Contacts of the helix formed by residues 180 - 204 (chain A) in PDB entry 1FPQ
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 LYS 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A MSE 1.3 68.1 + - - +
182A ASN* 4.0 21.8 - - + +
183A GLN* 3.2 24.7 + - + +
184A ILE* 3.3 24.6 + - - +
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Residues in contact with MSE 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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180A LYS* 1.3 73.1 - - - +
182A ASN* 1.3 64.4 + - - +
184A ILE* 3.2 10.2 + - - +
185A PHE* 2.9 29.9 + - + +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 3.2 20.4 - - + +
181A MSE 1.3 79.7 - - - +
183A GLN* 1.3 54.5 + - - +
185A PHE* 3.4 7.4 + - - +
186A ASN* 2.7 64.9 + - - +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 3.2 20.7 + - + +
182A ASN* 1.3 80.7 + - - +
184A ILE* 1.3 91.4 + - - +
186A ASN* 4.0 7.0 - - - +
187A LYS* 3.0 51.7 + - + +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS 3.6 19.5 - - - +
181A MSE 3.2 11.3 + - + +
183A GLN* 1.3 89.3 - - - +
185A PHE* 1.3 65.8 + - - +
187A LYS* 3.7 4.6 - - - +
188A SER* 3.0 25.5 + - - +
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Residues in contact with PHE 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 MSE 2.9 21.2 + - + +
182A ASN* 3.7 8.1 - - - +
184A ILE* 1.3 77.4 - - - +
186A ASN* 1.3 72.6 + - - +
188A SER* 2.7 23.8 + - - -
189A MSE 2.9 57.7 + - + +
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Residues in contact with ASN 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 ASN* 2.7 47.4 + - - +
183A GLN* 4.1 5.3 - - - +
185A PHE* 1.3 92.4 - - - +
187A LYS* 1.3 61.7 - - - +
189A MSE 3.9 5.5 - - - +
190A VAL* 3.1 31.0 + - + +
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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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183A GLN* 3.0 43.9 + - - +
184A ILE* 3.7 5.8 - - - +
185A PHE 3.1 0.2 - - - -
186A ASN* 1.3 74.3 - - - +
188A SER* 1.3 65.6 + - - +
190A VAL* 3.2 7.1 + - + +
191A ASP* 3.0 40.2 + - - +
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Residues in contact with SER 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 ILE* 3.0 17.2 + - - +
185A PHE* 2.7 24.4 + - - -
187A LYS* 1.3 77.1 - - - +
189A MSE 1.3 73.8 + - - +
191A ASP* 3.3 7.0 + - - +
192A VAL* 3.0 33.8 + - - +
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Residues in contact with MSE 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 PHE* 2.9 57.6 + - + +
186A ASN* 3.9 7.2 - - - +
188A SER* 1.3 88.3 + - - +
190A VAL* 1.3 63.4 + - + +
192A VAL* 4.3 11.5 - - + +
193A CYS* 3.1 29.9 + - - +
1699A SAM 4.0 29.4 - - - +
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Residues in contact with VAL 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 ASN* 3.1 23.0 + - + +
187A LYS* 3.2 6.9 + - - +
189A MSE 1.3 77.6 - - + +
191A ASP* 1.3 65.1 + - - +
193A CYS* 3.5 5.2 + - - +
194A ALA* 3.0 29.1 + - + +
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Residues in contact with ASP 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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187A LYS* 3.0 34.0 + - - +
188A SER* 3.7 7.4 - - - +
190A VAL* 1.3 81.5 - - - +
192A VAL* 1.3 67.6 + - + +
194A ALA* 3.3 7.1 + - - +
195A THR* 3.0 26.4 + - - -
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Residues in contact with VAL 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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29A MSE 6.2 5.4 - - + -
188A SER* 3.0 24.8 + - - +
189A MSE 4.3 12.1 - - + +
191A ASP* 1.3 76.5 - - + +
193A CYS* 1.3 57.5 + - - +
195A THR* 3.2 9.0 + - - -
196A GLU* 2.9 50.6 + - + +
307A PHE* 6.1 0.9 - - + -
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Residues in contact with CYS 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 MSE 3.1 22.0 + - - +
190A VAL* 3.6 7.0 - - - +
192A VAL* 1.3 75.7 - - - +
194A ALA* 1.3 59.3 + - - +
196A GLU* 3.4 6.8 + - - +
197A MSE 2.9 37.2 + - - +
223A ASN* 3.7 32.5 - - - +
274A LYS* 3.8 17.7 - - - -
1699A SAM 3.8 22.9 - - - -
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Residues in contact with ALA 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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190A VAL* 3.0 20.1 + - + +
191A ASP* 3.3 6.7 + - - +
193A CYS* 1.3 76.5 - - - +
195A THR* 1.3 57.9 + - - +
197A MSE 4.1 4.1 - - - +
198A LYS* 3.0 30.5 + - - +
226A LEU* 5.0 11.0 - - + +
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Residues in contact with THR 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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25A CYS* 3.9 27.6 - - - -
29A MSE 6.2 1.3 - - + -
191A ASP 3.0 15.2 + - - -
192A VAL* 3.4 11.1 - - - -
194A ALA* 1.3 77.6 - - - +
196A GLU* 1.3 67.3 + - + +
198A LYS* 3.5 10.1 + - - +
199A ARG* 3.5 8.3 + - - +
362A PHE* 3.7 8.6 - - + -
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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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29A MSE 5.6 2.9 - - - -
192A VAL* 2.9 38.4 + - + +
193A CYS* 3.8 7.4 - - - +
195A THR* 1.3 77.5 - - - +
197A MSE 1.3 56.9 + - - +
199A ARG* 3.4 3.8 + - - +
200A MSE 3.0 28.2 + - - +
274A LYS* 2.8 37.6 + - - -
307A PHE* 3.3 33.3 - - + -
361A ALA* 5.1 0.2 - - - +
362A PHE* 3.9 17.5 - - + -
365A LEU* 3.8 25.0 - - + +
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Residues in contact with MSE 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 CYS 2.9 20.7 + - - +
194A ALA 4.1 0.9 - - - +
196A GLU* 1.3 72.6 - - - +
198A LYS* 1.3 66.5 + - - +
200A MSE 3.7 34.5 - - + -
201A LEU* 3.1 36.1 + - + +
223A ASN* 3.5 33.7 - - + +
226A LEU* 3.9 20.9 - - + -
227A ILE* 3.9 30.5 - - + -
272A ILE* 5.8 1.3 - - - -
274A LYS* 4.0 23.3 - - - -
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Residues in contact with LYS 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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194A ALA 3.0 19.3 + - - +
195A THR* 3.8 7.0 - - - +
196A GLU 3.3 0.4 - - - -
197A MSE 1.3 78.6 - - - +
199A ARG* 1.3 63.5 + - - +
201A LEU* 3.6 6.8 + - - +
202A GLU* 3.1 42.0 + - + +
226A LEU* 5.6 0.8 - - - +
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Residues in contact with ARG 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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21A GLU* 5.5 11.0 - - - +
22A ASP* 2.9 42.3 + - - +
195A THR 3.5 2.3 + - - +
196A GLU 3.4 3.0 + - - +
197A MSE 3.2 0.2 - - - -
198A LYS* 1.3 76.5 - - - +
200A MSE 1.3 66.9 + - - +
202A GLU* 2.9 51.0 + - - +
203A ILE* 3.3 40.7 + - + +
361A ALA* 3.4 25.8 - - + -
362A PHE* 3.4 32.3 - - + -
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Residues in contact with MSE 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 GLU 3.0 17.8 + - - +
197A MSE 3.5 36.8 + - + +
199A ARG* 1.3 75.0 - - - +
201A LEU* 1.3 60.6 - - - +
203A ILE* 3.0 10.6 + - - -
204A TYR* 2.8 38.9 + - + +
207A PHE* 4.0 30.3 - - - -
272A ILE* 4.5 6.1 - - + -
274A LYS* 5.4 0.2 - - + -
303A ILE* 6.2 0.4 - - - -
305A VAL* 3.3 42.6 - - + -
361A ALA* 4.7 5.8 - - + +
365A LEU* 5.8 2.7 - - + -
367A VAL* 3.8 22.9 - - + -
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Residues in contact with LEU 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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197A MSE 3.1 26.2 + - + +
198A LYS* 3.9 6.3 - - - +
200A MSE 1.3 79.4 - - - +
202A GLU* 1.3 60.8 + - + +
204A TYR* 4.2 10.9 - - - +
207A PHE* 3.7 33.0 - - + -
226A LEU* 3.7 38.1 - - + +
227A ILE* 4.1 15.0 - - + -
229A SER 4.9 0.9 - - - +
230A LYS* 3.2 44.9 + - + -
231A TYR* 4.7 0.6 + - + -
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Residues in contact with GLU 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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198A LYS* 3.1 38.1 + - + +
199A ARG* 2.9 44.2 + - - +
201A LEU* 1.3 78.7 - - + +
203A ILE* 1.3 61.9 + - - +
230A LYS* 5.3 1.1 - - - +
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Residues in contact with ILE 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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22A ASP* 5.5 0.2 - - - +
199A ARG* 3.4 42.6 - - + +
200A MSE 3.0 12.3 + - - +
202A GLU* 1.3 80.1 - - - +
204A TYR* 1.3 66.4 + - - +
205A THR* 3.7 10.7 + - - +
359A CYS* 3.9 26.3 - - + +
360A ARG 3.4 33.4 - - - +
361A ALA* 4.0 14.6 - - + +
367A VAL* 5.7 1.1 - - + -
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Residues in contact with TYR 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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200A MSE 2.8 29.3 + - + +
201A LEU* 4.2 8.7 - - - +
203A ILE* 1.3 73.4 - - - +
205A THR* 1.3 60.7 + - - +
206A GLY* 3.2 33.0 - - - -
207A PHE* 3.7 33.2 - + + -
230A LYS* 5.4 0.2 + - - -
231A TYR* 3.9 13.0 + - - -
301A LYS* 3.3 5.9 + - - -
303A ILE* 3.2 32.7 - - + +
358A ALA* 3.6 24.0 - - + -
359A CYS* 3.9 14.1 - - - -
367A VAL* 3.7 25.1 - - + -
369A GLU* 2.6 30.8 + - - +
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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