Contacts of the helix formed by residues 201 - 213 (chain M) in PDB entry 5MS0
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 201 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166M ASP* 5.7 0.6 - - - +
198M THR* 4.1 20.8 - - - -
199M ARG 3.7 0.9 - - - +
200M SER* 1.3 81.9 - - - +
202M PRO* 1.3 66.2 - - - +
203M GLU* 3.2 9.5 + - + +
204M MET* 3.3 17.8 + - - +
205M LEU* 4.2 1.7 + - - +
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Residues in contact with PRO 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M SER 3.8 0.6 - - - -
201M LYS* 1.3 73.5 - - - +
203M GLU* 1.3 57.5 + - - +
205M LEU* 3.1 12.4 + - + +
206M ILE* 2.9 26.5 + - - +
226M ALA* 4.2 31.7 - - + +
228M ARG* 5.2 15.0 - - + -
37N ILE* 5.6 7.4 - - + -
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Residues in contact with GLU 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M VAL* 4.2 18.1 - - + +
201M LYS* 3.2 8.0 - - + +
202M PRO* 1.3 77.4 - - - +
204M MET* 1.3 57.0 + - - +
206M ILE* 3.7 10.2 - - + +
207M GLU* 2.9 31.4 + - - +
40N LEU* 4.6 18.2 - - + +
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Residues in contact with MET 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M GLY* 5.5 2.5 - - - -
182M VAL* 4.5 10.7 - - + +
198M THR* 4.2 10.0 - - - +
199M ARG* 4.0 29.8 - - - +
201M LYS* 3.3 13.4 + - - +
203M GLU* 1.3 76.2 - - - +
205M LEU* 1.3 59.9 + - - +
207M GLU* 3.9 2.1 - - - +
208M LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M LYS 4.2 1.0 + - - +
202M PRO* 3.1 14.3 + - + +
204M MET* 1.3 77.7 - - - +
206M ILE* 1.3 56.2 + - - +
208M LEU* 3.3 8.2 + - - +
209M PHE* 2.9 26.7 + - - +
234M ALA* 6.1 5.8 - - + -
262M VAL* 5.8 0.9 - - - +
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Residues in contact with ILE 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M PRO 2.9 15.3 + - - +
203M GLU* 3.7 10.8 - - - +
205M LEU* 1.3 77.6 - - - +
207M GLU* 1.3 56.9 + - - +
209M PHE* 3.1 10.6 + - - +
210M ARG* 2.9 24.0 + - - +
40N LEU 5.0 2.5 - - - +
41N ASN* 4.7 23.1 - - + +
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Residues in contact with GLU 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M GLY 5.8 3.6 - - - +
136M GLU 5.6 1.3 - - - -
137M ILE* 5.2 16.2 - - + +
182M VAL* 5.1 8.7 - - + -
203M GLU 2.9 18.3 + - - +
204M MET* 4.2 2.5 - - - +
206M ILE* 1.3 72.3 - - - +
208M LEU* 1.3 61.9 + - - +
210M ARG* 3.5 10.6 - - + +
211M ILE* 3.0 28.9 + - - +
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Residues in contact with LEU 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M MET 2.9 19.1 + - - +
205M LEU* 3.5 9.2 - - - +
207M GLU* 1.3 76.8 - - - +
209M PHE* 1.3 57.5 + - - +
211M ILE* 4.4 3.4 - - - +
212M GLU* 2.9 31.2 + - - +
262M VAL* 4.7 18.6 - - + +
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Residues in contact with PHE 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205M LEU 2.9 13.4 + - - +
206M ILE* 3.1 11.6 + - - +
208M LEU* 1.3 76.6 - - - +
210M ARG* 1.3 56.4 + - - +
212M GLU* 4.2 5.4 - - - -
213M VAL* 2.7 39.9 + - + +
216M ILE* 4.9 1.0 - - - +
262M VAL* 5.5 0.4 - - - +
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Residues in contact with ARG 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ILE 2.9 12.1 + - - +
207M GLU* 3.1 15.8 + - + +
209M PHE* 1.3 77.9 - - - +
211M ILE* 1.3 57.8 + - - +
213M VAL 3.0 19.2 - - - +
214M PRO* 5.1 0.3 - - - +
216M ILE* 4.4 18.2 - - + +
217M GLY* 5.1 2.3 + - - -
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Residues in contact with ILE 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ASP* 5.5 9.4 - - + +
93E ALA* 3.8 21.9 - - + +
207M GLU 3.0 14.8 + - - +
208M LEU* 4.4 3.4 - - - +
210M ARG* 1.3 75.8 - - - +
212M GLU* 1.3 65.4 + - - +
213M VAL 4.4 2.1 - - - +
214M PRO* 5.0 1.2 - - - +
53N ASN* 6.3 3.1 - - + -
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Residues in contact with GLU 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 5.9 3.5 - - - +
93E ALA* 4.9 9.5 - - - +
94E ALA* 5.5 8.0 - - + +
208M LEU 2.9 21.6 + - - +
209M PHE* 3.9 4.9 - - - +
211M ILE* 1.3 79.5 - - - +
213M VAL* 1.3 59.5 + - + +
214M PRO* 3.7 2.6 - - - +
258M ARG* 5.1 20.4 - - + +
261M ALA* 6.5 1.3 - - + -
262M VAL* 5.5 5.6 - - + -
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Residues in contact with VAL 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209M PHE* 2.7 23.3 + - + +
210M ARG 3.0 18.3 - - - +
211M ILE 4.5 0.7 - - - -
212M GLU* 1.3 72.9 - - + +
214M PRO* 1.3 63.2 - - - +
215M GLU* 3.5 7.3 + - + +
216M ILE* 3.6 14.6 + - + +
217M GLY 4.3 0.3 + - - -
250M ALA 5.3 8.7 - - - +
251M CYS* 5.8 5.4 - - + -
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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