Contacts of the helix formed by residues 181 - 193 (chain A) in PDB entry 1X1O
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 GLY 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A VAL* 2.9 19.9 + - - +
179A ALA 3.5 0.6 - - - -
180A GLY* 1.3 79.2 - - - +
182A VAL* 1.3 61.6 + - - -
184A GLU* 3.0 13.2 - - - -
185A ALA* 3.0 29.6 + - - +
211A GLU* 4.6 1.8 - - - -
285B ARG* 5.9 0.2 - - - +
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Residues in contact with VAL 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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176A VAL* 3.6 29.8 - - + +
181A GLY* 1.3 68.6 - - - -
183A GLY* 1.3 69.0 + - - +
185A ALA* 3.3 2.0 + - - +
186A VAL* 2.9 29.2 + - + +
201A VAL* 4.3 4.3 - - + -
202A GLU 4.4 0.9 - - - +
203A VAL* 4.2 9.2 - - + -
208A GLU* 3.6 52.9 - - + +
211A GLU* 3.5 15.3 + - + +
212A ALA* 3.7 22.9 - - + +
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Residues in contact with GLY 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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182A VAL* 1.3 76.6 - - - +
184A GLU* 1.3 57.1 + - - +
187A ARG* 2.9 55.0 + - - +
211A GLU* 2.9 29.0 + - - -
215A ALA* 3.9 10.8 - - - +
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Residues in contact with GLU 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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179A ALA* 3.5 23.8 - - - +
180A GLY 3.7 14.4 - - - +
181A GLY* 3.0 21.6 - - - +
182A VAL 3.6 0.2 + - - -
183A GLY* 1.3 78.3 + - - +
185A ALA* 1.3 62.1 + - - +
187A ARG* 4.0 22.1 + - - +
188A ARG* 3.1 34.2 + - - +
211A GLU* 3.7 6.3 - - - +
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Residues in contact with ALA 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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171A LEU* 3.7 20.8 - - + +
175A HIS 4.4 2.2 - - - +
176A VAL* 4.3 16.4 - - + -
179A ALA* 3.7 21.4 - - + +
181A GLY 3.0 17.7 + - - +
182A VAL* 3.8 4.3 - - - +
184A GLU* 1.3 76.2 - - - +
186A VAL* 1.3 63.6 + - + +
188A ARG* 3.4 0.9 + - - -
189A ALA* 3.0 24.4 + - - +
201A VAL* 5.5 0.2 - - + -
36B VAL* 3.6 10.8 - - + +
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Residues in contact with VAL 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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171A LEU* 4.0 7.9 - - + -
182A VAL* 2.9 26.2 + - + +
185A ALA* 1.3 74.5 - - - +
187A ARG* 1.3 60.8 + - - +
189A ALA* 3.2 2.0 + - - +
190A LYS* 2.9 35.2 + - + +
199A VAL* 4.8 3.1 - - + -
201A VAL* 3.8 37.9 - - + -
212A ALA* 4.4 4.7 - - - -
215A ALA* 3.4 34.8 - - + +
217A ALA* 3.7 23.3 - - + +
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Residues in contact with ARG 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 GLY* 2.9 40.6 + - - +
184A GLU* 3.7 25.1 + - - +
186A VAL* 1.3 77.3 - - - +
188A ARG* 1.3 62.1 + - + +
190A LYS* 3.5 6.4 + - - +
191A ALA* 3.2 23.4 + - - +
211A GLU 5.5 0.2 + - - -
214A GLU 5.9 0.2 - - - -
215A ALA* 3.9 24.3 - - + +
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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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178A ALA 4.8 2.6 + - - -
179A ALA* 3.8 32.3 + - - +
184A GLU* 3.1 23.6 + - - +
185A ALA 3.7 4.9 - - - +
186A VAL 3.2 0.4 - - - -
187A ARG* 1.3 78.2 - - + +
189A ALA* 1.3 61.9 + - - +
191A ALA* 3.3 14.1 + - - +
192A ARG* 3.5 13.0 + - - +
35B LEU 4.4 9.2 - - - +
36B VAL* 2.8 44.5 + - + +
38B PRO* 4.4 13.7 - - - +
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Residues in contact with ALA 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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169A ILE* 4.7 1.3 - - + -
171A LEU* 3.9 19.7 - - + -
185A ALA 3.0 17.4 + - - +
186A VAL 3.7 2.9 - - - +
188A ARG* 1.3 77.9 - - - +
190A LYS* 1.3 56.6 + - - +
192A ARG 3.2 0.3 + - - -
193A ALA* 2.6 38.9 + - - +
199A VAL* 4.0 12.6 - - + -
35B LEU* 3.9 23.3 - - + -
36B VAL* 4.0 7.8 - - + +
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Residues in contact with LYS 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 VAL* 2.9 25.7 + - + +
187A ARG* 3.9 5.6 - - - +
189A ALA* 1.3 76.2 - - - +
191A ALA* 1.3 61.8 + - - +
192A ARG 3.4 0.3 + - - -
193A ALA* 4.2 4.9 + - - +
199A VAL* 4.0 24.9 - - + -
215A ALA 3.9 14.1 - - - +
216A GLY* 3.0 32.5 + - - +
218A ASP* 3.5 18.0 + - - +
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Residues in contact with ALA 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 ARG 3.2 17.2 + - - +
188A ARG* 3.6 8.3 - - - +
189A ALA 3.1 0.6 - - - -
190A LYS* 1.3 78.9 - - - +
192A ARG* 1.3 68.1 + - + +
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Residues in contact with ARG 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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188A ARG 3.5 5.1 + - - +
189A ALA 3.2 1.8 + - - -
191A ALA* 1.3 87.7 - - + +
193A ALA* 1.3 69.1 + - - +
194A PRO* 3.6 2.3 - - - +
35B LEU* 3.3 22.9 - - + +
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Residues in contact with ALA 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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169A ILE* 4.6 3.8 - - + -
189A ALA 2.6 24.0 + - - +
190A LYS* 4.2 5.2 + - - +
191A ALA 3.9 0.4 - - - -
192A ARG* 1.3 74.7 - - - +
194A PRO* 1.3 80.7 - - + +
195A HIS* 3.2 4.3 + - - +
197A LEU 5.2 1.6 - - - +
199A VAL* 3.8 23.8 - - + -
35B LEU* 3.6 13.0 - - + +
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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