Contacts of the helix formed by residues 178 - 194 (chain A) in PDB entry 1B3U
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 PRO 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASP 3.4 8.0 - - - +
177A THR* 1.3 87.0 - - + +
179A MET* 1.3 66.0 + - - +
181A ARG* 3.1 25.0 + - + +
182A ARG* 2.8 47.7 + - - +
216A GLN* 4.4 24.7 - - + +
219A VAL* 4.2 3.3 - - + +
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Residues in contact with MET 179 (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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140A PHE* 3.8 45.1 - - + -
144A THR* 4.0 6.8 - - + +
177A THR* 3.2 20.8 - - + -
178A PRO* 1.3 86.8 - - - +
180A VAL* 1.3 62.1 + - - +
182A ARG* 3.5 28.1 + - - +
183A ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 180 (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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140A PHE* 4.2 4.9 - - + +
143A ARG* 4.0 27.1 - - + +
144A THR* 4.1 17.9 - - + -
147A CYS* 4.2 1.9 - - - -
172A LEU* 3.8 27.6 - - + +
175A ASP* 3.7 28.9 - - + +
177A THR* 2.9 29.5 + - + +
179A MET* 1.3 76.3 - - - +
181A ARG* 1.3 64.6 + - - +
183A ALA* 3.2 4.1 + - - +
184A ALA* 3.0 21.1 + - - +
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Residues in contact with ARG 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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172A LEU 4.3 5.2 - - - -
173A CYS 3.3 25.1 - - - +
174A SER* 4.2 3.1 - - - +
175A ASP 2.9 37.7 + - - +
176A ASP* 3.1 21.6 + - - +
177A THR 3.1 2.6 + - - +
178A PRO* 3.1 24.3 + - - +
180A VAL* 1.3 75.8 - - - +
182A ARG* 1.3 58.2 + - - +
184A ALA* 3.3 4.1 + - - +
185A ALA* 2.9 29.5 + - - +
211A LEU* 4.2 5.4 - - + +
214A ASP* 2.7 39.8 + - - -
215A GLU* 5.8 1.4 - - - +
216A GLN* 4.1 19.2 + - - +
219A VAL* 4.2 12.0 - - + +
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Residues in contact with ARG 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 PRO* 2.8 29.5 + - - +
179A MET* 3.7 41.5 - - - +
181A ARG* 1.3 77.7 - - - +
183A ALA* 1.3 60.9 + - - +
185A ALA* 3.4 1.8 + - - -
186A SER* 3.0 21.3 + - - -
218A SER* 3.3 45.7 + - - +
219A VAL* 3.6 15.3 - - + -
222A LEU* 3.4 23.6 - - + +
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Residues in contact with ALA 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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144A THR* 4.2 23.1 - - - +
147A CYS* 3.9 15.5 - - + -
179A MET 3.2 12.8 + - - +
180A VAL 3.6 7.4 - - - +
182A ARG* 1.3 78.6 - - - +
184A ALA* 1.3 61.2 + - - +
186A SER* 2.5 24.4 + - - -
187A LYS* 3.3 17.0 + - - +
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Residues in contact with ALA 184 (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 CYS* 3.7 15.2 - - - -
169A PHE* 3.5 17.0 - - + -
172A LEU* 4.3 2.7 - - + -
173A CYS* 3.8 39.5 - - - +
180A VAL 3.0 12.4 + - - +
181A ARG 3.6 7.4 - - - +
183A ALA* 1.3 75.3 - - - +
185A ALA* 1.3 65.8 + - - +
187A LYS 3.0 2.3 + - - -
188A LEU* 2.9 21.4 + - - +
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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
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181A ARG 2.9 16.5 + - - +
182A ARG* 3.7 4.7 - - - +
184A ALA* 1.3 77.2 - - - +
186A SER* 1.3 62.0 + - - +
187A LYS 3.3 0.5 + - - -
188A LEU* 3.3 16.1 + - - +
189A GLY 4.6 1.4 + - - -
211A LEU* 3.9 31.3 - - + +
219A VAL* 4.8 6.5 - - + +
222A LEU* 4.1 31.6 - - + +
223A ALA* 5.3 1.6 - - - +
226A ALA* 4.6 6.4 + - - +
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Residues in contact with SER 186 (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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182A ARG 3.0 12.0 + - - -
183A ALA* 2.5 26.7 + - - -
185A ALA* 1.3 78.1 - - - +
187A LYS* 1.3 77.2 + - - +
188A LEU 3.5 0.2 - - - -
189A GLY 4.9 2.1 + - - -
190A GLU* 5.5 1.0 + - - +
222A LEU* 4.7 13.0 - - - +
225A GLU* 6.2 0.3 - - - +
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Residues in contact with LYS 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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112A ARG* 5.2 3.1 - - - +
147A CYS* 3.6 28.8 - - + +
148A GLY* 4.1 14.1 - - - +
169A PHE* 4.2 9.2 - - + -
183A ALA* 3.5 13.8 + - - +
184A ALA 3.0 4.5 + - - +
186A SER* 1.3 95.1 + - - +
188A LEU* 1.3 66.6 + - - +
189A GLY 3.1 3.7 + - - -
190A GLU* 3.2 34.2 + - + +
191A PHE* 3.0 21.9 + - + +
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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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169A PHE* 3.9 23.8 - - + -
173A CYS* 5.0 1.3 - - - -
184A ALA 2.9 11.1 + - - +
185A ALA* 3.3 15.6 + - - +
187A LYS* 1.3 77.2 - - - +
189A GLY* 1.3 56.8 + - - +
191A PHE* 3.4 1.5 + - + +
192A ALA* 3.0 28.1 + - - +
204A ILE* 4.0 27.6 - - + -
207A MET* 4.1 13.5 - - + -
208A PHE* 3.9 34.3 - - + +
211A LEU* 4.1 15.0 - - + -
226A ALA* 4.2 18.8 - - + -
230A ILE* 4.5 4.9 - - + -
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Residues in contact with GLY 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 4.6 2.0 + - - -
186A SER 4.9 2.2 + - - -
187A LYS 3.2 1.0 - - - -
188A LEU* 1.3 79.8 - - - +
190A GLU* 1.3 61.9 + - - +
192A ALA* 3.1 8.5 + - - +
193A LYS* 3.1 21.0 + - - +
226A ALA* 5.0 6.1 - - - +
229A ASN* 3.7 36.2 + - - +
230A ILE* 5.6 2.0 - - - -
233A LEU* 4.7 2.9 - - - +
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Residues in contact with GLU 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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112A ARG* 3.1 33.6 + - - -
147A CYS 4.9 0.9 - - - +
148A GLY* 4.5 3.6 - - - +
151A SER* 3.6 28.2 + - - +
186A SER 5.5 0.8 + - - +
187A LYS* 3.2 42.3 + - + +
189A GLY* 1.3 75.3 - - - +
191A PHE* 1.3 64.7 + - + +
193A LYS* 3.5 18.0 + - - +
194A VAL* 3.8 6.4 + - - +
229A ASN* 5.0 0.2 + - - -
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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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150A PHE* 4.0 27.8 - + + -
151A SER* 4.4 6.1 - - - -
154A TYR* 4.0 21.5 - + + -
166A ARG* 4.3 22.9 - - + -
169A PHE* 3.6 51.1 - + + -
187A LYS* 3.0 17.7 + - + +
188A LEU 3.7 3.8 - - - +
190A GLU* 1.3 78.2 - - + +
192A ALA* 1.3 64.2 + - - +
193A LYS 3.1 0.2 - - - -
194A VAL* 3.2 23.3 + - + +
195A LEU* 3.5 34.0 - - + +
204A ILE* 4.6 11.4 - - + -
207A MET* 5.1 3.4 - - + -
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Residues in contact with ALA 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 3.0 14.3 + - - +
189A GLY* 3.1 11.0 + - - +
191A PHE* 1.3 77.3 - - - +
193A LYS* 1.3 61.7 + - - +
195A LEU* 3.2 19.6 + - - +
200A VAL* 3.7 13.9 - - + +
204A ILE* 4.0 35.4 - - + +
229A ASN 6.4 0.2 - - - -
230A ILE* 5.0 5.2 - - + -
233A LEU* 3.9 18.6 - - + +
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Residues in contact with LYS 193 (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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189A GLY 3.1 11.3 + - - +
190A GLU* 3.5 16.4 - - - +
191A PHE 3.1 0.4 - - - -
192A ALA* 1.3 77.8 - - - +
194A VAL* 1.3 63.1 + - + +
195A LEU 3.4 3.7 + - - +
233A LEU* 3.2 36.6 - - + +
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Residues in contact with VAL 194 (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 SER* 4.1 33.9 - - - +
154A TYR* 3.5 33.8 - - + -
155A PRO* 4.0 16.8 - - + +
162A LYS* 5.5 0.3 + - - -
190A GLU 3.8 9.4 + - - +
191A PHE* 3.2 16.6 + - + +
193A LYS* 1.3 82.0 - - + +
195A LEU* 1.3 63.0 + - - +
196A GLU* 5.4 0.2 - - - -
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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
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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