Contacts of the helix formed by residues 192 - 198 (chain E) in PDB entry 3IKM
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 HIS 192 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E VAL* 3.4 26.9 - - + -
129E ASP* 3.7 4.6 - - - +
188E GLY 3.9 0.7 - - - -
189E ALA 2.9 3.0 + - - -
191E GLU* 1.3 124.5 + - + +
193E TYR* 1.3 69.9 + - - +
194E VAL 3.0 3.1 - - - -
195E ASN* 3.6 16.1 - - - +
196E CYS* 2.7 43.4 + - + +
206E TYR* 4.2 2.2 - - - -
208E LEU* 3.7 17.9 - - + -
80F SER* 3.4 44.3 + - - -
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Residues in contact with TYR 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ALA 3.9 4.0 + - - -
190E LEU 3.9 10.5 + - - +
191E GLU 3.8 0.8 - - - -
192E HIS* 1.3 76.7 - - - +
194E VAL* 1.3 51.7 + - - +
197E LEU* 2.5 52.6 + - + +
204E LEU* 4.9 15.3 - - + -
206E TYR* 3.1 24.2 + + - +
208E LEU* 4.9 0.4 - - - +
242E PHE* 4.2 25.1 - + + -
311E LEU* 5.1 13.0 - - + -
315E TYR* 5.0 6.1 - + + -
322E LEU* 2.6 74.7 + - + +
324E GLY* 2.8 16.2 + - - -
331E VAL 3.6 4.0 + - - -
332E VAL* 3.8 11.5 - - + -
333E PRO* 4.9 3.0 - - + +
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLU 4.5 0.2 - - - +
192E HIS 2.9 0.2 + - - -
193E TYR* 1.3 84.6 - - + +
195E ASN* 1.3 90.0 + - - +
196E CYS 3.2 0.9 + - - -
197E LEU* 4.1 5.5 - - - +
198E ASP* 3.4 22.5 + - - +
315E TYR* 2.9 38.6 - - + +
321E LYS* 3.4 36.6 - - + +
322E LEU* 5.1 1.8 - - + -
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Residues in contact with ASN 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLU* 2.6 31.5 + - - -
192E HIS* 3.2 21.7 + - + +
194E VAL* 1.3 96.1 - - - +
196E CYS* 1.3 60.2 + - - +
198E ASP* 3.8 12.2 - - - +
315E TYR* 3.5 5.1 + - - -
77F HIS* 3.9 15.1 + - - -
80F SER 4.6 12.6 + - - +
82F SER* 5.8 3.8 - - - -
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Residues in contact with CYS 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 6.2 1.1 - - - -
128E VAL* 6.1 0.7 - - - -
192E HIS* 2.7 39.1 + - + +
195E ASN* 1.3 73.9 - - - +
197E LEU* 1.3 56.3 + - - +
198E ASP 2.8 2.5 - - - -
199E LEU* 2.5 35.0 + - + +
200E VAL* 5.1 1.4 - - - +
206E TYR* 4.6 7.9 - - + -
208E LEU* 4.2 21.3 - - + -
77F HIS* 4.4 15.7 - - - -
101F PRO* 4.5 22.0 - - - -
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TYR* 2.5 46.7 + - + +
194E VAL* 4.1 4.9 - - - +
196E CYS* 1.3 71.2 - - - +
198E ASP* 1.3 55.2 + - - +
199E LEU 2.6 25.9 + - - +
202E LYS* 3.4 52.5 + - + +
203E ARG 3.9 9.2 - - - +
204E LEU* 5.1 4.5 - - + -
206E TYR* 4.2 14.2 + - + +
321E LYS 4.9 5.8 - - - +
322E LEU 3.7 23.1 - - - +
323E HIS* 5.0 1.1 - - + -
324E GLY* 4.0 8.7 - - - -
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Residues in contact with ASP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E VAL 3.4 15.8 + - - +
195E ASN* 3.8 10.8 - - - +
197E LEU* 1.3 80.5 - - - +
199E LEU* 1.3 57.3 + - - +
201E ASN* 4.4 3.1 + - - -
202E LYS* 4.3 24.0 + - - +
77F HIS* 4.4 11.8 - - - -
422F GLN* 5.7 2.6 + - - -
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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