Contacts of the helix formed by residues 180 - 191 (chain A) in PDB entry 3OM0
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ILE* 5.8 0.2 - - + -
174A LEU* 3.4 29.2 - - + -
178A ARG 4.0 1.6 - - - +
179A ASP* 1.3 89.6 - - - +
181A THR* 1.3 63.7 + - - +
182A PRO* 3.3 1.6 - - - -
183A LEU* 3.0 10.4 + - + +
184A LEU* 2.9 29.8 + - + +
206A LEU* 3.9 25.4 - - + -
207A VAL* 4.1 26.2 - - + -
210A LYS* 3.8 18.8 - - + -
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Residues in contact with THR 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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179A ASP* 3.1 22.3 + - - -
180A PRO* 1.3 76.9 - - - +
182A PRO* 1.3 72.4 - - + +
184A LEU* 3.1 9.4 + - - +
185A LYS* 2.9 45.7 + - + +
210A LYS* 3.6 20.3 - - - +
214A LEU* 4.1 14.1 - - + +
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Residues in contact with PRO 182 (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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179A ASP* 3.2 20.0 - - + +
180A PRO 3.5 1.3 - - - -
181A THR* 1.3 96.1 - - + +
183A LEU* 1.3 60.9 + - - +
185A LYS* 3.4 10.5 + - + +
186A GLU* 3.2 28.2 + - - +
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Residues in contact with LEU 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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145A ILE* 3.7 20.9 - - + -
172A ARG* 3.5 35.1 - - + +
173A MET 3.7 30.1 - - - +
174A LEU* 4.0 19.3 - - + +
179A ASP 5.5 0.4 - - - +
180A PRO* 3.0 13.8 + - + +
182A PRO* 1.3 82.0 - - + +
184A LEU* 1.3 63.3 + - + +
186A GLU* 3.2 9.0 + - - +
187A ILE* 3.1 41.7 + - + +
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Residues in contact with LEU 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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145A ILE* 4.0 26.0 - - + -
180A PRO* 2.9 23.7 + - + +
181A THR 3.6 2.5 - - - +
183A LEU* 1.3 77.1 - - + +
185A LYS* 1.3 58.8 + - - +
187A ILE* 3.2 7.3 + - + +
188A ARG* 2.8 25.1 + - - +
195A ILE* 5.0 2.5 - - + -
207A VAL* 3.6 13.9 - - + +
210A LYS* 3.7 16.2 - - + -
211A ALA* 3.5 42.2 - - + +
214A LEU* 3.6 16.8 - - + -
216A MET* 3.4 25.9 - - + +
223A TYR* 4.9 3.4 - - + +
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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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181A THR* 2.9 33.0 + - + +
182A PRO* 3.8 8.7 - - + +
183A LEU 3.2 0.2 - - - -
184A LEU* 1.3 77.1 - - - +
186A GLU* 1.3 62.1 + - + +
188A ARG* 3.3 29.2 + - - +
189A ASP* 3.1 29.5 + - - +
214A LEU* 3.6 29.1 - - + +
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Residues in contact with GLU 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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172A ARG* 2.9 40.0 + - - +
182A PRO* 3.2 16.1 + - - +
183A LEU* 3.2 6.2 + - - +
185A LYS* 1.3 78.1 - - + +
187A ILE* 1.3 63.8 + - - +
189A ASP* 3.1 18.2 + - - +
190A ASP* 3.2 16.1 + - - +
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Residues in contact with ILE 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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143A SER* 3.7 26.0 - - - +
144A LEU 5.5 0.4 - - - +
145A ILE* 3.5 36.6 - - + -
172A ARG* 3.5 23.1 - - + +
183A LEU* 3.1 22.7 + - + +
184A LEU* 3.5 12.1 - - + +
186A GLU* 1.3 76.2 - - - +
188A ARG* 1.3 66.2 + - - +
190A ASP* 3.0 15.9 + - - +
191A LYS* 3.3 6.8 + - - -
192A VAL 4.4 10.9 + - - +
195A ILE* 3.8 26.9 - - + -
216A MET* 4.1 4.7 - - + -
221A TYR* 5.4 1.0 - - + -
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Residues in contact with ARG 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 LEU 2.8 16.9 + - - +
185A LYS* 3.5 37.2 + - - +
186A GLU 3.2 0.2 - - - -
187A ILE* 1.3 77.0 - - - +
189A ASP* 1.3 69.6 + - - +
191A LYS* 3.0 21.9 + - - +
214A LEU* 3.3 36.0 + - - +
216A MET* 3.9 21.3 - - + -
221A TYR* 3.7 23.3 + - - +
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Residues in contact with ASP 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 LYS* 3.1 19.5 + - - +
186A GLU* 3.1 11.4 + - - +
188A ARG* 1.3 85.2 + - - +
190A ASP* 1.3 64.4 + - - +
191A LYS* 3.2 11.7 + - - +
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Residues in contact with ASP 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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143A SER* 5.3 2.9 - - - +
170A SER* 4.1 11.3 + - - -
172A ARG* 3.1 29.1 + - - -
186A GLU 3.2 8.9 + - - +
187A ILE* 3.0 11.6 + - - +
189A ASP* 1.3 77.2 - - - +
191A LYS* 1.3 71.1 + - - +
192A VAL* 3.2 20.5 + - + +
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Residues in contact with LYS 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 ILE 3.3 2.5 + - - -
188A ARG* 3.0 21.7 + - - +
189A ASP* 3.6 11.7 - - - +
190A ASP* 1.3 80.5 - - - +
192A VAL* 1.3 61.1 + - - +
220A PHE* 3.8 20.3 - - + -
221A TYR* 6.0 1.6 - - - -
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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
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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