Contacts of the helix formed by residues 193 - 205 (chain A) in PDB entry 6J95
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 ASP 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A TYR 4.2 4.9 - - - +
173A SER* 3.5 24.3 - - - -
174A LYS* 2.8 32.2 + - - +
175A GLY 4.7 0.2 + - - -
178A ALA* 6.1 0.2 - - - +
191A PRO 4.0 2.9 + - - +
192A ALA* 1.3 79.8 - - - +
194A GLY* 1.3 68.5 + - - +
195A GLU 3.7 0.3 + - - -
196A ILE* 3.5 18.6 - - - +
197A TRP* 3.7 7.2 - - - -
514A ARG* 3.0 20.9 + - - +
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Residues in contact with GLY 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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193A ASP* 1.3 76.0 + - - +
195A GLU* 1.3 65.9 + - - -
197A TRP* 3.2 12.9 + - - +
198A ARG* 3.0 19.4 + - - +
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Residues in contact with GLU 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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193A ASP 3.7 0.6 + - - -
194A GLY* 1.3 71.1 - - - -
196A ILE* 1.3 58.1 + - - +
198A ARG* 3.7 6.5 - - - +
199A ARG* 2.8 33.0 + - - +
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Residues in contact with ILE 196 (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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187A LYS* 3.3 34.8 - - + +
192A ALA* 4.1 11.4 - - + -
193A ASP 3.5 14.1 - - - +
195A GLU* 1.3 78.4 - - - +
197A TRP* 1.3 66.0 + - - +
199A ARG* 4.6 4.5 - - + +
200A ARG* 3.2 25.9 + - + +
366A GLN* 3.6 24.7 - - - +
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Residues in contact with TRP 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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189A LEU* 3.6 20.7 - - + +
192A ALA* 3.9 8.5 - - + -
193A ASP* 3.6 23.3 + - - +
194A GLY* 3.2 16.7 + - - +
195A GLU 3.2 0.6 - - - -
196A ILE* 1.3 83.3 - - - +
198A ARG* 1.3 83.8 + - + +
201A ARG* 2.9 46.1 + - + +
513A PRO* 3.4 39.9 - - + -
514A ARG* 3.1 38.4 - - - +
601A HEM 2.8 20.7 + - - -
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Residues in contact with ARG 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 GLY 3.0 13.0 + - - +
195A GLU* 3.1 9.8 + - - +
197A TRP* 1.3 96.8 - - + +
199A ARG* 1.3 62.8 + - - +
201A ARG* 3.5 3.2 + - - +
202A ARG* 3.1 24.9 + - - +
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Residues in contact with ARG 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 GLU 2.8 21.4 + - - +
196A ILE* 4.2 4.7 - - + +
198A ARG* 1.3 75.2 - - - +
200A ARG* 1.3 68.9 + - - +
202A ARG* 3.5 5.4 + - - +
203A ALA* 3.2 21.1 + - - +
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Residues in contact with ARG 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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187A LYS 4.9 0.9 - - - +
189A LEU* 3.9 15.0 - - + -
196A ILE* 3.2 26.4 + - + +
199A ARG* 1.3 79.2 + - + +
201A ARG* 1.3 66.8 + - - +
203A ALA* 3.2 14.3 + - - +
204A ILE* 3.0 47.1 + - + +
355A LEU* 4.6 7.3 - - - +
360A ASP* 2.7 40.8 + - - -
362A VAL* 3.2 27.0 - - - +
366A GLN* 3.4 29.7 - - - +
367A LEU* 4.7 1.6 - - - +
370A ASP* 2.7 30.0 + - - +
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Residues in contact with ARG 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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189A LEU* 3.5 14.0 - - + +
197A TRP* 2.9 37.3 + - + +
198A ARG* 3.8 4.3 - - - +
200A ARG* 1.3 77.4 - - - +
202A ARG* 1.3 62.4 + - - +
205A VAL* 3.2 42.2 + - + +
513A PRO* 3.2 20.6 + - - +
514A ARG 3.9 0.2 - - - -
515A LYS* 2.9 34.1 + - - +
516A CYS 5.0 2.0 + - - -
517A ILE* 3.5 15.6 - - - +
601A HEM 2.7 40.2 + - - +
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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 ARG 3.1 17.8 + - - +
199A ARG* 3.9 5.2 - - - +
201A ARG* 1.3 77.5 - - - +
203A ALA* 1.3 57.7 + - - +
205A VAL* 5.3 0.9 - - - -
206A PRO* 3.1 24.2 - - - +
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Residues in contact with ALA 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 ARG 3.2 12.2 + - - +
200A ARG* 3.2 34.2 + - - +
201A ARG 3.1 0.8 - - - -
202A ARG* 1.3 79.2 - - - +
204A ILE* 1.3 62.5 + - - +
206A PRO* 3.5 11.1 - - - +
354A PHE* 4.6 4.5 - - - -
355A LEU* 3.5 13.3 - - - +
358A SER* 5.5 1.6 + - - -
360A ASP* 3.8 13.5 - - - +
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Residues in contact with ILE 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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189A LEU* 4.1 20.4 - - + -
200A ARG* 3.0 31.4 + - + +
201A ARG 4.4 0.4 - - - +
203A ALA* 1.3 77.3 - - - +
205A VAL* 1.3 57.0 + - - +
206A PRO* 3.2 2.2 - - - -
207A ALA* 2.8 33.1 + - - +
208A LEU* 3.8 6.1 - - + +
351A ILE* 4.8 6.1 - - + -
355A LEU* 4.0 17.7 - - + -
370A ASP* 3.9 35.7 - - + +
374A MET* 3.9 22.4 - - + -
517A ILE* 3.8 22.9 - - + -
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Residues in contact with VAL 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 ARG* 3.2 35.5 + - + +
202A ARG* 5.2 1.6 - - - -
204A ILE* 1.3 76.0 - - - +
206A PRO* 1.3 68.5 - - + +
207A ALA 3.0 0.9 + - - -
208A LEU* 3.1 25.3 + - - +
517A ILE* 3.7 31.2 - - + -
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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