Contacts of the helix formed by residues 186 - 202 (chain C) in PDB entry 3Q29
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 ASN 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C GLY 2.6 27.2 + - - +
168C TYR* 3.2 29.2 - - + -
183C GLY* 3.7 9.7 + - - +
184C VAL 4.5 0.4 - - - +
185C ASP* 1.3 83.4 - - - +
187C ALA* 1.3 65.7 + - - +
188C GLY 3.5 1.9 + - - -
189C ALA* 3.2 23.7 + - - +
190C LYS* 3.3 19.5 + - - +
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Residues in contact with ALA 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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165C ASP* 5.1 1.6 - - - +
186C ASN* 1.3 77.7 - - - +
188C GLY* 1.3 62.2 + - - +
190C LYS* 3.4 10.6 + - - +
191C ALA* 3.1 23.2 + - - +
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Residues in contact with GLY 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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162C ILE 3.7 9.1 - - - +
165C ASP* 3.2 43.2 + - - +
166C GLY* 4.1 1.5 - - - -
167C GLY 4.4 0.2 - - - -
186C ASN* 3.3 6.4 + - - -
187C ALA* 1.3 76.0 - - - +
189C ALA* 1.3 65.5 + - - +
191C ALA* 3.1 4.0 + - - +
192C GLY* 2.9 19.8 + - - -
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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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162C ILE* 3.6 30.3 + - + +
167C GLY* 4.1 2.9 - - - +
183C GLY 4.3 2.2 - - - +
184C VAL* 3.6 32.3 - - - +
186C ASN* 3.2 19.1 + - - +
188C GLY* 1.3 74.9 - - - +
190C LYS* 1.3 63.2 + - - +
192C GLY* 3.1 1.6 + - - -
193C LEU* 2.9 26.5 + - - +
362C LEU* 3.9 4.5 - - + -
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Residues in contact with LYS 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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185C ASP* 3.2 31.5 + - - +
186C ASN 3.3 15.1 + - - +
187C ALA* 3.7 10.5 - - - +
188C GLY 3.3 0.2 - - - -
189C ALA* 1.3 76.1 - - - +
191C ALA* 1.3 55.4 + - - +
194C THR* 2.5 38.8 + - - +
358C VAL* 3.8 8.9 - - + +
359C ASP* 3.0 34.5 + - - +
362C LEU* 3.9 18.8 - - + -
363C LYS* 5.0 8.9 - - - +
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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
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165C ASP* 4.3 3.6 - - - +
187C ALA 3.1 12.5 + - - +
188C GLY 3.1 9.1 + - - +
190C LYS* 1.3 75.4 - - - +
192C GLY* 1.3 64.4 + - - +
194C THR* 3.3 5.5 + - - -
195C PHE* 3.0 19.4 + - - +
251C PHE* 3.5 14.3 - - + -
252C LYS* 3.6 31.4 - - - +
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Residues in contact with GLY 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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161C LEU* 3.4 40.0 - - - +
162C ILE* 4.2 5.8 - - - -
188C GLY 2.9 13.2 + - - -
189C ALA 3.7 2.2 - - - -
191C ALA* 1.3 78.4 - - - +
193C LEU* 1.3 59.9 + - - +
195C PHE* 3.5 1.2 + - - +
196C LEU* 3.2 16.3 + - - +
251C PHE* 3.6 12.6 - - - -
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Residues in contact with LEU 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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162C ILE* 4.2 22.7 - - + +
189C ALA 2.9 16.2 + - - +
190C LYS 4.3 2.0 - - - +
192C GLY* 1.3 73.5 - - - +
194C THR* 1.3 61.4 + - - +
196C LEU* 3.3 25.9 + - + -
197C VAL* 2.9 41.7 + - + +
347C ALA* 4.7 6.7 - - + +
348C VAL* 4.5 14.4 - - + +
351C ALA* 4.2 18.4 - - + -
358C VAL* 4.2 16.2 - - + +
361C ALA* 5.3 0.9 - - + -
362C LEU* 3.6 35.2 - - + -
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Residues in contact with THR 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 LYS* 2.5 26.1 + - - +
191C ALA* 3.7 6.1 - - - -
192C GLY 3.3 0.2 - - - -
193C LEU* 1.3 75.6 - - - +
195C PHE* 1.3 59.8 + - - +
197C VAL* 3.3 2.1 + - + +
198C ASP* 2.9 45.6 + - - +
358C VAL* 3.6 24.5 - - + +
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Residues in contact with PHE 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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130C TRP* 3.1 48.9 - + + -
131C GLU* 3.8 19.5 - - + -
134C PRO* 4.1 19.3 - - + -
161C LEU* 4.3 9.2 - - + -
191C ALA 3.0 16.5 + - - +
192C GLY 3.8 4.9 - - - +
193C LEU 3.3 0.2 - - - -
194C THR* 1.3 75.8 - - - +
196C LEU* 1.3 62.3 + - - +
198C ASP* 3.5 11.0 + - + +
199C LEU* 3.0 46.1 + - + +
251C PHE* 3.8 22.9 - + + -
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Residues in contact with LEU 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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150C PHE* 4.0 17.7 - - + -
152C LEU* 4.2 8.1 - - + -
158C THR* 3.7 26.7 - - + +
161C LEU* 3.9 19.0 - - + +
192C GLY 3.2 11.7 + - - +
193C LEU* 3.5 24.7 - - + +
194C THR 3.2 0.2 - - - -
195C PHE* 1.3 80.0 - - - +
197C VAL* 1.3 62.8 + - + +
199C LEU* 3.3 11.1 - - + +
200C ILE* 3.3 31.4 + - + +
205C MET* 3.7 26.2 - - + -
348C VAL* 4.1 14.1 - - + +
352C ALA* 5.3 1.6 - - + -
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Residues in contact with VAL 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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193C LEU* 2.9 26.9 + - + +
194C THR* 3.8 4.5 - - + +
196C LEU* 1.3 75.3 - - + +
198C ASP* 1.3 53.9 + - - +
200C ILE* 3.0 10.4 + - + +
201C LYS* 2.7 59.1 + - + +
351C ALA* 3.7 46.9 - - + +
352C ALA* 4.2 7.2 - - - +
358C VAL* 4.0 13.5 - - + -
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Residues in contact with ASP 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 THR* 2.9 36.8 + - - +
195C PHE* 3.8 11.0 - - + +
197C VAL* 1.3 73.6 - - - +
199C LEU* 1.3 66.5 + - - +
201C LYS* 3.6 28.0 + - - +
202C ASN* 2.8 40.6 + - - +
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Residues in contact with LEU 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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130C TRP* 4.1 18.6 - - + -
133C ILE* 4.7 8.1 - - + -
134C PRO* 4.0 26.5 - - + -
148C LEU* 5.0 3.8 - - + -
195C PHE* 3.0 45.4 + - + +
196C LEU* 3.3 13.0 - - + +
197C VAL 3.3 0.2 - - - -
198C ASP* 1.3 76.5 - - - +
200C ILE* 1.3 58.3 + - - +
202C ASN 3.6 0.5 + - - -
203C LYS 3.4 1.6 + - - -
204C HIS* 2.9 48.6 + - + +
205C MET* 3.3 35.9 + - + -
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Residues in contact with ILE 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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152C LEU* 4.1 18.4 - - + -
196C LEU* 3.3 23.1 + - + +
197C VAL* 3.0 10.4 + - + +
199C LEU* 1.3 76.3 - - - +
201C LYS* 1.3 64.2 + - + +
202C ASN 3.2 0.4 - - - -
203C LYS* 3.2 15.8 + - - +
205C MET* 3.5 35.2 - - + +
206C ASN* 4.4 0.4 - - - -
207C ALA* 3.8 17.7 - - + +
352C ALA* 3.6 46.9 - - + +
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Residues in contact with LYS 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 VAL* 2.7 38.6 + - + +
198C ASP* 3.0 29.7 + - - +
200C ILE* 1.3 74.2 - - + +
202C ASN* 1.3 65.4 + - - +
203C LYS* 3.2 17.9 + - - +
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Residues in contact with ASN 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 ASP* 2.8 30.9 + - - +
201C LYS* 1.3 82.3 + - - +
203C LYS* 1.3 70.9 + - - +
204C HIS* 3.2 32.6 + - + +
395C SO4 4.9 7.2 + - - +
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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