Contacts of the helix formed by residues 182 - 194 (chain E) in PDB entry 4KYI
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 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178E ASN 4.7 5.4 - - - -
179E LEU 3.3 8.3 + - - +
180E THR 3.1 1.2 - - - -
181E LYS* 1.3 81.5 - - - +
183E VAL* 1.3 57.6 + - - +
184E LYS* 3.2 19.2 - - - +
185E ASP* 2.7 42.9 + - - -
186E LEU* 3.2 29.8 + - - +
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Residues in contact with VAL 183 (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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117E ARG* 5.2 11.7 - - - +
181E LYS 5.5 1.6 - - - +
182E SER* 1.3 73.0 - - - +
184E LYS* 1.3 75.1 + - + +
186E LEU* 3.6 9.1 - - + +
187E GLU* 3.2 44.7 + - + +
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Residues in contact with LYS 184 (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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181E LYS 5.3 1.0 + - - -
182E SER* 3.2 21.0 + - - +
183E VAL* 1.3 109.4 - - + +
185E ASP* 1.3 64.9 + - - +
186E LEU 3.1 1.6 - - - -
187E GLU* 3.0 12.1 + - - +
188E LYS* 2.9 42.0 + - - +
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Residues in contact with ASP 185 (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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168E ILE* 3.8 9.5 - - + +
178E ASN 5.5 0.7 - - - +
179E LEU* 4.3 23.8 - - + +
182E SER* 2.7 27.9 + - - +
184E LYS* 1.3 81.5 - - - +
186E LEU* 1.3 57.9 + - - +
188E LYS* 3.3 25.3 + - - +
189E LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 186 (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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102E LYS 4.3 10.5 - - - +
103E LEU* 5.1 1.1 - - + -
117E ARG* 3.4 46.0 - - + +
121E ILE* 4.7 6.3 - - + -
179E LEU* 3.2 37.0 - - + +
180E THR* 3.9 25.8 - - + +
182E SER 3.2 20.4 + - - +
183E VAL* 3.6 10.5 - - + +
184E LYS 3.1 0.2 - - - -
185E ASP* 1.3 78.5 - - - +
187E GLU* 1.3 57.3 + - - +
189E LEU* 3.5 5.9 + - + +
190E ASP* 2.9 34.8 + - - +
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Residues in contact with GLU 187 (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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117E ARG* 4.6 12.1 - - - +
183E VAL* 3.2 23.9 + - + +
184E LYS* 3.0 13.8 + - - +
186E LEU* 1.3 77.2 - - - +
188E LYS* 1.3 62.8 + - + +
189E LEU 3.2 0.2 - - - -
190E ASP* 3.6 6.5 + - - +
191E LYS* 3.2 24.4 + - - +
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Residues in contact with LYS 188 (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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166E ALA* 3.2 40.5 - - + +
168E ILE* 4.0 8.5 - - + -
184E LYS* 2.9 27.5 + - - +
185E ASP* 3.3 31.9 + - - +
187E GLU* 1.3 77.4 - - + +
189E LEU* 1.3 61.8 + - - +
191E LYS* 3.6 6.7 + - - +
192E ALA* 3.2 24.1 + - - +
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Residues in contact with LEU 189 (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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117E ARG* 4.9 1.3 - - + +
120E ASN* 4.1 20.6 - - + +
121E ILE* 3.8 30.7 - - + -
124E VAL* 3.8 10.1 - - + -
163E LEU* 3.8 21.1 - - + -
168E ILE* 3.7 11.4 - - + +
179E LEU* 3.8 15.5 - - + -
185E ASP 2.9 16.4 + - - +
186E LEU* 3.6 9.0 - - + +
187E GLU 3.2 0.2 - - - -
188E LYS* 1.3 75.7 - - - +
190E ASP* 1.3 70.1 + - - +
192E ALA* 3.3 2.6 + - - +
193E LEU* 3.1 46.3 + - + +
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Residues in contact with ASP 190 (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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105E ASP* 3.7 19.8 - - - +
114E ARG* 5.6 1.0 - - - -
116E ASP* 4.1 4.3 - - - +
117E ARG* 3.7 30.2 + - - +
120E ASN* 3.7 19.1 + - - +
186E LEU 2.9 19.1 + - - +
187E GLU* 4.0 5.8 - - - +
188E LYS 3.4 0.2 - - - -
189E LEU* 1.3 80.6 - - - +
191E LYS* 1.3 63.2 + - - +
194E ASN* 2.9 41.3 + - - +
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Residues in contact with LYS 191 (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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166E ALA* 6.6 0.7 - - + -
187E GLU 3.2 16.9 + - - +
188E LYS* 3.8 8.1 - - - +
189E LEU 3.3 0.2 - - - -
190E ASP* 1.3 79.7 - - - +
192E ALA* 1.3 63.4 + - - +
194E ASN* 4.8 2.0 - - - +
195E SER* 4.0 13.5 + - - -
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Residues in contact with ALA 192 (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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162E LYS* 3.2 43.0 - - + +
163E LEU* 4.9 3.8 - - + -
165E ARG* 5.9 0.4 - - + -
166E ALA* 4.4 6.3 - - + -
188E LYS 3.2 18.2 + - - +
189E LEU* 3.7 5.4 - - - +
190E ASP 3.2 0.2 - - - -
191E LYS* 1.3 76.5 - - - +
193E LEU* 1.3 62.8 + - + +
195E SER* 2.2 32.1 + - - -
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Residues in contact with LEU 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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120E ASN* 3.3 47.8 - - + +
123E ASP* 4.3 13.0 - - + +
124E VAL* 4.1 8.5 - - + -
159E TYR* 4.4 17.9 - - + +
162E LYS* 3.9 21.8 - - + -
163E LEU* 4.6 8.1 - - + -
189E LEU* 3.1 28.5 + - + +
192E ALA* 1.3 75.7 - - + +
194E ASN* 1.3 56.1 + - - +
195E SER 3.0 5.6 - - - -
196E ILE* 3.0 35.7 + - + +
212E ARG* 3.1 19.3 + - - +
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Residues in contact with ASN 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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114E ARG* 5.7 0.6 - - - +
116E ASP* 3.9 17.8 + - - +
119E ARG* 3.3 31.0 + - - -
120E ASN* 3.5 7.1 + - - +
190E ASP* 2.9 39.3 + - - +
191E LYS* 4.8 2.9 - - - +
193E LEU* 1.3 76.1 - - - +
195E SER* 1.3 60.1 + - - +
196E ILE 3.1 8.8 + - - +
212E ARG* 4.6 3.4 - - - +
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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