Contacts of the helix formed by residues 191 - 199 (chain A) in PDB entry 1IK2
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.6 7.6 - - + +
157A ILE* 5.7 0.4 - - + -
158A SER* 4.1 16.8 - - - -
174A ILE* 4.6 13.9 - - + -
176A ILE* 4.4 19.1 - - + -
187A ASN* 3.2 18.4 + - + +
190A ARG* 1.3 92.5 - - + +
192A ILE* 1.3 67.9 + - + +
194A TYR* 3.0 2.9 + - - +
195A PHE* 2.9 53.8 + - + -
459A VAL* 4.3 19.5 - - + -
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Residues in contact with ILE 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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187A ASN 5.2 0.2 - - - +
188A THR* 3.3 30.9 + - + +
191A VAL* 1.3 80.2 - - + +
193A GLN* 1.3 61.9 + - - +
194A TYR 3.1 4.5 + - - -
195A PHE* 3.7 5.7 + - + +
196A ALA* 3.3 21.1 + - - +
220A ILE* 4.0 27.6 - - + -
246A LYS* 6.0 0.9 - - + -
248A ILE* 4.1 24.0 - - + -
250A ILE* 3.9 32.4 - - + +
459A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN 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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139A VAL* 5.0 5.7 - - - +
188A THR* 2.9 31.8 + - + +
189A LYS* 4.1 8.7 - - + +
190A ARG* 3.1 12.8 + - - +
192A ILE* 1.3 83.0 - - - +
194A TYR* 1.3 59.2 + - - +
196A ALA* 4.1 15.7 - - - +
197A VAL* 5.1 4.9 - - - +
220A ILE* 5.3 4.3 - - - +
221A ILE* 3.7 33.5 - - - +
224A ASN* 5.2 4.3 + - - -
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Residues in contact with TYR 194 (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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139A VAL* 2.9 45.7 + - + -
140A ALA* 3.7 11.0 + - - -
142A TYR 4.8 0.7 - - - -
143A ARG* 3.9 15.2 + - - +
155A PHE* 3.9 22.7 - + + -
158A SER* 4.3 15.3 - - - -
159A ASP* 4.4 18.4 - - + -
190A ARG 2.9 18.9 + - - +
191A VAL 3.0 2.0 + - - +
192A ILE 3.1 0.4 + - - -
193A GLN* 1.3 76.3 - - - +
195A PHE* 1.3 69.7 + - - +
196A ALA 2.9 0.9 - - - -
197A VAL* 3.1 39.1 + - + -
198A ILE* 3.3 42.6 + - + +
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Residues in contact with PHE 195 (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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158A SER* 3.4 28.5 - - - -
161A ALA* 4.4 6.7 - - + -
162A TYR 4.9 1.8 - - - -
174A ILE* 4.0 12.8 - - + -
191A VAL* 2.9 42.0 + - + +
192A ILE* 4.1 1.6 - - + +
194A TYR* 1.3 75.6 - - - +
196A ALA* 1.3 62.2 + - - +
197A VAL 3.3 0.9 + - - -
198A ILE* 4.0 10.5 - - + -
199A ALA* 3.4 20.1 + - - +
250A ILE* 3.8 42.6 - - + -
252A PHE* 3.9 26.2 - + + -
258A LEU* 3.6 12.1 - - + +
457A ILE* 3.5 33.2 - - + -
459A VAL* 5.0 0.2 - - + -
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Residues in contact with ALA 196 (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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192A ILE 3.3 17.4 + - - +
193A GLN* 4.1 23.8 - - - +
195A PHE* 1.3 79.3 - - - +
197A VAL* 1.3 61.9 + - + +
200A ALA* 3.3 23.7 - - - +
217A GLU* 4.0 19.9 - - + +
221A ILE* 6.0 2.2 - - + -
250A ILE* 5.5 0.6 - - - +
258A LEU* 4.4 8.9 - - - +
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Residues in contact with VAL 197 (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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139A VAL* 5.3 3.4 - - + -
193A GLN 5.1 4.9 - - - +
194A TYR* 3.1 39.0 + - + +
196A ALA* 1.3 80.9 - - + +
198A ILE* 1.3 64.3 + - + +
199A ALA 3.0 10.4 + - - -
200A ALA* 3.4 15.2 + - - +
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Residues in contact with ILE 198 (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 ARG* 5.3 10.5 - - - +
158A SER 4.4 3.6 - - - +
159A ASP* 5.1 3.4 - - - +
162A TYR* 3.8 55.6 + - + -
194A TYR* 3.4 55.4 - - + +
195A PHE* 4.0 21.3 - - + +
197A VAL* 1.3 78.0 - - + +
199A ALA* 1.3 61.4 + - + +
200A ALA 3.8 0.2 - - - -
252A PHE* 4.6 1.1 - - + -
256A GLY 4.3 0.2 - - - +
257A LYS* 5.9 0.4 + - - -
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Residues in contact with ALA 199 (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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195A PHE 3.4 12.7 + - - +
197A VAL 3.1 0.6 - - - -
198A ILE* 1.3 78.5 - - - +
200A ALA* 1.3 66.1 + - - +
201A ILE 3.3 2.4 + - - -
252A PHE* 3.6 22.0 - - + -
256A GLY 3.1 26.9 - - - +
257A LYS* 3.8 8.9 - - - +
258A LEU* 3.0 35.2 + - + +
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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