Contacts of the helix formed by residues 208 - 221 (chain A) in PDB entry 6M0X
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 THR 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLN* 3.6 2.9 - - - +
205A PRO 4.5 6.5 - - - +
206A GLN* 3.1 14.6 + - - +
207A ILE* 1.3 76.6 - - - +
209A ASP* 1.3 64.3 + - - +
210A GLU* 3.3 9.6 + - - +
211A PHE* 3.0 24.0 + - + +
212A ILE* 3.2 20.4 + - - +
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Residues in contact with ASP 209 (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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201A GLN* 3.6 20.3 + - - +
208A THR* 1.3 74.8 - - - +
210A GLU* 1.3 57.1 + - - +
212A ILE* 3.3 9.3 + - - +
213A ASN* 2.9 37.7 + - - +
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Residues in contact with GLU 210 (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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208A THR* 3.2 7.9 + - - +
209A ASP* 1.3 76.6 - - - +
211A PHE* 1.3 61.1 + - - +
213A ASN* 2.9 19.5 + - - +
214A ARG* 2.8 70.7 + - + +
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Residues in contact with PHE 211 (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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69A LEU* 3.5 39.0 - - + +
70A PHE* 3.9 33.4 - + - -
73A SER* 3.3 28.5 - - - +
75A LEU* 4.5 9.6 - - + -
105A LEU* 4.6 3.1 - - + -
109A LEU* 4.2 7.2 - - + -
197A LEU* 4.1 28.5 - - + -
206A GLN 4.9 1.6 - - - +
207A ILE* 3.9 27.4 - - + -
208A THR* 3.0 26.5 + - - +
210A GLU* 1.3 77.1 - - - +
212A ILE* 1.3 65.7 + - - +
214A ARG* 3.4 1.3 + - - +
215A TYR* 3.2 24.2 + - + +
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Residues in contact with ILE 212 (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 LEU* 4.2 23.6 - - + -
197A LEU* 4.0 40.6 - - + -
198A GLN* 4.3 9.0 - - + +
201A GLN* 3.7 32.1 - - - +
207A ILE* 4.0 12.1 - - + -
208A THR 3.2 10.6 + - - +
209A ASP* 3.6 9.0 - - - +
210A GLU 3.2 0.8 - - - -
211A PHE* 1.3 78.7 - - + +
213A ASN* 1.3 65.8 + - - +
215A TYR* 3.7 1.2 + - - +
216A LEU* 3.3 30.2 + - + +
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Residues in contact with ASN 213 (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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209A ASP* 2.9 28.8 + - - +
210A GLU* 2.9 24.0 + - - +
212A ILE* 1.3 80.0 - - - +
214A ARG* 1.3 63.4 + - + +
216A LEU* 3.4 5.6 + - - +
217A GLU* 3.3 19.9 + - - +
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Residues in contact with ARG 214 (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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68A ARG 5.0 0.2 - - - -
69A LEU* 3.5 40.1 - - + +
72A GLU* 2.4 34.9 + - - +
210A GLU* 2.8 59.1 + - + +
211A PHE 4.1 0.2 - - - +
213A ASN* 1.3 73.2 - - + +
215A TYR* 1.3 62.5 + - - +
217A GLU* 3.3 8.6 + - - +
218A ILE* 3.0 28.0 + - + +
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Residues in contact with TYR 215 (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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66A LEU* 3.8 22.0 - - + -
69A LEU* 3.9 9.5 - - + +
109A LEU* 3.1 49.5 + - + -
112A MET* 3.3 14.4 - - - +
113A VAL* 4.1 13.2 - - + -
193A ALA* 3.8 22.2 - - + -
197A LEU* 4.1 18.4 - - + -
211A PHE* 3.2 19.5 + - + +
212A ILE 4.2 2.0 - - - +
214A ARG* 1.3 77.2 - - - +
216A LEU* 1.3 63.0 + - + +
218A ILE* 2.8 15.3 + - + +
219A LEU* 2.7 63.6 + - + +
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Residues in contact with LEU 216 (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 ARG* 3.6 52.7 - - + +
193A ALA* 4.2 14.8 - - + -
194A LEU* 4.3 27.8 - - + +
197A LEU* 5.5 0.9 - - + -
212A ILE* 3.3 23.3 + - + +
213A ASN* 3.4 6.0 + - - +
215A TYR* 1.3 97.7 - - + +
217A GLU* 1.3 50.9 + - - +
219A LEU* 4.3 6.5 - - + -
220A THR* 2.3 40.7 + - - +
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Residues in contact with GLU 217 (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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65A ARG* 4.6 10.0 + - - +
213A ASN 3.3 12.3 + - - +
214A ARG* 3.6 10.1 - - - +
215A TYR 3.1 0.8 - - - -
216A LEU* 1.3 75.5 - - - +
218A ILE* 1.3 59.2 + - - +
220A THR* 3.9 4.2 + - - -
221A GLY* 2.7 47.3 + - - -
222A LYS 5.1 1.0 + - - +
60B U 4.7 16.8 + - - +
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Residues in contact with ILE 218 (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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62A ARG* 3.1 52.8 - - + +
65A ARG* 3.7 59.0 + - + +
66A LEU* 4.1 6.5 - - + +
69A LEU* 4.1 15.7 - - + -
113A VAL* 3.8 15.7 - - + -
116A ARG* 4.3 0.7 + - - -
214A ARG* 3.0 18.4 + - + +
215A TYR* 2.8 16.7 + - + +
217A GLU* 1.3 77.8 - - + +
219A LEU* 1.3 61.3 + - - +
221A GLY* 4.0 2.9 + - - +
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Residues in contact with LEU 219 (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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62A ARG* 4.8 0.2 - - - +
112A MET* 3.6 33.4 - - + +
113A VAL* 3.7 13.2 - - + -
116A ARG* 2.8 42.0 + - + +
186A THR* 5.2 1.3 - - + +
189A TYR* 4.2 10.1 - - + +
190A ARG* 3.9 31.9 - - - +
193A ALA* 4.4 2.0 - - + -
215A TYR* 2.7 55.6 + - + +
216A LEU* 4.0 7.4 - - + +
218A ILE* 1.3 74.8 - - - +
220A THR* 1.3 66.1 + - + +
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Residues in contact with THR 220 (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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116A ARG* 3.8 1.8 + - - -
186A THR* 4.0 23.1 - - + +
190A ARG* 3.7 40.3 + - + -
216A LEU* 2.3 33.7 + - - +
217A GLU* 3.9 5.9 + - - -
219A LEU* 1.3 80.9 - - + +
221A GLY* 1.3 66.8 + - - +
222A LYS* 3.3 12.6 + - - +
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Residues in contact with GLY 221 (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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62A ARG* 5.5 0.9 - - - -
65A ARG* 5.8 1.1 + - - -
116A ARG* 3.0 23.6 + - - -
217A GLU* 2.7 44.6 + - - -
218A ILE 4.0 1.8 + - - +
219A LEU 3.5 1.2 - - - -
220A THR* 1.3 71.6 + - - +
222A LYS* 1.3 58.7 + - - -
17B G 4.6 1.0 + - - -
60B U 4.1 13.7 + - - -
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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