Contacts of the helix formed by residues 185 - 192 (chain A) in PDB entry 1I9G
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 VAL 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP* 3.9 1.6 - - - +
162A LEU* 3.9 17.3 - - + -
163A ALA* 3.9 20.9 - - - +
177A LEU* 3.7 32.3 - - + -
179A MET* 3.9 12.8 - - - -
182A PRO 3.2 14.6 - - - +
184A GLU* 1.3 82.9 - - + +
186A LEU* 1.3 60.5 + - - +
187A ASP 3.4 2.2 - - - -
188A ALA* 3.2 7.4 + - - +
189A VAL* 3.0 26.1 + - + +
301A SAM 3.4 29.6 - - - +
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Residues in contact with LEU 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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177A LEU* 5.2 3.6 - - + -
182A PRO 3.5 6.5 + - - +
183A TRP 3.4 13.7 + - - +
184A GLU 3.6 0.4 - - - -
185A VAL* 1.3 74.3 - - - +
187A ASP* 1.3 58.2 + - - +
189A VAL* 3.7 6.5 - - + +
190A SER* 2.6 39.6 + - - +
199A LEU* 4.1 15.0 - - + -
212A ILE* 4.1 15.5 - - + -
215A ALA* 3.8 31.0 - - + -
216A LEU* 3.5 30.7 - - + +
219A LYS* 3.7 33.7 - - + -
222A TRP* 4.2 9.0 - - + +
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Residues in contact with ASP 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 TRP 5.0 0.2 + - - -
184A GLU 5.4 0.8 + - - -
185A VAL 3.4 0.8 - - - -
186A LEU* 1.3 77.8 - - - +
188A ALA* 1.3 63.0 + - - +
190A SER* 3.8 5.5 - - - -
191A ARG* 3.1 24.6 + - - +
219A LYS* 2.4 40.8 + - - +
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Residues in contact with ALA 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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162A LEU* 3.6 31.0 - - + +
163A ALA* 4.0 17.3 - - - +
165A SER* 5.0 0.7 - - - -
185A VAL 3.2 10.0 + - - +
187A ASP* 1.3 79.0 - - - +
189A VAL* 1.3 57.5 + - - +
191A ARG* 3.2 20.1 + - - +
192A LEU* 2.9 36.0 + - + +
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Residues in contact with VAL 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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104A LEU* 4.4 8.3 - - + -
162A LEU* 3.8 23.8 - - + -
175A ALA* 4.2 13.0 - - + -
177A LEU* 4.2 17.3 - - + -
185A VAL* 3.0 20.3 + - + +
186A LEU* 3.7 7.9 - - + +
188A ALA* 1.3 74.7 - - - +
190A SER* 1.3 56.8 + - - +
192A LEU* 3.2 5.1 + - - -
193A LEU* 2.9 32.8 + - + +
199A LEU* 4.1 21.1 - - + -
222A TRP* 4.0 22.2 - - + -
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Residues in contact with SER 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 LEU* 2.6 30.9 + - - +
187A ASP* 3.8 7.0 - - - -
189A VAL* 1.3 73.4 - - - +
191A ARG* 1.3 61.4 + - - +
193A LEU 3.7 4.9 - - - +
219A LYS* 4.9 5.1 - - - +
221A CYS* 3.8 21.1 - - - -
222A TRP* 3.2 31.3 + - - -
260A ARG* 2.9 31.9 + - - +
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Residues in contact with ARG 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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163A ALA 5.6 1.0 + - - -
165A SER* 3.4 23.4 + - - -
166A GLU* 4.4 1.4 - - - +
167A LEU 2.4 32.7 + - - -
168A PRO 4.1 0.4 - - - -
169A ASP* 3.0 38.6 + - - +
170A GLY* 2.9 21.0 + - - -
187A ASP 3.1 12.5 + - - +
188A ALA* 3.4 23.8 - - - +
190A SER* 1.3 79.7 - - - +
192A LEU* 1.3 75.9 + - - +
193A LEU 4.4 1.4 - - - +
260A ARG* 5.0 2.5 - - - +
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Residues in contact with LEU 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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104A LEU* 3.8 29.4 - - + -
162A LEU* 4.0 8.5 - - + -
165A SER* 3.7 24.2 - - - +
167A LEU* 3.5 20.2 - - + +
168A PRO 3.4 20.9 - - - +
170A GLY* 3.1 4.7 - - - +
171A SER* 2.9 28.6 + - - +
172A VAL* 3.1 19.6 + - + -
188A ALA* 2.9 21.4 + - + +
189A VAL 3.9 2.2 - - - +
191A ARG* 1.3 104.3 - - - +
193A LEU* 1.3 57.5 + - - +
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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