Contacts of the helix formed by residues 189 - 200 (chain C) in PDB entry 6B3I
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C ALA* 3.0 53.0 - - + +
182C GLY* 4.2 5.4 - - - +
184C GLY* 4.9 4.3 - - - +
187C GLY 3.6 5.3 + - - +
188C THR* 1.3 69.4 - - - +
190C GLU* 1.3 82.8 + - - +
191C LEU 3.1 6.4 + - - -
192C ALA* 3.1 12.0 + - - +
193C PHE* 3.5 9.3 - - + -
227C GLU* 4.5 14.0 - - - +
228C THR* 5.6 0.9 - - - +
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Residues in contact with GLU 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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147C ASN* 2.9 35.7 + - + +
188C THR* 3.5 8.1 - - + +
189C ASP* 1.3 92.0 + - - +
191C LEU* 1.3 59.0 + - - +
192C ALA 3.3 0.4 - - - -
193C PHE* 3.9 6.5 - - + +
194C ASN* 3.0 35.8 + - - +
227C GLU 5.2 2.1 - - - +
228C THR* 4.6 10.3 - - + +
232C LEU* 3.4 29.8 - - + +
236C TYR* 3.2 17.6 + - + +
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Residues in contact with LEU 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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169B ASP* 5.4 11.1 - - - +
176B LYS* 5.9 5.8 - - - +
147C ASN* 4.3 3.6 - - - +
150C LYS* 4.2 34.1 - - + +
188C THR* 3.6 38.7 + - + +
189C ASP 3.1 1.4 + - - -
190C GLU* 1.3 77.0 - - - +
192C ALA* 1.3 65.0 + - - +
194C ASN* 3.4 9.2 + - + +
195C GLU* 3.1 23.0 + - - +
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Residues in contact with ALA 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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173B GLN* 4.5 18.4 + - - +
177C ASP* 4.4 11.9 - - + +
178C LEU* 3.8 8.5 - - + -
181C ALA* 3.8 17.9 - - + -
188C THR 4.4 2.5 + - - +
189C ASP 3.1 11.1 + - - +
191C LEU* 1.3 77.4 - - - +
193C PHE* 1.3 65.1 + - - +
195C GLU* 3.3 5.4 + - - +
196C VAL* 3.0 30.0 + - + +
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Residues in contact with PHE 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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178C LEU* 3.5 48.9 - - + -
181C ALA* 3.6 11.9 - - + -
182C GLY* 4.3 1.3 - - - -
189C ASP* 3.5 17.3 - - + -
190C GLU* 3.6 3.7 + - + +
191C LEU 3.4 0.2 - - - -
192C ALA* 1.3 77.9 - - - +
194C ASN* 1.3 64.6 + - - +
197C LEU* 3.0 47.8 + - + +
212C TYR* 5.8 0.2 - - - -
220C ILE* 4.3 14.4 - - + -
223C ALA* 5.7 2.5 - - + -
224C ILE* 4.0 23.8 - - + -
227C GLU* 3.7 22.4 - - + -
228C THR* 6.0 4.3 - - + -
236C TYR* 3.6 34.5 - + + +
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Residues in contact with ASN 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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147C ASN* 4.0 9.3 + - - +
150C LYS* 3.7 33.7 - - - +
151C ILE* 3.7 25.9 - - + +
154C SER* 4.9 5.7 + - - +
190C GLU 3.0 23.7 + - - +
191C LEU* 3.7 10.5 - - + +
192C ALA 3.3 0.2 - - - -
193C PHE* 1.3 78.1 - - - +
195C GLU* 1.3 60.6 + - - +
198C ALA* 3.2 28.2 + - - +
199C LYS* 5.0 0.3 - - - +
236C TYR* 2.4 34.2 + - - -
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Residues in contact with GLU 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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167B ASP* 2.8 38.5 - - - +
169B ASP* 3.5 20.8 - - + +
170B LEU* 3.7 16.2 - - + +
173B GLN* 5.7 6.1 - - + -
191C LEU 3.1 16.6 + - - +
192C ALA* 3.8 4.9 - - - +
193C PHE 3.3 0.4 - - - -
194C ASN* 1.3 76.8 - - - +
196C VAL* 1.3 65.7 + - + +
199C LYS* 3.1 42.4 + - - +
200C ARG* 3.0 31.8 + - - +
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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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174C ASP* 3.7 36.6 - - + +
177C ASP* 5.7 3.1 - - + -
178C LEU* 4.0 33.9 - - + -
192C ALA* 3.0 18.6 + - + +
193C PHE 4.4 0.2 - - - +
195C GLU* 1.3 80.1 - - + +
197C LEU* 1.3 63.9 + - + +
198C ALA 3.3 0.9 + - - -
200C ARG* 3.2 43.5 + - + +
205C LEU* 3.4 19.4 - - + +
208C THR* 4.5 4.3 - - + +
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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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160C ARG* 2.9 23.5 + - - -
178C LEU* 5.0 6.5 - - + -
193C PHE* 3.0 37.5 + - + +
194C ASN* 4.9 0.4 - - - +
196C VAL* 1.3 82.3 - - + +
198C ALA* 1.3 57.1 + - + +
205C LEU* 3.9 15.2 - - + +
209C PHE* 4.2 18.2 - - + -
220C ILE* 5.7 0.9 - - + -
224C ILE* 4.5 1.6 - - + -
236C TYR* 3.8 45.5 - - + +
239C LEU* 3.8 24.3 - - + +
240C VAL* 4.0 22.2 - - + +
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Residues in contact with ALA 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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151C ILE* 3.7 12.8 - - + -
154C SER* 4.2 14.1 - - - +
155C LEU* 3.7 22.8 - - + +
160C ARG* 3.3 33.4 + - - +
194C ASN 3.2 20.1 + - - +
196C VAL 3.2 0.4 - - - -
197C LEU* 1.3 80.5 - - - +
199C LYS* 1.3 67.1 + - - +
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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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167B ASP* 3.9 11.0 - - - +
154C SER* 3.0 43.4 + - - +
155C LEU* 5.1 0.4 - - - +
157C GLN* 4.4 3.0 - - - +
159C ASN* 2.7 42.8 + - - +
160C ARG* 3.8 2.7 - - - +
161C ASN* 2.9 39.8 + - - +
194C ASN 5.3 0.7 - - - -
195C GLU* 3.1 45.5 + - - +
198C ALA* 1.3 88.3 + - + +
200C ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 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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170B LEU* 3.7 28.8 - - - +
173B GLN* 6.1 2.2 - - - +
160C ARG* 2.7 33.7 + - - +
161C ASN* 4.1 12.0 - - - +
170C LEU* 4.0 25.9 - - - +
174C ASP* 2.7 41.2 + - - +
195C GLU* 3.0 40.0 + - - +
196C VAL* 3.2 31.5 + - + +
199C LYS* 1.3 82.6 - - - +
201C SER* 1.3 63.6 + - - +
204C GLN* 4.1 14.4 - - + -
205C LEU* 3.8 13.8 - - + +
208C THR* 5.6 0.7 - - - +
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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