Contacts of the helix formed by residues 183 - 190 (chain I) in PDB entry 6O85
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ARG 5.4 0.4 - - - -
224A PHE* 5.3 0.2 - - - -
169I PHE* 6.0 1.0 - - - -
181I VAL* 4.3 2.4 - - - +
182I ILE* 1.3 83.5 - - - +
184I GLY* 1.3 65.8 + - - +
185I SER* 3.4 24.7 - - - +
186I ILE* 3.3 30.3 - - + +
187I LEU* 3.7 5.0 + - - +
234I ARG 4.5 4.4 + - - -
237I PHE* 2.7 47.3 + - + +
238I SER 5.1 2.3 + - - -
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Residues in contact with GLY 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG 4.1 16.2 + - - -
224A PHE* 4.5 13.0 - - - -
182I ILE 3.7 1.0 + - - -
183I LYS* 1.3 75.7 - - - +
185I SER* 1.3 60.5 + - - +
187I LEU* 3.3 4.2 + - - +
188I GLN* 2.9 36.0 + - - +
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Residues in contact with SER 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I LYS* 3.4 24.2 - - - +
184I GLY* 1.3 76.9 - - - +
186I ILE* 1.3 58.9 + - - +
188I GLN* 3.3 11.3 + - - +
189I LYS* 2.9 40.5 + - - +
237I PHE 5.4 1.8 - - - -
238I SER 5.0 13.7 + - - -
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Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I LEU* 4.5 37.9 - - + +
169I PHE* 5.1 12.1 - - + -
182I ILE* 4.0 20.2 - - + -
183I LYS* 3.3 29.1 - - + +
185I SER* 1.3 76.9 - - - +
187I LEU* 1.3 59.2 + - - +
189I LYS* 4.5 4.3 - - + +
190I HIS* 2.9 35.2 + - + +
193I ILE* 4.3 15.2 - - + +
237I PHE* 3.7 31.4 - - + -
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Residues in contact with LEU 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 3.6 8.8 - - - +
202A VAL* 4.2 10.1 - - + -
224A PHE* 3.8 33.0 - - + -
226A PHE* 5.6 0.4 - - + -
240A VAL* 4.3 14.6 - - + -
242A TYR* 3.8 39.1 - - + -
182I ILE* 3.8 23.3 - - + -
183I LYS 3.7 2.4 + - - +
184I GLY* 3.3 9.0 + - - +
185I SER 3.2 0.4 - - - -
186I ILE* 1.3 79.4 - - - +
188I GLN* 1.3 63.9 + - - +
190I HIS 3.5 19.6 - - - +
191I PRO* 3.6 17.4 - - - +
193I ILE* 4.1 16.4 - - + -
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Residues in contact with GLN 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 4.2 28.7 - - + +
191A SER* 5.5 3.1 + - - -
242A TYR* 5.1 7.9 - - + -
184I GLY* 2.9 21.5 + - - +
185I SER* 3.3 10.6 + - - +
187I LEU* 1.3 80.1 - - + +
189I LYS* 1.3 62.2 + - + +
191I PRO* 5.3 0.3 - - - +
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Residues in contact with LYS 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I SER* 2.9 25.2 + - - +
186I ILE* 4.7 1.6 - - + -
188I GLN* 1.3 81.8 - - + +
190I HIS* 1.3 82.1 + - + +
191I PRO* 4.0 6.2 - - - +
238I SER 6.0 6.3 - - - -
258I LEU 5.0 13.0 - - - +
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Residues in contact with HIS 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I ASP* 3.3 37.4 + - - +
166I ARG* 4.3 24.3 - - - -
168I LEU* 3.7 35.4 - - + +
186I ILE* 2.9 26.4 + - + +
187I LEU* 3.5 12.7 - - - +
189I LYS* 1.3 99.6 + - + +
191I PRO* 1.3 68.7 - - - +
192I ARG 3.4 2.5 + - - -
193I ILE* 3.9 5.0 - - + +
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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