Contacts of the helix formed by residues 186 - 192 (chain A) in PDB entry 1IZC
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 SER 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A HIS* 5.5 5.2 - - - -
126A VAL 4.7 1.0 + - - -
127A GLU* 2.6 34.0 + - - +
184A ILE 3.9 0.2 - - - -
185A GLU* 1.3 81.1 + - - +
187A VAL* 1.3 65.3 + - - +
188A LYS 3.7 0.8 + - - -
189A GLY* 3.0 14.1 + - - +
190A VAL* 3.0 24.8 + - - +
212A TYR* 3.9 8.8 - - - -
215A ASP* 3.5 18.6 - - - -
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Residues in contact with VAL 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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186A SER* 1.3 71.6 - - - +
188A LYS* 1.3 59.6 + - + +
190A VAL* 3.3 3.6 + - - +
191A GLU* 2.8 54.6 + - + +
212A TYR* 4.2 13.2 - - + +
215A ASP* 2.7 26.3 + - - +
216A ALA* 3.8 34.5 - - + +
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Residues in contact with LYS 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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127A GLU* 3.7 33.5 - - + +
186A SER* 3.3 1.4 + - - -
187A VAL* 1.3 78.9 - - + +
189A GLY* 1.3 62.5 + - - +
191A GLU* 3.3 18.6 + - - +
192A ASN* 3.1 24.3 + - - +
215A ASP* 4.4 1.0 + - - +
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Residues in contact with GLY 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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126A VAL 3.7 20.9 - - - -
127A GLU* 4.0 7.3 - - - +
184A ILE* 3.6 15.8 - - - +
186A SER* 3.0 20.6 + - - -
188A LYS* 1.3 77.8 - - - +
190A VAL* 1.3 60.9 + - - +
192A ASN* 3.2 4.5 + - - +
193A VAL* 3.0 22.2 + - - +
196A ILE* 4.2 0.5 - - - +
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Residues in contact with VAL 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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184A ILE* 3.9 9.0 - - + -
186A SER 3.0 16.8 + - - +
187A VAL* 3.7 7.2 - - - +
189A GLY* 1.3 75.4 - - - +
191A GLU* 1.3 63.5 + - + +
192A ASN 3.1 0.9 + - - -
193A VAL* 3.2 18.1 + - + +
207A PHE* 3.7 30.1 - - + -
212A TYR* 3.7 18.8 - - + +
235A ALA* 4.1 25.8 - - + +
238A LYS* 2.9 31.3 + - + -
239A PHE* 5.7 1.6 - - + +
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Residues in contact with GLU 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 VAL* 2.8 42.8 + - + +
188A LYS* 3.7 23.4 - - - +
189A GLY 3.2 0.2 - - - -
190A VAL* 1.3 79.6 - - + +
192A ASN* 1.3 59.0 + - + +
194A ASP* 5.2 1.0 + - - +
238A LYS* 3.1 19.4 + - - +
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Residues in contact with ASN 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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127A GLU 2.9 25.5 + - - +
128A THR* 3.8 14.3 - - - +
129A VAL* 4.5 3.2 - - - +
188A LYS 3.1 15.2 + - - +
189A GLY 3.5 3.8 - - - +
190A VAL 3.1 0.4 - - - -
191A GLU* 1.3 76.3 - - - +
193A VAL* 1.3 64.7 + - - +
194A ASP* 3.3 3.6 - - - -
195A ALA* 3.3 27.5 + - - +
196A ILE* 3.3 16.6 + - + +
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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