Contacts of the helix formed by residues 188 - 199 (chain K) in PDB entry 1I43
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 ASP 188 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184K ILE* 3.3 24.1 - - - +
185K ASP* 3.2 28.5 + - + +
186K PRO 4.9 1.0 - - - +
187K ALA* 1.3 73.1 - - - +
189K VAL* 1.3 59.6 + - - +
190K GLY* 3.2 6.1 + - - -
191K ALA* 2.7 43.4 + - + +
192K LEU 3.7 1.6 + - - -
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Residues in contact with VAL 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K PRO 5.5 1.3 - - - +
187K ALA 2.6 19.7 + - - +
188K ASP* 1.3 71.2 - - - +
190K GLY* 1.3 65.6 + - - +
191K ALA 3.3 0.4 - - - -
192K LEU* 3.3 9.1 + - + +
193K GLU* 3.0 23.9 + - + +
218K ASP* 6.0 2.2 - - + -
221K LEU* 4.0 26.9 - - + -
222K VAL* 5.4 8.5 - - + -
225K LEU* 3.5 27.8 - - + +
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Residues in contact with GLY 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K ASP* 3.2 5.0 + - - -
189K VAL* 1.3 80.6 - - - +
191K ALA* 1.3 55.6 + - - +
193K GLU* 3.3 11.0 + - - +
194K LEU* 2.9 30.4 + - - +
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Residues in contact with ALA 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K THR* 5.5 0.2 - - - +
184K ILE* 3.7 27.7 - - + +
188K ASP* 2.7 35.9 + - + +
189K VAL 3.3 0.2 - - - -
190K GLY* 1.3 72.5 - - - +
192K LEU* 1.3 58.2 + - - +
194K LEU* 3.6 9.8 - - - +
195K ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K VAL* 3.8 13.9 - - + -
184K ILE* 3.6 15.7 - - + +
188K ASP 3.7 3.6 + - - +
189K VAL* 3.3 10.0 + - + +
190K GLY 3.2 0.2 - - - -
191K ALA* 1.3 77.3 - - - +
193K GLU* 1.3 54.4 + - - +
195K ALA* 3.4 4.5 + - - +
196K LEU* 2.7 60.8 + - + +
201K VAL* 6.4 0.2 - - + -
204K PHE* 3.8 35.2 - - + -
222K VAL* 3.6 40.8 - - + +
225K LEU* 4.0 20.0 - - + -
226K CYS* 4.3 1.6 - - - -
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Residues in contact with GLU 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K VAL* 3.0 19.7 + - - +
190K GLY* 3.6 8.9 - - - +
192K LEU* 1.3 78.1 - - - +
194K LEU* 1.3 62.6 + - - +
196K LEU* 3.4 9.4 - - + +
197K ASN* 3.1 37.8 + - - +
225K LEU* 4.7 24.9 - - + +
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Residues in contact with LEU 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K GLY 2.9 17.6 + - - +
191K ALA* 3.6 8.3 - - - +
193K GLU* 1.3 74.2 - - - +
195K ALA* 1.3 57.1 + - - +
197K ASN* 2.8 27.7 + - + +
198K GLN* 2.9 49.0 + - + +
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Residues in contact with ALA 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K VAL* 4.6 14.4 - - + -
182K THR* 4.0 28.5 - - + +
184K ILE* 5.2 0.2 - - + -
191K ALA 2.9 19.0 + - - +
192K LEU* 3.7 5.6 - - - +
194K LEU* 1.3 77.3 - - - +
196K LEU* 1.3 62.9 + - - +
197K ASN 3.1 0.9 + - - -
198K GLN* 4.0 12.7 + - - +
199K LYS* 3.2 28.9 + - + +
201K VAL* 3.7 7.4 - - + +
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Residues in contact with LEU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K LEU* 2.7 54.0 + - + +
193K GLU* 3.4 14.1 - - + +
195K ALA* 1.3 78.0 - - + +
197K ASN* 1.3 57.8 + - - +
199K LYS 3.5 9.4 - - - +
200K LYS* 5.2 0.3 - - - -
201K VAL* 3.8 29.6 + - + +
225K LEU* 4.2 9.6 - - + +
226K CYS* 3.9 17.0 - - - +
229K LYS* 3.6 47.7 - - + +
231K ALA* 4.0 13.7 - - + -
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Residues in contact with ASN 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K GLU* 3.1 27.4 + - - +
194K LEU* 2.8 12.1 + - + +
196K LEU* 1.3 81.4 - - - +
198K GLN* 1.3 69.4 + - + +
199K LYS 3.8 2.5 - - - +
229K LYS* 3.3 32.1 + - - +
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Residues in contact with GLN 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K LEU* 2.9 56.3 + - + +
195K ALA* 4.0 6.3 - - - +
197K ASN* 1.3 76.9 - - + +
199K LYS* 1.3 86.0 + - + +
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Residues in contact with LYS 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K HIS* 3.7 35.7 - - + +
180K THR* 5.6 0.2 - - - -
182K THR* 2.9 31.1 + - - +
195K ALA* 3.2 23.2 + - - +
196K LEU 3.5 10.2 - - - +
197K ASN 3.8 2.2 - - - +
198K GLN* 1.3 107.5 + - + +
200K LYS* 1.3 61.5 + - - +
201K VAL 3.4 3.9 + - - -
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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