Contacts of the helix formed by residues 179 - 199 (chain A) in PDB entry 3P3B
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 1.3 92.9 - - + +
180A LEU* 1.3 57.0 + - - +
181A TRP 3.5 0.7 - - - -
182A GLU* 3.4 36.3 - - + +
183A GLY* 2.7 33.4 + - - -
215B ASN* 4.3 4.3 - - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY* 3.3 27.6 + - - +
178A MET 3.5 1.2 + - - -
179A PRO* 1.3 72.4 - - - +
181A TRP* 1.3 62.2 + - - +
184A THR* 2.8 36.6 + - - +
212A TYR* 6.3 0.2 - - + -
216A LEU* 3.8 18.4 - - + -
180B LEU* 4.6 2.2 - - + -
181B TRP* 3.5 31.0 - - + -
213B ASN* 3.5 20.6 - - - +
215B ASN* 4.3 9.3 - - + +
216B LEU* 3.3 42.6 - - + +
219B GLU* 5.3 3.4 - - - +
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Residues in contact with TRP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A PRO 3.5 0.2 - - - -
180A LEU* 1.3 78.2 - - - +
182A GLU* 1.3 97.3 + - + +
184A THR* 3.3 5.6 + - - -
185A LYS* 3.0 72.2 + - + +
219A GLU* 5.4 7.4 + - - -
181B TRP* 3.9 34.2 - + + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A MET* 3.8 14.9 - - + +
179A PRO* 3.4 35.7 + - + +
181A TRP* 1.3 110.8 + - + +
183A GLY* 1.3 61.3 + - - +
185A LYS* 3.6 5.3 + - - +
186A ARG* 3.1 23.6 + - - +
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Residues in contact with GLY 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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173A ARG* 3.6 3.5 - - - +
174A GLY* 3.6 20.6 - - - -
178A MET* 3.9 17.9 - - - +
179A PRO 2.7 22.3 + - - -
182A GLU* 1.3 73.1 - - - +
184A THR* 1.3 57.6 + - - +
186A ARG* 3.3 3.3 + - - +
187A ASP* 2.9 31.7 + - - +
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Residues in contact with THR 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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174A GLY* 4.6 2.8 + - - -
180A LEU* 2.8 26.1 + - - +
181A TRP* 3.3 4.9 + - - -
183A GLY* 1.3 74.1 - - - +
185A LYS* 1.3 65.9 + - - +
187A ASP* 3.3 12.6 + - - +
188A ILE* 3.1 28.9 + - + +
212A TYR* 4.8 5.3 - - + +
216A LEU* 3.8 26.6 - - + +
219A GLU* 4.6 11.9 - - - +
220A VAL* 3.5 30.1 - - + -
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Residues in contact with LYS 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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145A GLU* 3.9 22.5 + - - +
181A TRP* 3.0 66.0 + - + +
182A GLU* 3.8 6.5 - - - +
184A THR* 1.3 75.6 - - - +
186A ARG* 1.3 62.7 + - - +
188A ILE* 3.3 11.9 + - + +
189A ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 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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139A ASP* 3.0 29.7 + - - +
140A LEU* 5.0 1.0 - - - +
142A LEU 2.8 29.8 + - - -
143A ALA* 3.1 21.0 + - - +
144A ASP 3.8 4.0 - - - -
145A GLU* 3.7 24.4 + - - +
148A ALA* 3.3 24.5 - - - +
173A ARG* 3.4 22.7 - - - +
178A MET* 4.2 25.2 - - + +
182A GLU 3.1 19.1 + - - +
183A GLY 3.5 5.8 - - - +
185A LYS* 1.3 73.8 - - - +
187A ASP* 1.3 65.7 + - - +
189A ALA* 3.3 2.5 + - - +
190A ILE* 2.9 34.0 + - + +
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Residues in contact with ASP 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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171A VAL* 3.7 9.2 - - + -
172A GLY* 2.7 29.6 + - - -
173A ARG* 3.1 46.4 + - - +
174A GLY 4.6 0.3 + - - -
183A GLY 2.9 16.0 + - - +
184A THR* 3.3 12.2 + - - +
186A ARG* 1.3 74.2 - - - +
188A ILE* 1.3 66.1 + - + +
190A ILE* 3.2 2.1 + - - +
191A VAL* 2.9 28.9 + - - +
212A TYR* 2.8 23.9 + - - +
220A VAL* 5.3 1.8 - - + -
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Residues in contact with ILE 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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184A THR* 3.1 22.9 + - + +
185A LYS* 3.6 10.5 - - + +
186A ARG 3.2 0.2 - - - -
187A ASP* 1.3 80.1 - - - +
189A ALA* 1.3 56.9 + - - +
191A VAL* 3.3 2.2 + - - -
192A ARG* 3.0 49.8 + - - +
219A GLU* 4.7 7.6 - - + +
220A VAL* 4.3 32.5 - - + +
223A ALA* 3.6 31.4 - - + -
224A LEU* 3.6 20.7 - - + +
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Residues in contact with ALA 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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145A GLU* 3.5 35.7 - - + +
149A VAL* 3.6 22.4 - - + +
185A LYS 3.1 10.7 + - - +
186A ARG 3.7 3.4 - - - +
188A ILE* 1.3 77.7 - - - +
190A ILE* 1.3 57.5 + - - +
192A ARG* 3.5 8.9 + - - +
193A GLY* 2.9 25.1 + - - -
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Residues in contact with ILE 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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139A ASP* 4.2 0.7 - - - +
148A ALA* 3.7 10.3 - - + +
149A VAL* 3.6 38.5 - - + +
152A MET* 3.7 27.6 - - + -
169A ILE* 4.1 13.7 - - + -
173A ARG* 4.0 26.2 - - - +
186A ARG* 2.9 35.3 + - - +
187A ASP 3.5 4.5 - - - +
189A ALA* 1.3 77.2 - - - +
191A VAL* 1.3 63.3 + - - +
193A GLY* 3.2 1.4 + - - -
194A ILE* 2.9 34.6 + - + +
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Residues in contact with VAL 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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169A ILE* 4.0 22.7 - - + +
171A VAL* 3.7 25.4 - - + -
187A ASP 2.9 21.0 + - - +
188A ILE 3.8 3.8 - - - +
190A ILE* 1.3 75.6 - - - +
192A ARG* 1.3 64.1 + - - +
194A ILE* 3.9 1.6 - - - +
195A SER* 3.0 22.2 + - - -
204A ILE* 4.2 2.7 - - + -
206A ILE* 3.8 15.0 - - + -
220A VAL* 6.1 0.4 - - + -
224A LEU* 3.8 29.4 - - + -
227A VAL* 4.5 3.1 - - + -
229A LEU* 4.0 20.6 - - + -
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Residues in contact with ARG 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 ILE* 3.0 34.7 + - - +
189A ALA* 3.9 7.0 - - - +
191A VAL* 1.3 75.3 - - - +
193A GLY* 1.3 63.0 + - - +
195A SER* 3.2 9.3 + - - -
196A GLU* 2.9 35.3 + - - +
223A ALA* 2.5 33.7 + - - +
224A LEU* 3.7 14.8 - - + -
226A ASP* 3.8 21.8 + - - -
227A VAL* 3.9 11.2 - - + +
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Residues in contact with GLY 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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149A VAL* 3.9 12.1 - - - -
153A GLN* 2.8 37.4 + - - +
189A ALA 2.9 16.2 + - - -
190A ILE 3.6 3.4 - - - -
192A ARG* 1.3 76.5 - - - +
194A ILE* 1.3 61.1 + - - +
196A GLU* 3.3 15.2 + - - +
197A VAL 3.3 3.6 + - - -
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Residues in contact with ILE 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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135A LEU* 3.7 26.9 - - + -
149A VAL 5.8 0.2 - - - +
152A MET* 4.0 31.0 - - + +
153A GLN* 4.5 1.1 - - - +
156A ALA* 3.9 17.7 - - + -
167A PHE* 4.4 7.4 - - + -
169A ILE* 3.7 37.7 - - + -
190A ILE* 2.9 30.3 + - + +
193A GLY* 1.3 73.5 - - - +
195A SER* 1.3 60.9 + - - +
197A VAL* 3.0 7.8 + - - +
198A ALA* 2.8 27.2 + - - +
204A ILE* 4.4 10.5 - - + -
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Residues in contact with SER 195 (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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191A VAL 3.0 13.9 + - - -
192A ARG 3.2 11.2 - - - -
194A ILE* 1.3 76.5 - - - +
196A GLU* 1.3 62.6 + - - +
198A ALA* 3.3 1.3 + - - +
199A GLY* 3.1 23.9 + - - +
204A ILE* 4.3 15.7 - - - +
227A VAL* 3.4 38.6 - - - +
228A ASN* 4.6 2.8 + - - +
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Residues in contact with GLU 196 (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 GLN* 4.1 8.9 + - - +
192A ARG* 2.9 28.1 + - - +
193A GLY* 3.3 13.0 - - - +
195A SER* 1.3 78.3 + - - +
197A VAL* 1.3 63.0 + - + +
198A ALA 3.5 0.2 + - - -
199A GLY* 3.5 8.8 + - - -
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Residues in contact with VAL 197 (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 GLN* 3.7 37.5 - - + +
156A ALA* 4.0 20.4 - - + -
157A MET* 3.0 48.4 - - + +
160A TYR* 5.0 5.3 - - + -
167A PHE* 5.9 1.1 - - + -
193A GLY 3.3 3.3 + - - +
194A ILE* 3.0 9.5 + - - +
196A GLU* 1.3 81.2 - - + +
198A ALA* 1.3 63.7 + - + +
199A GLY* 3.6 0.3 + - - -
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Residues in contact with ALA 198 (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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160A TYR* 4.6 14.3 - - - -
165A ARG* 4.8 1.6 - - - +
167A PHE* 4.1 25.1 - - + -
194A ILE* 2.8 18.0 + - + +
195A SER 3.3 2.9 + - - +
197A VAL* 1.3 76.1 - - + +
199A GLY* 1.3 67.7 + - - +
201A ALA* 4.6 2.4 + - - +
202A GLY* 3.9 14.4 + - - -
204A ILE* 4.0 23.1 - - + -
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Residues in contact with GLY 199 (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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195A SER 3.1 15.5 + - - +
196A GLU 3.5 6.6 + - - -
197A VAL 3.4 3.0 - - - -
198A ALA* 1.3 79.4 - - - +
200A PRO* 1.3 71.1 - - - +
201A ALA 3.3 0.7 - - - -
202A GLY* 3.1 21.5 + - - +
204A ILE* 6.0 0.5 - - - +
228A ASN* 5.4 1.9 + - - +
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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