Contacts of the helix formed by residues 174 - 192 (chain A) in PDB entry 5UDJ
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 ASN 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO* 4.7 10.9 - - - +
143A CYS* 4.5 2.8 - - - -
167A VAL* 3.8 14.8 - - + +
168A LEU* 4.1 0.9 - - - +
171A ASP* 3.2 35.2 + - - +
172A PRO 3.5 1.4 - - - -
173A GLU* 1.3 74.7 - - - +
175A PRO* 1.3 72.1 - - - +
176A GLU* 3.4 9.3 + - - +
177A SER* 2.8 42.8 + - - +
178A SER* 3.0 23.0 + - - -
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Residues in contact with PRO 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU 3.1 9.9 - - - +
174A ASN* 1.3 87.3 - - + +
176A GLU* 1.3 62.9 + - - +
178A SER* 3.3 1.4 + - - -
179A ALA* 3.1 12.1 + - - +
212A LEU* 3.6 28.0 - - + +
213A ASN* 3.0 37.6 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.2 1.8 - - - -
93A ARG* 2.7 45.7 + - - -
143A CYS* 3.5 17.3 - - - +
147A TRP* 2.9 38.3 + - + +
174A ASN* 3.3 7.8 + - - +
175A PRO* 1.3 79.4 - - - +
177A SER* 1.3 60.3 + - - +
179A ALA* 3.2 7.6 + - - +
180A GLY 3.0 22.5 + - - -
213A ASN* 4.8 2.5 - - - -
1B G3A 4.7 5.3 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 3.8 10.1 - - - -
164A PHE* 3.6 22.2 - - - +
167A VAL* 3.3 27.7 - - - +
168A LEU* 3.3 9.7 - - - +
174A ASN* 2.8 34.0 + - - +
176A GLU* 1.3 76.3 - - - +
178A SER* 1.3 62.1 + - - +
181A TYR* 2.8 32.7 + - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.1 16.2 - - - -
172A PRO 5.3 0.2 - - - -
174A ASN 3.0 20.8 + - - -
175A PRO 3.5 4.9 - - - -
177A SER* 1.3 78.3 + - - +
179A ALA* 1.3 56.9 + - - +
181A TYR* 3.8 2.6 - - - +
182A ALA* 3.0 30.3 + - - +
205A PRO* 4.3 1.6 + - - +
208A GLN* 3.8 7.4 - - - +
209A ALA* 3.3 26.8 + - - -
212A LEU* 3.7 20.1 - - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TRP* 4.1 12.1 - - + -
175A PRO 3.1 13.2 + - - +
176A GLU* 3.5 9.6 - - - +
178A SER* 1.3 76.8 + - - +
180A GLY* 1.3 56.5 + - - +
182A ALA* 3.2 2.9 + - - +
183A ILE* 2.9 34.3 + - + +
209A ALA* 3.9 10.7 - - - +
213A ASN* 4.0 14.1 - - - +
216A ASN* 4.9 7.4 - - - +
219A ILE* 4.5 15.5 - - + -
1B G3A 5.2 2.7 - - + +
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TRP* 3.5 23.2 - - - -
150A LEU* 4.3 0.2 - - - +
164A PHE* 3.3 25.1 - - - -
176A GLU 3.0 12.1 + - - -
179A ALA* 1.3 75.9 - - - +
181A TYR* 1.3 61.8 + - - +
183A ILE* 3.4 1.7 + - - +
184A SER* 2.9 30.5 + - - -
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Residues in contact with TYR 181 (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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161A LYS* 3.5 43.1 + - + +
164A PHE* 3.5 11.2 - - + +
165A GLU* 3.5 41.3 + - + -
168A LEU* 3.7 19.5 - - + -
177A SER 2.8 23.8 + - - +
178A SER 3.8 2.5 - - - +
180A GLY* 1.3 71.2 - - - +
182A ALA* 1.3 58.8 + - - +
184A SER* 3.4 3.6 + - - -
185A ALA* 2.9 35.9 + - + +
205A PRO* 3.8 31.4 - - + +
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Residues in contact with ALA 182 (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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178A SER 3.0 18.1 + - - +
179A ALA 3.7 3.8 - - - +
181A TYR* 1.3 78.5 - - - +
183A ILE* 1.3 58.2 + - - +
185A ALA* 3.4 2.0 + - - +
186A TYR* 2.8 30.7 + - - +
202A SER* 4.2 2.8 - - - -
205A PRO* 3.6 38.6 - - - +
206A LEU* 3.8 20.1 - - + +
209A ALA* 4.0 6.1 - - + -
219A ILE* 5.1 0.7 - - + -
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Residues in contact with ILE 183 (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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147A TRP* 3.9 12.8 - - + -
150A LEU* 3.9 7.2 - - + -
179A ALA* 2.9 21.7 + - + +
180A GLY 4.0 2.9 - - - +
182A ALA* 1.3 72.4 - - - +
184A SER* 1.4 65.1 + - - +
186A TYR* 3.3 6.5 + - - +
187A ARG* 3.0 45.5 + - - +
206A LEU* 5.5 0.2 - - + -
218A TYR* 4.0 10.1 - - + -
219A ILE* 4.0 15.9 - - + -
222A LEU* 4.0 24.7 - - + -
1B G3A 3.6 47.8 - - + +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.7 24.0 - - - +
157A TYR* 4.4 6.1 - - - +
160A ALA* 3.8 1.2 - - - +
161A LYS* 3.7 32.0 + - - -
164A PHE* 3.7 13.9 - - - -
180A GLY 2.9 20.9 + - - -
181A TYR 3.7 2.2 - - - -
183A ILE* 1.4 76.9 - - - +
185A ALA* 1.3 57.6 + - - +
187A ARG* 3.3 4.3 + - - +
188A LEU* 3.0 35.0 + - - +
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 4.3 19.2 - - + +
181A TYR* 2.9 29.5 + - + +
182A ALA* 3.7 5.4 - - - +
184A SER* 1.3 74.1 - - - +
186A TYR* 1.3 61.3 + - - +
188A LEU* 3.3 5.8 + - - +
189A ASP* 2.8 33.4 + - - +
201A PHE* 4.9 4.0 - - + +
202A SER* 3.5 21.1 - - - +
205A PRO* 4.8 0.9 - - + -
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 2.8 19.0 + - - +
183A ILE* 3.3 6.5 + - - +
185A ALA* 1.3 75.7 - - - +
187A ARG* 1.3 72.4 + - + +
189A ASP* 3.2 4.0 + - - +
190A GLY* 3.0 19.1 + - - -
202A SER* 3.3 12.0 - - - +
206A LEU* 3.9 17.0 - - + -
222A LEU* 3.7 49.1 - - + -
225A LEU* 3.5 26.3 - - + +
226A LYS* 3.8 34.3 + - - -
229A ASP* 4.7 4.5 + - - -
259A LYS* 4.0 13.9 + - - -
263A ARG* 5.5 0.2 + - - -
2B A 3.4 22.6 + - - -
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Residues in contact with ARG 187 (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 LEU* 3.4 17.5 + - - +
157A TYR* 3.1 37.3 + - + -
183A ILE* 3.0 32.8 + - - +
184A SER 3.8 2.5 - - - +
186A TYR* 1.3 86.0 - - + +
188A LEU* 1.3 63.5 + - - +
190A GLY* 3.0 12.3 + - - +
191A PHE* 3.2 21.6 + - - -
218A TYR* 2.9 27.1 + - - -
222A LEU* 5.8 1.2 - - - +
256A TYR* 4.4 0.8 + - - -
1B G3A 2.9 87.3 + - - +
2B A 4.0 10.0 + - - +
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Residues in contact with LEU 188 (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 GLY 5.4 0.2 - - - +
157A TYR* 3.8 36.8 - - + +
158A GLU* 3.7 36.3 - - + +
161A LYS* 3.9 27.6 - - + +
184A SER 3.0 20.2 + - - +
185A ALA* 3.7 4.3 - - - +
187A ARG* 1.3 75.4 - - - +
189A ASP* 1.3 64.5 + - - +
191A PHE* 3.2 37.6 + - + +
192A LYS* 3.6 10.9 + - - +
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Residues in contact with ASP 189 (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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185A ALA 2.8 16.1 + - - +
186A TYR 3.4 9.4 - - - +
188A LEU* 1.3 75.2 - - - +
190A GLY* 1.3 63.3 + - - +
192A LYS* 3.1 16.6 + - - +
193A LEU* 3.1 15.7 + - + +
198A HIS* 5.8 0.5 - - - +
199A LYS 3.6 10.9 - - - +
200A PRO* 3.6 5.9 - - - +
201A PHE* 3.3 32.1 + - - +
202A SER* 2.7 33.9 + - - +
226A LYS* 3.9 18.2 - - - +
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Residues in contact with GLY 190 (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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186A TYR* 3.0 14.8 + - - -
187A ARG* 3.0 6.6 + - - -
189A ASP* 1.3 77.5 - - - +
191A PHE* 1.3 63.3 + - - +
192A LYS 3.2 0.5 + - - -
193A LEU* 3.3 16.0 + - - -
226A LYS* 5.1 1.7 - - - +
4B A 2.9 29.1 + - - +
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Residues in contact with PHE 191 (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 GLY* 3.9 25.1 - - - -
157A TYR* 3.5 22.4 - + - -
187A ARG 3.2 13.4 + - - -
188A LEU* 3.2 34.2 + - + +
190A GLY* 1.3 78.4 - - - +
192A LYS* 1.3 67.1 + - + +
193A LEU 3.8 0.2 + - - -
194A ALA 5.2 0.3 + - - -
195A THR* 4.9 4.0 - - - +
372A VAL* 4.3 11.0 - - + -
373A VAL* 3.6 42.1 - - + +
375A GLU* 4.9 2.6 - - - +
1B G3A 3.6 38.6 - + - -
4B A 4.7 6.0 - - - +
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Residues in contact with LYS 192 (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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188A LEU 3.6 10.3 + - - +
189A ASP* 3.1 11.4 + - - +
191A PHE* 1.3 83.8 - - + +
193A LEU* 1.3 63.4 + - - +
194A ALA 3.2 2.7 - - - -
195A THR* 2.7 44.9 + - + +
198A HIS* 3.3 13.1 - - + +
375A GLU* 3.9 26.7 + - - -
410A GLN* 4.4 14.3 - - - +
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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
------------------------------------------------------------
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