 + - - +
223A PRO* 3.6 21.4 - - + +
224A PRO* 4.0 10.3 - - + -
243A PRO* 4.0 17.7 - - + -
262A LEU* 3.7 25.1 - - + -
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Residues in contact with THR 214 (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 VAL* 3.7 4.5 + - - +
153A LYS* 3.2 23.0 + - - -
154A ALA* 3.5 28.5 - - + +
157A ILE* 3.7 22.9 - - + -
188A TRP* 3.7 1.4 - - - +
210A SER 2.9 20.7 + - - -
211A LEU* 3.1 13.9 + - + -
213A ILE* 1.3 77.5 - - - +
215A CYS* 1.3 59.6 + - - +
217A GLU* 3.1 10.3 + - - +
218A LEU* 2.8 37.3 + - + +
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Residues in contact with CYS 215 (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 ILE* 4.8 0.2 - - - -
132A THR* 3.5 38.1 - - - -
211A LEU* 2.8 19.5 + - - -
212A GLY* 3.3 10.3 - - - +
214A THR* 1.3 77.7 - - - +
216A ILE* 1.3 61.5 + - - +
218A LEU* 3.3 10.7 + - - +
219A ALA* 3.0 23.0 + - - +
254A PHE* 3.7 16.9 - - + -
257A PHE* 3.9 19.7 - - - -
258A VAL* 3.7 17.7 - - + -
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Residues in contact with ILE 216 (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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212A GLY 3.3 7.4 + - - +
213A ILE* 3.1 9.0 + - + +
215A CYS* 1.3 73.4 - - - +
217A GLU* 1.3 56.3 + - - +
219A ALA* 2.9 1.6 + - - +
220A GLU* 2.6 67.8 + - - +
222A LYS 4.2 3.4 - - - +
224A PRO* 3.9 29.6 - - + -
243A PRO* 4.3 0.4 - - + -
244A ALA 3.8 24.0 - - - +
245A LEU* 4.1 16.2 - - + +
258A VAL* 3.9 12.6 - - + -
262A LEU* 3.7 27.8 - - + -
84B ARG* 3.6 7.4 - - - +
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Residues in contact with GLU 217 (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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113A SER* 4.8 5.4 + - - -
116A LEU* 3.5 9.3 - - + +
153A LYS* 5.1 0.2 - - - +
154A ALA* 3.0 36.1 + - - +
155A GLY 4.6 2.3 + - - -
188A TRP* 2.8 44.0 + - - +
213A ILE 2.9 12.1 + - - +
214A THR* 3.1 8.6 + - - +
216A ILE* 1.3 76.7 - - - +
218A LEU* 1.3 56.2 + - - +
221A ARG* 2.6 46.9 + - - +
222A LYS* 3.4 22.4 + - - -
223A PRO* 4.1 3.7 - - + +
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Residues in contact with LEU 218 (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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112A ALA* 3.7 27.6 - - + -
116A LEU* 3.7 13.2 - - + +
122A PRO* 3.5 4.3 - - - +
123A LEU* 3.1 39.9 + - + -
128A ILE* 3.8 32.0 - - + +
131A VAL* 3.8 28.0 - - + -
132A THR* 4.3 7.4 - - - +
154A ALA* 3.8 14.8 - - + -
157A ILE* 5.5 0.4 - - + -
214A THR* 2.8 30.0 + - + +
215A CYS* 3.7 6.5 - - - +
216A ILE 3.2 0.2 - - - -
217A GLU* 1.3 77.5 - - - +
219A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 219 (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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122A PRO* 2.9 24.3 - - - +
128A ILE* 3.7 13.2 - - + -
215A CYS 3.0 16.6 + - - +
216A ILE 2.9 2.3 + - - +
218A LEU* 1.3 77.4 - - - +
220A GLU* 1.3 61.1 + - + +
245A LEU* 3.5 27.4 - - + -
250A TRP* 3.5 28.5 - - + +
254A PHE* 4.0 1.8 - - + -
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Residues in contact with GLU 220 (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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122A PRO* 4.2 3.4 - - - -
216A ILE* 2.6 31.0 + - - +
219A ALA* 1.3 84.7 - - + +
221A ARG* 1.3 67.9 + - - +
222A LYS* 3.1 16.4 + - - +
245A LEU* 3.5 10.6 - - - +
246A GLN* 2.9 53.2 + - + +
247A SER 4.6 0.7 + - - -
250A TRP* 5.1 4.0 + - - +
84B ARG* 2.9 24.6 + - - -
90B GLN* 4.8 11.3 + - - +
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Residues in contact with ARG 221 (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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116A LEU* 4.1 26.0 + - + +
117A GLU* 5.4 1.8 - - - +
120A LYS* 3.2 39.4 + - - +
121A LYS* 3.8 32.5 - - - +
122A PRO* 4.0 8.5 - - + -
217A GLU* 2.6 30.7 + - - +
218A LEU 4.4 0.6 - - - -
219A ALA 3.8 0.6 - - - -
220A GLU* 1.3 75.0 - - - +
222A LYS* 1.3 70.7 + - + +
52B GLU* 2.6 43.4 + - - -
92B ARG* 5.5 4.2 - - - +
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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
------------------------------------------------------------
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