Contacts of the helix formed by residues 189 - 209 (chain C) in PDB entry 3LOC
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY 4.6 0.9 - - - +
185C ALA* 3.1 16.7 - - + +
186C THR* 3.0 34.6 + - - +
187C LEU 4.1 1.3 - - - -
188C ARG* 1.3 77.8 - - - +
190C GLU* 1.3 56.9 + - - +
191C VAL* 3.1 3.1 - - + +
192C PHE* 3.0 11.8 + - + +
193C PHE* 2.8 32.6 + - - +
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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
----------------------------------------------------------
187C LEU 5.1 0.4 - - - -
188C ARG 3.4 6.6 + - - -
189C ASP* 1.3 70.9 - - - +
191C VAL* 1.3 64.5 + - + +
193C PHE* 3.3 10.0 + - - +
194C ASN* 3.0 24.6 + - - +
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Residues in contact with VAL 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ASP* 3.1 3.6 - - + +
190C GLU* 1.3 77.9 - - + +
192C PHE* 1.3 59.1 + - - +
194C ASN* 3.3 6.2 + - - +
195C GLN* 2.9 53.6 + - + +
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Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 4.4 3.4 - + - -
179C VAL* 3.6 31.4 - - + -
183C THR* 3.4 23.8 - - + -
185C ALA* 3.6 21.3 - - + -
186C THR* 3.3 28.9 - - - +
187C LEU* 4.0 11.9 - - + -
189C ASP* 3.0 12.4 + - + +
191C VAL* 1.3 77.3 - - - +
193C PHE* 1.3 66.6 + - - +
195C GLN* 3.2 19.3 + - - +
196C THR* 2.8 43.8 + - - -
159D GLN* 5.6 1.1 - - - -
160D HIS* 3.7 24.0 - + - -
163D PHE* 5.1 0.2 - + - -
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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
----------------------------------------------------------
98C ARG* 4.6 10.8 - - + -
101C LEU* 3.6 29.4 - - + -
102C GLU* 4.0 23.6 - - + -
105C ARG* 3.7 32.3 - - + +
187C LEU* 3.5 43.3 + - + +
189C ASP 2.8 11.7 + - - +
190C GLU* 3.5 13.5 - - - +
192C PHE* 1.3 74.1 - - - +
194C ASN* 1.3 69.6 + - + +
196C THR* 3.0 13.7 + - - -
197C VAL* 3.0 35.7 + - + +
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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
----------------------------------------------------------
98C ARG* 4.1 20.4 - - - +
190C GLU 3.0 16.8 + - - +
191C VAL* 3.7 5.8 - - - +
193C PHE* 1.3 83.6 - - + +
195C GLN* 1.3 64.9 + - - +
197C VAL* 3.4 3.2 + - - +
198C GLU* 3.0 42.4 + - - +
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Residues in contact with GLN 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 2.9 37.5 + - + +
192C PHE* 3.5 24.0 - - - +
194C ASN* 1.3 77.5 - - + +
196C THR* 1.3 62.1 + - - +
198C GLU* 3.4 5.4 + - - +
199C ASN* 2.9 35.6 + - - +
157D ASP* 5.5 4.9 - - - +
160D HIS* 4.3 10.8 + - - +
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Residues in contact with THR 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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101C LEU* 4.0 13.5 - - + -
172C TYR* 3.6 41.3 - - + -
187C LEU* 3.7 7.0 - - + +
192C PHE* 2.8 31.7 + - - -
193C PHE* 3.3 8.3 - - - -
195C GLN* 1.3 77.5 - - - +
197C VAL* 1.3 65.1 + - - +
199C ASN* 3.6 1.0 - - - +
200C VAL* 2.9 32.2 + - + +
160D HIS* 3.4 21.0 - - - -
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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
----------------------------------------------------------
98C ARG* 3.8 30.5 - - + +
101C LEU* 3.5 26.9 - - + -
193C PHE* 3.0 41.4 + - + +
194C ASN* 3.8 7.4 - - - +
196C THR* 1.3 74.7 - - - +
198C GLU* 1.3 61.7 + - + +
201C GLN* 2.8 59.3 + - + +
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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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98C ARG* 5.2 4.2 + - - -
194C ASN* 3.0 40.7 + - - +
195C GLN* 3.9 5.6 - - - +
196C THR 3.2 0.2 - - - -
197C VAL* 1.3 78.9 - - + +
199C ASN* 1.3 59.6 + - - +
201C GLN* 4.1 11.1 - - - +
202C ARG* 3.0 29.6 + - - +
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Residues in contact with ASN 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 GLN* 2.9 31.0 + - - +
196C THR 3.6 2.5 - - - +
198C GLU* 1.3 77.4 - - - +
200C VAL* 1.3 65.3 + - + +
202C ARG* 3.3 4.1 + - - +
203C ILE* 3.1 32.4 + - + +
156D ILE* 4.0 11.4 - - - +
157D ASP* 2.9 51.5 + - - +
160D HIS* 3.5 35.8 + - + +
161D LEU 5.3 0.2 + - - -
164D MSE 4.8 0.2 - - - -
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 3.3 27.4 - - + -
101C LEU* 4.1 6.1 - - + -
168C SER* 3.8 20.2 - - - +
169C THR* 4.4 5.8 - - + -
172C TYR* 4.3 15.3 - - + +
196C THR* 2.9 39.5 + - + +
199C ASN* 1.3 70.5 - - + +
201C GLN* 1.3 65.6 + - - +
203C ILE* 4.1 0.5 - - - +
204C ILE* 3.1 31.1 + - + +
164D MSE 3.7 21.3 - - + -
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Residues in contact with GLN 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LYS* 2.9 60.2 + - + +
95C GLU* 5.5 0.4 + - - -
97C ILE* 4.0 22.7 - - + -
98C ARG* 3.5 27.4 + - - +
197C VAL* 2.8 36.3 + - + +
198C GLU* 4.1 12.3 - - - +
200C VAL* 1.3 77.8 - - - +
202C ARG* 1.3 55.3 + - - +
205C ILE* 2.7 38.6 + - - +
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Residues in contact with ARG 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C GLU 3.0 20.9 + - - +
199C ASN* 3.3 4.2 + - - +
201C GLN* 1.3 74.9 - - - +
203C ILE* 1.3 59.5 + - - +
205C ILE* 4.9 1.1 - - - -
206C GLU* 2.9 57.4 + - + +
154D ALA* 3.3 26.9 - - - +
155D PRO* 3.6 31.5 + - - +
156D ILE* 3.5 20.8 - - + +
207D GLY 3.0 24.2 + - - -
209D ARG 5.1 2.4 + - - -
211D ARG* 5.4 9.5 - - - +
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Residues in contact with ILE 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 ASN* 3.1 16.8 + - - +
202C ARG* 1.3 72.6 - - - +
204C ILE* 1.3 66.1 + - - +
207C GLY* 3.0 19.4 + - - -
156D ILE* 3.8 30.7 - - + -
160D HIS 5.0 0.9 - - - -
161D LEU* 4.1 24.5 - - + +
164D MSE 3.5 42.8 - - + -
203D ILE* 3.8 3.1 - - + +
204D ILE* 4.1 29.2 - - + +
207D GLY* 3.3 13.7 - - - -
208D ILE* 4.1 11.7 - - + -
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Residues in contact with ILE 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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93C ILE* 4.4 9.9 - - + -
97C ILE* 3.8 27.8 - - + -
161C LEU* 3.9 26.9 - - + -
164C MSE 4.0 21.8 - - + -
165C ILE* 4.3 11.7 - - + -
168C SER* 3.7 23.6 - - - +
200C VAL* 3.1 23.3 + - + +
203C ILE* 1.3 74.6 - - - +
205C ILE* 1.3 66.2 + - - +
207C GLY* 3.2 2.4 + - - -
208C ILE* 3.0 24.8 + - + +
164D MSE 4.5 8.7 - - - -
203D ILE* 4.1 8.9 - - + +
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Residues in contact with ILE 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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90C LEU* 3.5 49.4 - - + +
93C ILE* 4.0 25.8 - - + -
94C LYS* 3.9 26.7 - - + +
97C ILE* 4.6 3.8 - - + -
201C GLN* 2.7 28.9 + - + +
202C ARG* 4.4 1.3 - - - +
204C ILE* 1.3 71.5 - - - +
206C GLU* 1.3 60.6 + - + +
208C ILE* 2.9 7.7 + - + +
209C ARG* 2.8 47.4 + - - +
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Residues in contact with GLU 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 ARG* 2.9 60.1 + - + +
205C ILE* 1.3 78.3 - - - +
207C GLY* 1.3 60.8 + - - +
208C ILE 3.5 0.3 + - - -
209C ARG* 2.9 49.7 + - - +
211C ARG* 3.2 32.3 + - - +
206D GLU* 3.8 5.9 - - - +
207D GLY* 3.8 9.2 - - - +
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Residues in contact with GLY 207 (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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154C ALA* 4.3 8.1 - - - +
156C ILE* 5.1 3.6 - - - +
203C ILE 3.0 11.4 + - - -
204C ILE 3.5 4.9 - - - -
205C ILE 3.1 0.4 - - - -
206C GLU* 1.3 78.1 - - - +
208C ILE* 1.3 61.6 + - - +
209C ARG 5.1 0.7 - - - -
202D ARG* 4.6 2.4 - - - +
203D ILE* 3.4 35.8 - - - +
206D GLU* 3.7 15.1 - - - +
207D GLY* 3.4 7.0 - - - -
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.7 12.8 - - + -
93C ILE* 3.4 36.3 - - + -
153C LEU* 3.5 20.8 - - + +
154C ALA* 3.0 28.3 + - + +
156C ILE* 4.6 13.0 - - + -
161C LEU* 3.9 31.2 - - + -
204C ILE* 3.0 18.8 + - + +
205C ILE* 2.9 16.6 + - + +
207C GLY* 1.3 79.6 - - - +
209C ARG* 1.3 60.7 + - - +
210C PRO 3.5 0.5 - - - -
203D ILE* 4.5 12.3 - - + -
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Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.1 26.9 - - + +
154C ALA* 4.1 6.7 - - - +
205C ILE* 2.8 28.7 + - - +
206C GLU* 2.9 48.9 + - - +
207C GLY 3.5 1.5 - - - -
208C ILE* 1.3 78.1 - - - +
210C PRO* 1.4 82.6 - - + +
211C ARG* 3.4 23.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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