Contacts of the helix formed by residues 186 - 200 (chain C) in PDB entry 5A0Q
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 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ALA* 4.4 2.5 - - + -
41C ASP* 3.4 23.1 + - - +
42C GLY* 4.5 21.3 - - - -
43C VAL 5.1 1.8 - - - +
44C LEU* 5.8 2.5 - - + +
185C THR* 1.4 74.2 + - - +
187C LYS* 1.3 60.8 + - - +
189C ALA* 3.1 14.3 + - + +
190C LEU* 3.0 46.6 + - + +
215C THR* 4.8 14.4 - - + -
216C LEU 4.9 0.4 - - - +
217C THR* 4.1 26.5 - - + -
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Residues in contact with LYS 187 (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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185C THR* 4.0 14.8 + - + +
186C LEU* 1.3 79.7 - - - +
188C SER* 1.4 60.6 + - - +
190C LEU* 3.3 14.4 + - + +
191C ALA* 3.2 26.8 + - - +
236C LEU* 5.5 2.2 - - - +
239C LYS* 3.6 35.0 - - - +
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Residues in contact with SER 188 (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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183C GLU* 4.7 4.5 + - - -
184C MET* 3.5 30.6 - - - -
185C THR* 3.0 24.6 + - - +
187C LYS* 1.4 78.7 - - - +
189C ALA* 1.4 57.1 + - - +
191C ALA* 3.7 6.9 - - - +
192C LEU* 3.1 36.9 + - - +
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Residues in contact with ALA 189 (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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37C ILE* 4.3 32.7 - - + +
38C LEU 5.0 0.2 - - - +
39C ALA* 4.4 14.8 - - + -
42C GLY 5.8 0.2 - - - +
44C LEU* 4.0 12.1 - - + +
184C MET* 4.7 2.6 - - + +
185C THR 3.5 2.4 + - - -
186C LEU* 3.1 24.7 + - + +
188C SER* 1.4 75.5 - - - +
190C LEU* 1.3 59.3 + - - +
192C LEU* 3.7 2.8 + - - +
193C ALA* 3.0 29.6 + - - +
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Residues in contact with LEU 190 (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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44C LEU* 3.7 22.7 - - + -
186C LEU* 3.0 37.8 + - + +
187C LYS* 3.3 16.4 + - + +
189C ALA* 1.3 75.1 - - - +
191C ALA* 1.3 62.7 + - - +
193C ALA* 3.7 0.2 - - - +
194C ILE* 3.1 31.5 + - + +
213C ILE* 4.4 7.2 - - + -
215C THR* 4.6 7.6 - - + -
228C LEU* 4.6 7.6 - - + -
236C LEU* 3.8 42.6 - - + -
239C LYS* 5.1 0.8 + - - -
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LYS* 3.2 21.2 + - - +
188C SER* 3.7 12.1 - - - +
189C ALA 3.3 0.2 - - - -
190C LEU* 1.3 78.5 - - - +
192C LEU* 1.4 60.3 + - + +
194C ILE* 3.9 2.1 - - - +
195C LYS* 3.0 28.1 + - - +
239C LYS* 4.8 7.0 - - - +
243C GLU* 4.6 19.7 - - - +
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Residues in contact with LEU 192 (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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37C ILE* 4.0 16.7 - - + +
175C LEU* 4.4 5.6 - - + -
178C ASP* 3.1 30.3 - - + +
179C TYR* 4.0 17.9 - - + -
184C MET* 3.7 28.3 - - + -
188C SER* 3.1 19.3 + - - +
189C ALA 4.3 0.4 - - - +
191C ALA* 1.4 78.5 - - + +
193C ALA* 1.3 64.4 + - - +
195C LYS* 3.5 31.2 - - + +
196C VAL* 3.1 27.0 + - - +
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Residues in contact with ALA 193 (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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35C LEU* 4.0 9.8 - - + +
37C ILE* 3.9 8.9 - - + +
44C LEU* 3.5 35.7 - - + -
46C ALA* 4.8 0.7 - - + -
189C ALA 3.0 20.9 + - - +
190C LEU 3.7 3.8 - - - +
192C LEU* 1.3 76.5 - - - +
194C ILE* 1.4 62.0 - - + +
196C VAL* 3.3 0.5 + - - -
197C LEU* 3.0 40.0 + - + +
213C ILE* 5.3 0.4 - - + -
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Residues in contact with ILE 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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190C LEU* 3.1 19.0 + - - +
191C ALA 3.9 2.7 - - - +
193C ALA* 1.4 75.6 - - + +
195C LYS* 1.3 61.9 + - - +
197C LEU* 3.5 17.4 - - + +
198C ASN* 2.8 48.1 + - - +
211C VAL* 5.1 8.5 - - + -
213C ILE* 4.0 25.6 - - + -
236C LEU* 4.2 32.8 - - + +
237C ILE* 5.3 5.2 - - + -
239C LYS* 4.3 9.9 - - - +
240C HIS* 3.9 20.0 - - + +
243C GLU* 4.4 3.8 - - - +
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Residues in contact with LYS 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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174C MET* 4.2 6.5 - - + -
178C ASP* 3.7 32.3 + - + +
191C ALA 3.0 15.9 + - - +
192C LEU* 3.5 34.0 - - + +
194C ILE* 1.3 76.0 - - - +
196C VAL* 1.4 70.0 + - + +
198C ASN* 3.0 7.4 + - - +
199C LYS* 3.0 57.2 + - + +
240C HIS* 5.8 0.2 - - - -
243C GLU* 5.0 4.7 + - - +
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Residues in contact with VAL 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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35C LEU* 3.6 20.4 - - + -
171C ALA* 3.6 39.0 - - + +
174C MET* 4.2 19.1 - - + -
175C LEU* 3.6 26.2 - - + -
178C ASP* 5.6 0.2 - - + -
192C LEU 3.1 16.4 + - - +
195C LYS* 1.4 86.4 - - + +
197C LEU* 1.3 57.6 + - - +
199C LYS* 3.1 6.0 + - - +
200C THR* 3.0 27.8 + - - +
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Residues in contact with LEU 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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33C THR* 5.5 2.5 - - + -
35C LEU* 3.9 10.9 - - + +
46C ALA* 3.3 33.2 - - + -
193C ALA* 3.0 29.9 + - + +
194C ILE* 3.5 27.1 - - + +
196C VAL* 1.3 76.3 - - - +
198C ASN* 1.3 70.0 + - - +
200C THR* 3.1 24.2 - - + +
201C MET* 3.7 3.9 - - + +
206C LEU* 3.1 32.4 - - + +
211C VAL* 3.6 28.9 - - + -
213C ILE* 5.1 0.7 - - + -
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Residues in contact with ASN 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 ILE* 2.8 30.7 + - - +
195C LYS* 3.0 7.9 + - - +
197C LEU* 1.3 90.4 - - - +
199C LYS* 1.3 65.1 + - - +
201C MET 3.6 3.8 - - - +
203C VAL 3.4 20.1 - - - +
204C SER* 3.4 8.0 - - - +
205C LYS* 3.6 0.4 - - - +
206C LEU* 3.4 24.8 - - - +
240C HIS* 2.2 59.2 + - + +
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Residues in contact with LYS 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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174C MET* 3.6 39.0 - - + -
195C LYS* 3.0 50.4 + - - +
196C VAL 3.1 3.8 + - - +
198C ASN* 1.3 89.2 - - + +
200C THR* 1.4 61.4 + - - +
201C MET 3.4 6.4 - - - +
204C SER 5.8 1.1 - - - +
240C HIS* 4.6 7.9 + - - -
243C GLU* 6.0 0.6 + - - -
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Residues in contact with THR 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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33C THR* 3.3 35.1 + - + +
166C ASN 3.8 0.7 + - - -
167C ASN* 3.4 37.5 + - - +
170C ALA* 6.6 0.2 - - - -
171C ALA* 4.8 10.5 - - - -
196C VAL* 3.0 16.0 + - + +
197C LEU* 3.1 27.1 - - - +
199C LYS* 1.4 74.6 - - - +
201C MET* 1.3 70.6 + - + +
202C ASP 4.0 0.5 + - - -
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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