Contacts of the helix formed by residues 204 - 212 (chain A) in PDB entry 6RKU
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ASP 3.7 1.2 + - - -
203A ILE* 1.3 81.7 - - - +
205A ILE* 1.3 66.4 + - - +
206A GLU* 3.5 9.6 + - - +
207A GLY* 3.2 16.8 + - - -
208A LEU* 3.2 21.9 + - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE 5.7 0.2 - - - +
204A SER* 1.3 75.6 - - - +
206A GLU* 1.3 57.5 + - - +
208A LEU* 3.4 11.5 + - + +
209A MET* 2.9 34.2 + - + +
230A GLU* 5.9 1.3 - - - +
233A TYR* 5.1 13.2 - - + +
234A ARG* 4.9 30.1 - - + +
346A ASN* 4.9 11.7 - - - +
347A LEU* 5.8 5.6 - - + -
348A LYS* 4.5 29.2 - - + +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A SER* 3.2 9.5 + - - +
205A ILE* 1.3 79.4 - - - +
207A GLY* 1.3 62.0 + - - +
209A MET* 3.3 18.9 + - - +
210A GLU* 3.0 23.9 + - - +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.1 13.5 - - - -
204A SER* 3.2 15.6 + - - -
206A GLU* 1.3 80.2 - - - +
208A LEU* 1.3 61.2 + - - +
210A GLU* 3.1 15.2 + - - +
211A HIS* 3.0 23.7 + - - -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY* 4.2 25.4 - - - +
196A ALA* 5.1 1.1 - - + -
197A TYR* 4.9 4.9 - - + -
203A ILE* 3.7 36.7 - - + +
204A SER 3.2 12.6 + - - +
205A ILE* 3.9 15.9 - - + +
207A GLY* 1.3 75.6 - - - +
209A MET* 1.3 61.8 + - - +
211A HIS* 3.1 7.4 + - - +
212A ILE* 3.0 29.0 + - + +
347A LEU* 4.4 20.2 - - + -
348A LYS* 4.7 20.0 - - + -
351A ILE* 4.4 23.3 - - + -
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Residues in contact with MET 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ILE* 2.9 24.4 + - + +
206A GLU* 3.7 21.8 - - - +
207A GLY 3.3 0.2 - - - -
208A LEU* 1.3 76.9 - - - +
210A GLU* 1.3 61.6 + - - +
212A ILE* 2.8 27.4 - - - +
213A PRO* 3.9 11.7 - - - +
226A ARG* 3.6 32.5 - - + +
229A ILE* 5.0 6.7 - - + -
230A GLU* 4.1 38.4 - - + -
233A TYR* 5.3 15.0 - - + -
347A LEU* 5.8 1.1 - - - +
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLU* 3.0 15.2 + - - +
207A GLY* 3.1 12.5 + - - +
209A MET* 1.3 79.3 - - - +
211A HIS* 1.3 85.9 + - - +
213A PRO* 4.6 7.4 - - - +
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLU* 4.0 16.4 - - - +
192A ASN* 4.6 16.4 + - + +
193A GLY* 4.5 18.2 - - - +
196A ALA* 4.0 29.8 - - + +
203A ILE* 4.8 5.1 - - + +
207A GLY* 3.0 26.1 + - - -
208A LEU* 3.1 9.1 + - - +
210A GLU* 1.3 94.3 + - + +
212A ILE* 1.3 60.0 + - + +
213A PRO* 3.2 10.4 - - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU* 6.0 0.9 - - + -
185A HIS* 4.5 17.0 - - + -
189A GLU* 3.8 33.0 - - + +
190A VAL* 4.5 18.6 - - + +
193A GLY* 5.0 7.9 - - - -
208A LEU* 3.0 14.7 + - + +
209A MET* 2.8 21.9 - - - +
211A HIS* 1.3 80.7 - - + +
213A PRO* 1.3 64.6 - - - +
214A GLY* 4.3 15.3 - - - +
233A TYR* 4.8 13.5 - - + +
347A LEU* 4.4 28.3 - - + -
351A ILE* 5.5 5.4 - - + -
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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