Contacts of the helix formed by residues 193 - 207 (chain A) in PDB entry 1O6K
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 GLU 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE* 5.6 9.5 - - + -
188A ILE* 2.9 25.0 + - + +
191A LYS* 3.7 25.3 - - + +
192A ASP* 1.3 81.5 - - - +
194A VAL* 1.3 61.5 + - - +
195A ALA 3.4 2.2 - - - -
196A HIS* 2.7 41.7 + - + +
197A THR* 2.9 26.6 + - - +
296A LEU* 5.0 1.2 - - - +
11C ALA* 3.7 27.6 - - - +
12C GLU 4.9 5.4 - - - +
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Residues in contact with VAL 194 (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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188A ILE* 4.0 6.7 - - - +
189A ILE* 4.3 26.2 - - + +
192A ASP* 3.5 5.5 - - - +
193A GLU* 1.3 77.7 - - - +
195A ALA* 1.3 59.4 + - - +
197A THR* 3.2 4.0 + - - -
198A VAL* 3.0 41.1 + - + +
470A PHE* 3.7 32.5 - - + -
471A PRO* 5.4 6.5 - - + -
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Residues in contact with ALA 195 (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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192A ASP 5.2 2.2 + - - +
193A GLU 3.4 0.4 - - - -
194A VAL* 1.3 77.7 - - - +
196A HIS* 1.3 62.7 + - + +
198A VAL* 3.5 7.5 + - - +
199A THR* 2.8 33.1 + - - -
298A LYS* 6.3 1.3 - - - +
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Residues in contact with HIS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 2.7 42.1 + - + +
194A VAL 3.3 0.4 - - - -
195A ALA* 1.3 83.2 - - + +
197A THR* 1.3 58.0 + - - +
199A THR* 3.4 7.4 + - - -
200A GLU* 3.0 26.9 + - - +
274A ARG* 4.0 8.7 + - - -
295A GLY 3.7 22.8 - - - +
296A LEU* 4.1 16.3 - - + +
297A CYS 4.7 7.6 - - - -
298A LYS* 5.6 4.3 - - + -
309A TPO 2.7 49.3 + - + -
11C ALA* 4.3 2.9 - - + -
12C GLU 5.9 0.2 - - - -
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Residues in contact with THR 197 (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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183A LEU* 3.8 22.3 - - + +
188A ILE* 3.5 19.4 - - + +
193A GLU* 2.9 15.3 + - - +
194A VAL 3.2 7.7 + - - -
196A HIS* 1.3 73.8 - - - +
198A VAL* 1.3 65.4 + - - +
200A GLU* 3.4 11.0 + - - +
201A SER* 3.2 20.4 + - - -
225A LEU* 3.8 28.9 - - + -
227A PHE* 4.1 3.4 - - + -
470A PHE* 4.5 3.8 - - + -
473A PHE* 4.2 10.4 - - + -
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Residues in contact with VAL 198 (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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194A VAL* 3.0 35.6 + - + +
195A ALA* 3.8 7.2 - - - +
197A THR* 1.3 74.8 - - - +
199A THR* 1.3 58.2 + - - +
201A SER* 3.2 7.7 + - - -
202A ARG* 2.9 43.5 + - - +
470A PHE* 4.5 10.3 - - + -
471A PRO* 3.9 34.5 - - + +
472A GLN* 4.2 14.6 - - + +
473A PHE* 4.9 3.6 - - + -
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Residues in contact with THR 199 (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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195A ALA 2.8 22.6 + - - -
196A HIS* 3.6 8.2 - - - -
197A THR 3.3 0.2 - - - -
198A VAL* 1.3 75.0 - - - +
200A GLU* 1.3 57.9 + - - +
202A ARG* 3.2 2.4 + - - +
203A VAL* 2.8 39.9 + - + +
294A PHE 5.7 0.2 - - - -
297A CYS* 3.4 33.0 - - + +
298A LYS* 4.4 2.1 - - + +
299A GLU* 3.6 38.6 + - + +
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Residues in contact with GLU 200 (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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181A LYS* 2.8 35.4 + - - +
183A LEU* 4.1 10.0 - - - +
196A HIS 3.0 14.3 + - - +
197A THR* 3.5 14.0 + - - +
198A VAL 3.3 0.2 - - - -
199A THR* 1.3 74.8 - - - +
201A SER* 1.3 57.8 + - - +
203A VAL* 3.7 1.9 + - - +
204A LEU* 3.1 38.6 + - + +
227A PHE* 3.7 23.4 - - + -
293A ASP* 4.6 1.0 - - - -
294A PHE* 3.6 31.9 + - + +
295A GLY* 3.5 20.2 + - - -
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Residues in contact with SER 201 (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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197A THR 3.2 8.9 + - - -
198A VAL* 3.4 8.3 - - - -
199A THR 3.2 0.2 - - - -
200A GLU* 1.3 77.3 - - - +
202A ARG* 1.3 58.0 + - - +
204A LEU* 3.3 3.7 + - - +
205A GLN* 2.9 58.1 + - - +
215A LEU* 4.6 0.4 - - - +
218A ALA* 4.3 5.0 - - - +
227A PHE* 3.7 26.9 - - - -
472A GLN 3.6 6.2 + - - -
473A PHE* 3.9 21.8 - - - -
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Residues in contact with ARG 202 (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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198A VAL* 2.9 27.1 + - - +
199A THR* 3.2 5.6 + - - +
201A SER* 1.3 75.9 - - - +
203A VAL* 1.3 55.5 - - - +
205A GLN* 4.2 4.9 - - - +
206A ASN* 2.9 49.6 + - - +
299A GLU* 2.8 44.7 + - - +
472A GLN* 2.7 64.8 + - + +
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Residues in contact with VAL 203 (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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199A THR* 2.8 28.5 + - + +
200A GLU 4.1 3.4 - - - +
202A ARG* 1.3 74.1 - - - +
204A LEU* 1.3 57.4 + - - +
206A ASN* 5.2 1.1 - - - -
207A THR* 2.7 54.1 + - + +
266A LEU* 4.4 2.0 - - + -
271A VAL* 4.2 16.2 - - + -
294A PHE* 3.8 33.4 - - + -
297A CYS* 4.0 24.2 - - + -
299A GLU* 4.1 15.5 - - + -
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Residues in contact with LEU 204 (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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181A LYS* 6.4 0.2 - - + -
200A GLU* 3.1 33.8 + - + +
201A SER 3.6 4.0 - - - +
203A VAL* 1.3 76.4 - - - +
205A GLN* 1.3 61.4 + - - +
207A THR* 4.0 13.1 + - - +
208A ARG* 4.5 2.4 + - - -
213A THR* 3.7 23.7 - - + +
214A ALA* 5.4 0.2 - - - -
215A LEU* 3.6 46.4 + - + +
227A PHE* 3.9 33.0 - - + -
229A MET* 4.5 20.2 - - + -
294A PHE* 3.8 24.7 - - + -
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Residues in contact with GLN 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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201A SER* 2.9 38.8 + - - +
202A ARG* 3.8 9.0 - - - +
204A LEU* 1.3 77.9 - - - +
206A ASN* 1.3 66.8 + - - +
207A THR 3.5 0.2 - - - -
208A ARG* 3.1 24.3 + - - -
215A LEU* 3.9 10.1 - - + -
472A GLN 2.8 29.7 + - - +
473A PHE* 4.4 5.6 - - - +
475A TYR* 3.5 58.6 + - + +
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Residues in contact with ASN 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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202A ARG* 2.9 43.0 + - - +
203A VAL* 5.2 0.9 - - - -
205A GLN* 1.3 87.6 + - - +
207A THR* 1.3 60.8 + - + +
208A ARG* 4.2 3.8 + - - +
265A TYR* 4.0 1.9 + - - -
269A ARG* 3.1 34.4 + - - +
299A GLU* 5.6 1.3 + - - +
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Residues in contact with THR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 2.7 41.6 + - + +
204A LEU* 4.0 9.9 + - - +
205A GLN 3.5 0.8 - - - -
206A ASN* 1.3 82.4 - - + +
208A ARG* 1.3 80.6 + - - +
209A HIS 4.2 0.4 - - - -
212A LEU* 3.9 15.3 - - - +
213A THR 5.0 4.7 + - - -
214A ALA* 5.6 5.4 - - - +
265A TYR* 3.6 21.3 - - + +
266A LEU* 4.1 11.9 - - + -
269A ARG* 5.4 5.8 - - + +
271A VAL* 5.5 5.6 - - + -
294A PHE* 5.3 3.1 - - - -
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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