Contacts of the helix formed by residues 193 - 206 (chain C) in PDB entry 5CLQ
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 LEU 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.2 45.8 - - + +
75B LYS* 5.4 3.1 - - - +
190C ASP* 3.6 22.0 - - - +
192C ALA* 1.3 77.2 - - + +
194C ALA* 1.3 58.1 + - - +
195C ALA 2.8 6.1 - - - -
196C GLN* 2.8 27.8 + - + +
197C TYR* 3.1 57.3 + - + +
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C MET* 4.6 17.5 - - + -
190C ASP 3.1 8.9 + - - +
191C PRO* 3.5 26.9 - - + +
192C ALA 3.5 1.0 - - - -
193C LEU* 1.3 78.4 - - - +
195C ALA* 1.3 61.1 + - - +
196C GLN 3.3 0.4 + - - -
197C TYR* 3.6 19.2 + - - +
198C GLU* 3.4 20.1 + - - +
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C PRO 4.2 5.6 + - - +
192C ALA 4.2 13.7 - - - +
194C ALA* 1.3 80.0 - - - +
196C GLN* 1.3 61.1 + - - +
198C GLU* 3.4 28.2 - - - +
199C HIS* 4.0 4.2 + - - +
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU* 2.8 17.5 + - + +
195C ALA* 1.3 76.0 - - - +
197C TYR* 1.3 71.5 + - - +
198C GLU 2.8 11.4 + - - -
199C HIS* 2.9 28.1 + - + +
200C ASP* 3.0 45.4 + - - +
52D VAL* 5.8 0.6 - - - +
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Residues in contact with TYR 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.0 29.9 + - - +
189C MET* 3.7 27.6 - - + -
193C LEU* 3.1 36.4 + - + +
194C ALA* 3.6 10.7 + - - +
195C ALA 3.6 0.4 - - - -
196C GLN* 1.3 87.6 + - - +
198C GLU* 1.3 55.3 + - - +
200C ASP* 3.8 10.8 - - - +
201C LEU* 2.9 27.1 + - - +
113D HIS* 3.5 36.3 - + + +
124D PRO* 3.3 35.3 - - + +
126D GLN* 4.1 9.0 + - - -
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA 3.4 15.9 - - - +
195C ALA* 3.4 21.5 - - - +
196C GLN 2.8 5.3 + - - -
197C TYR* 1.3 71.1 - - - +
199C HIS* 1.3 60.5 + - - +
201C LEU* 2.6 30.1 + - - +
202C GLU* 2.9 15.7 + - - +
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Residues in contact with HIS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ALA 4.0 2.8 + - - +
196C GLN* 2.9 24.0 + - + +
198C GLU* 1.3 77.1 - - - +
200C ASP* 1.3 81.1 + - - +
202C GLU* 2.6 49.7 + - - +
203C VAL* 3.0 27.0 + - + +
55D LYS* 5.9 1.6 + - - -
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Residues in contact with ASP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLN* 3.0 40.1 + - - +
197C TYR* 3.8 13.3 - - - +
199C HIS* 1.3 94.7 + - - +
201C LEU* 1.3 61.2 + - - +
203C VAL* 3.3 14.4 + - - +
204C ALA* 3.0 20.3 + - - +
50D PHE* 4.8 2.9 - - - -
52D VAL* 3.4 33.8 - - + +
126D GLN* 4.0 15.9 + - - +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C TYR 2.9 14.0 + - - +
198C GLU* 2.6 22.5 + - - +
200C ASP* 1.3 74.6 - - - +
202C GLU* 1.3 58.3 + - - -
204C ALA* 3.1 4.7 + - + +
205C GLN* 2.9 40.9 + - - +
99D LYS 5.7 2.7 - - - +
101D THR* 5.9 0.9 - - - +
111D VAL* 4.7 9.0 - - + +
112D TRP* 3.9 28.5 - - - +
113D HIS* 3.9 18.2 - - + +
126D GLN* 3.7 28.3 - - + -
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Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLU* 2.9 10.4 + - - +
199C HIS* 2.6 39.7 + - - +
201C LEU* 1.3 69.8 - - - +
203C VAL* 1.3 64.5 + - + +
204C ALA 2.9 1.7 + - - -
205C GLN* 3.4 19.6 + - - +
206C THR* 2.8 36.3 + - + +
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C HIS* 3.4 42.4 - - + +
200C ASP* 3.3 15.7 - - + +
202C GLU* 1.3 75.9 - - + +
204C ALA* 1.3 52.7 + - - +
206C THR* 3.0 13.3 + - - -
207C THR* 2.7 28.1 + - - +
50D PHE* 3.8 9.1 - - + -
52D VAL* 5.6 1.3 - - + +
55D LYS* 3.7 44.2 - - + +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP 3.0 12.4 + - - +
201C LEU* 3.2 12.1 - - + +
202C GLU 2.9 1.2 - - - -
203C VAL* 1.3 73.6 - - - +
205C GLN* 1.3 54.0 + - - +
206C THR 2.7 3.9 + - - -
207C THR* 2.6 35.0 + - - -
50D PHE* 3.9 18.8 - - + -
57D TRP* 3.7 25.3 + - + -
111D VAL* 5.7 0.2 - - + -
126D GLN* 3.9 21.1 - - + -
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Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C LEU* 2.9 30.5 + - - +
202C GLU* 3.4 26.4 - - - +
204C ALA* 1.3 73.5 - - - +
206C THR* 1.3 60.6 + - + +
207C THR 3.2 2.6 + - - -
57D TRP* 5.0 0.2 - - - -
101D THR* 3.7 32.5 + - + +
102D PRO 5.2 3.6 - - - +
103D ASN* 4.1 15.6 - - - +
104D ALA* 4.5 5.9 + - - -
111D VAL* 3.4 32.2 - - + +
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLU* 2.8 28.9 + - + +
203C VAL* 3.0 16.5 + - - -
204C ALA 2.7 3.6 + - - -
205C GLN* 1.3 81.3 - - + +
207C THR* 1.3 59.1 + - - +
208C ALA 4.1 1.7 + - - -
103D ASN* 5.5 0.4 - - - -
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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