Contacts of the helix formed by residues 185 - 204 (chain A) in PDB entry 3PMM
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 ARG 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.5 44.5 + - - +
137A GLU* 4.1 8.3 + - - +
180A GLY* 2.8 17.3 + - - +
183A LEU* 3.6 23.6 + - - +
184A ASN* 1.3 78.8 - - - +
186A PRO* 1.3 66.9 - - - +
187A GLN* 3.2 3.6 - - + +
188A TYR* 2.9 72.7 + - + +
189A VAL 3.9 0.7 + - - -
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Residues in contact with PRO 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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180A GLY 5.0 0.4 - - - +
184A ASN* 3.4 12.8 - - - +
185A ARG* 1.3 84.9 - - - +
187A GLN* 1.3 60.6 + - + +
188A TYR 3.1 0.2 - - - -
189A VAL* 3.0 13.7 + - + +
190A GLU* 2.9 39.6 + - + +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MSE 3.8 17.4 - - + +
185A ARG* 3.2 2.1 + - + -
186A PRO* 1.3 79.1 - - + +
188A TYR* 1.3 60.8 + - + +
190A GLU* 3.7 19.8 - - - +
191A GLU* 2.9 29.8 + - - +
383A FMT 3.8 15.1 - - - +
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.4 24.6 - - + +
137A GLU* 2.4 32.0 + - - +
140A MSE 3.4 36.1 - - + -
141A HIS* 5.6 0.7 - - - -
176A LEU* 3.6 28.5 - - + +
177A ALA* 4.7 0.2 - - - -
179A ILE* 4.1 7.0 - - + -
180A GLY* 3.6 28.7 - - - -
185A ARG* 2.9 55.6 + - + +
187A GLN* 1.3 80.7 - - + +
189A VAL* 1.3 58.7 + - - +
191A GLU* 3.5 2.8 + - - +
192A ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA* 3.7 27.8 - - + +
180A GLY* 3.9 6.7 - - - +
181A LYS* 3.9 37.0 - - + +
185A ARG 4.3 1.8 - - - +
186A PRO* 3.0 12.8 + - + +
188A TYR* 1.3 76.0 - - - +
190A GLU* 1.3 60.0 + - - +
192A ALA* 3.3 6.7 + - - +
193A THR* 2.9 36.5 + - - +
242A PHE* 5.2 0.4 - - + -
246A VAL* 4.1 26.2 - - + -
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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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186A PRO* 2.9 25.5 + - + +
187A GLN* 3.7 17.2 - - - +
189A VAL* 1.3 77.5 - - + +
191A GLU* 1.3 61.2 + - - +
193A THR* 3.4 7.0 + - - -
194A TYR* 3.0 23.6 + - - +
383A FMT 2.6 35.4 - - - +
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Residues in contact with GLU 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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140A MSE 3.5 25.4 - - - +
145A ARG* 3.0 27.0 + - - +
149A GLY 4.3 1.0 - - - +
151A MSE 4.3 4.3 - - + -
176A LEU* 4.1 10.5 - - + -
187A GLN 2.9 18.6 + - - +
188A TYR 3.7 2.2 - - - +
190A GLU* 1.3 76.8 - - - +
192A ALA* 1.3 62.7 + - - +
194A TYR* 3.2 13.7 + - - +
195A GLN* 2.9 49.3 + - - +
383A FMT 4.0 14.6 - - - +
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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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173A VAL* 3.5 28.0 - - + +
176A LEU* 4.6 4.2 - - + +
177A ALA* 3.7 25.1 - - + +
188A TYR 3.0 18.2 + - - +
189A VAL 3.6 5.4 - - - +
191A GLU* 1.3 75.8 - - - +
193A THR* 1.3 63.2 + - - +
195A GLN* 3.1 6.9 + - - +
196A PHE* 3.0 27.7 + - - -
242A PHE* 4.0 5.6 - - + -
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 2.9 23.8 + - - +
190A GLU* 3.7 7.4 - - - -
191A GLU 3.3 0.2 - - - -
192A ALA* 1.3 76.2 - - - +
194A TYR* 1.3 62.6 + - - +
196A PHE* 3.1 5.7 + - + +
197A LEU* 3.1 27.1 + - + +
242A PHE* 3.5 23.0 - - + -
246A VAL* 4.8 2.1 - - - +
248A LEU* 6.2 0.7 - - + -
254A VAL* 3.8 35.9 - - + -
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Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 2.6 37.9 + - - +
149A GLY* 4.3 8.1 - - - -
190A GLU 3.0 13.3 + - - +
191A GLU* 3.5 15.7 - - - +
193A THR* 1.3 77.6 - - - +
195A GLN* 1.3 75.3 + - - +
197A LEU* 3.2 16.3 + - + +
198A LEU* 3.0 43.8 + - + +
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Residues in contact with GLN 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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149A GLY 2.9 23.8 + - - -
150A GLY* 3.8 4.3 - - - -
151A MSE 3.0 46.9 + - + +
164A MSE 4.3 0.7 - - - +
169A LEU* 4.1 0.7 - - - -
173A VAL* 4.0 18.2 - - + -
191A GLU* 2.9 42.1 + - - +
192A ALA* 3.1 8.0 + - - +
194A TYR* 1.3 84.2 - - - +
196A PHE* 1.3 57.7 + - - +
198A LEU* 4.6 2.1 - - - +
199A HIS* 2.7 52.6 + - + -
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Residues in contact with PHE 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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169A LEU* 3.9 28.4 - - + +
173A VAL* 3.7 19.5 - - + -
174A LEU 5.3 0.9 - - - -
192A ALA 3.0 23.1 + - - -
193A THR* 3.1 9.1 + - - +
195A GLN* 1.3 77.4 - - - +
197A LEU* 1.3 64.9 + - + +
199A HIS* 3.9 1.2 - - - +
200A VAL* 3.0 31.1 + - + +
211A TRP* 6.4 0.2 - + - -
238A VAL* 4.0 22.9 - - + -
239A ILE* 4.0 24.5 - - + -
242A PHE* 3.5 55.6 - + + -
258A LEU* 4.3 26.7 - - + -
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Residues in contact with LEU 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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193A THR* 3.1 22.9 + - + +
194A TYR* 3.7 18.8 - - + +
196A PHE* 1.3 78.6 - - + +
198A LEU* 1.3 58.2 + - - +
200A VAL* 3.4 5.0 + - - +
201A GLN* 3.0 26.5 + - - +
254A VAL* 4.9 18.8 - - + -
257A TYR* 4.1 29.1 - - + -
258A LEU* 4.7 10.1 - - + -
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Residues in contact with LEU 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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148A GLN* 3.5 27.8 - - + +
150A GLY* 3.5 33.2 - - - +
164A MSE 4.0 7.6 - - + -
194A TYR* 3.0 39.0 + - + +
195A GLN* 4.1 4.3 - - - +
197A LEU* 1.3 74.0 - - - +
199A HIS* 1.3 67.1 + - - +
201A GLN* 3.3 34.9 + - - +
202A ASN* 3.1 29.4 + - - +
217A TYR* 3.9 11.2 - - - +
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Residues in contact with HIS 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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151A MSE 4.4 4.9 + - - -
164A MSE 3.2 38.7 - - + +
165A TRP 3.6 15.1 + - - -
168A THR* 3.6 37.5 - - + +
169A LEU* 3.6 31.8 - - + +
195A GLN* 2.7 46.6 + - - +
196A PHE 4.0 2.0 - - - +
198A LEU* 1.3 74.2 - - - +
200A VAL* 1.3 66.7 + - - +
202A ASN* 3.3 0.4 + - - -
203A LEU* 2.9 43.4 + - + +
211A TRP* 4.0 4.7 - - + -
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Residues in contact with VAL 200 (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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196A PHE* 3.0 23.0 + - + +
197A LEU* 3.6 8.3 - - - +
199A HIS* 1.3 77.0 - - - +
201A GLN* 1.3 65.7 + - - +
204A MSE 3.1 43.3 + - + +
211A TRP* 3.5 27.8 - - + -
239A ILE* 5.9 1.6 - - + -
257A TYR* 3.5 30.3 - - + +
258A LEU* 4.6 12.3 - - + -
261A VAL* 4.2 14.4 - - + -
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Residues in contact with GLN 201 (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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148A GLN* 3.0 29.8 + - - +
197A LEU 3.0 14.6 + - - +
198A LEU* 3.4 21.6 - - - +
199A HIS 3.3 0.2 - - - -
200A VAL* 1.3 80.6 - - - +
202A ASN* 1.3 80.0 + - - +
204A MSE 4.8 4.2 - - - +
217A TYR* 5.2 0.2 - - - -
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Residues in contact with ASN 202 (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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164A MSE 3.4 23.5 - - + -
198A LEU* 3.1 15.1 + - - +
199A HIS* 4.3 1.6 - - - +
200A VAL 3.2 0.2 - - - -
201A GLN* 1.3 103.2 + - - +
203A LEU* 1.3 62.7 + - + +
204A MSE 5.0 0.4 - - - -
215A TRP* 3.6 44.4 - - + +
217A TYR* 2.9 29.0 + - - -
222A ASN* 3.0 24.4 + - - +
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Residues in contact with LEU 203 (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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164A MSE 3.7 6.7 - - + +
165A TRP* 3.7 29.2 - - - +
166A ASP* 3.8 8.5 - - - +
199A HIS* 2.9 33.5 + - + +
202A ASN* 1.3 83.2 - - + +
204A MSE 1.3 66.1 + - - +
205A ASP 3.6 0.2 + - - -
211A TRP* 3.5 15.9 - - + -
212A PHE* 2.9 43.9 + - - +
213A HIS 3.9 0.7 - - - +
214A GLY* 3.3 42.6 - - - +
215A TRP* 3.5 10.5 - - + +
222A ASN* 4.2 2.0 - - - +
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Residues in contact with MSE 204 (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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199A HIS 4.1 0.2 + - - -
200A VAL* 3.1 37.0 + - + +
201A GLN 4.8 3.5 - - - +
202A ASN 5.0 0.9 - - - -
203A LEU* 1.3 82.2 + - - +
205A ASP* 1.3 88.4 + - - +
206A ARG* 3.6 14.2 + - + -
209A GLY* 4.4 11.7 - - - +
210A LEU 3.8 4.7 - - - +
211A TRP* 3.5 37.4 - - + +
212A PHE* 4.9 3.3 - - - -
257A TYR* 4.3 9.9 - - - +
261A VAL* 4.5 15.9 - - + -
264A ALA* 6.1 3.6 - - + -
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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