Contacts of the helix formed by residues 183 - 190 (chain E) in PDB entry 6K71
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 LYS 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E VAL* 4.1 19.2 + - + +
182E ILE* 1.3 92.3 - - - +
184E GLY* 1.3 66.8 + - - +
185E SER* 3.6 7.9 - - - +
186E ILE* 4.7 18.4 - - + +
187E LEU* 4.1 5.2 + - - +
231E TYR* 3.2 22.7 + - - +
234E ARG* 5.1 12.8 - - + -
235E LYS 6.0 1.6 - - - +
236E GLN* 3.4 27.0 + - - -
222J ARG 4.2 3.4 - - - -
223J ARG* 5.3 3.8 - - - +
224J PHE* 4.6 3.3 - - - -
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Residues in contact with GLY 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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183E LYS* 1.3 77.3 - - - +
185E SER* 1.3 57.7 + - - +
187E LEU* 3.2 6.1 + - - +
188E GLN* 2.9 48.1 + - - +
222J ARG* 3.7 18.8 + - - -
224J PHE* 5.7 3.4 - - - -
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Residues in contact with SER 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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183E LYS* 3.6 5.6 - - - +
184E GLY* 1.3 73.0 - - - +
186E ILE* 1.3 65.0 + - - +
188E GLN* 3.7 11.3 + - - -
189E LYS* 2.9 35.7 + - - +
234E ARG* 3.6 27.2 - - - +
235E LYS* 6.0 3.4 - - - +
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Residues in contact with ILE 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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168E LEU* 3.7 34.5 - - + -
169E PHE* 5.2 14.4 - - + -
182E ILE* 5.1 7.6 - - + -
183E LYS* 4.8 24.0 - - + +
184E GLY 3.4 0.2 - - - -
185E SER* 1.3 78.4 + - - +
187E LEU* 1.3 58.9 + - + +
189E LYS* 5.2 0.2 - - - -
190E HIS* 2.9 36.4 + - + +
193E ILE* 4.9 7.2 - - + -
231E TYR* 6.1 2.7 - - + +
234E ARG* 3.3 47.8 - - + +
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Residues in contact with LEU 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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182E ILE* 4.0 20.0 - - + -
183E LYS 4.1 1.8 + - - +
184E GLY 3.2 7.9 + - - +
185E SER 3.2 0.2 - - - -
186E ILE* 1.3 78.3 - - - +
188E GLN* 1.3 65.2 + - + +
189E LYS 3.3 2.0 + - - -
190E HIS 3.7 8.7 - - - +
191E PRO* 3.8 23.7 - - + +
193E ILE* 5.7 1.3 - - + -
202J VAL* 4.6 8.5 - - + -
224J PHE* 3.8 28.3 - - + -
240J VAL* 4.5 17.5 - - + -
242J TYR* 3.5 54.9 - - + +
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Residues in contact with GLN 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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184E GLY* 2.9 33.9 + - - +
185E SER* 3.3 9.0 + - - +
187E LEU* 1.3 84.3 - - + +
189E LYS* 1.3 59.0 + - - +
190J PRO* 3.4 30.0 - - + +
222J ARG* 5.2 13.3 + - - +
224J PHE* 6.1 2.8 - - + -
242J TYR* 4.9 11.4 + - + +
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Residues in contact with LYS 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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185E SER* 2.9 16.1 + - - +
186E ILE 4.5 0.2 - - - +
188E GLN* 1.3 79.3 - - - +
190E HIS* 1.3 82.5 + - + +
191E PRO* 3.2 11.6 - - - +
190J PRO* 5.5 1.4 - - - +
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Residues in contact with HIS 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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161E ASP* 4.0 19.7 + - + +
166E ARG* 3.1 31.9 + - - -
168E LEU* 4.4 7.2 - - + +
186E ILE* 2.9 30.2 + - + +
187E LEU* 3.7 6.5 - - - +
189E LYS* 1.3 91.8 + - + +
191E PRO* 1.3 66.1 - - - +
192E ARG 3.4 3.0 + - - +
193E ILE* 3.6 26.4 - - + +
234E ARG* 3.9 18.3 + - - -
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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