Contacts of the helix formed by residues 165 - 184 (chain C) in PDB entry 1J1J
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 SER 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASP* 3.0 7.6 + - - -
164C TYR* 1.3 79.2 - - - +
166C ARG* 1.3 67.6 + - - +
167C PRO 3.3 0.7 - - - -
168C LEU* 3.0 19.0 + - - +
169C HIS* 3.1 28.1 + - - -
217C PHE* 5.0 3.6 - - - -
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 4.3 28.1 - - - +
107C TYR* 4.2 18.9 + - - -
108C LEU* 4.5 22.4 + - - +
111C GLU* 4.4 18.5 + - - +
154C LEU* 4.4 9.7 - - + +
158C SER* 3.0 29.0 + - - +
163C ASP* 3.5 20.5 + - - +
165C SER* 1.3 77.9 - - - +
167C PRO* 1.3 69.9 - - + +
169C HIS* 3.0 12.2 + - - +
170C ILE* 2.9 51.3 + - + +
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Residues in contact with PRO 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C SER* 3.4 41.2 + - - +
158C SER* 4.2 1.3 - - - -
159C VAL* 3.7 18.4 - - + -
163C ASP 4.2 4.7 - - - +
164C TYR 3.7 11.2 - - - +
165C SER 3.4 4.5 - - - -
166C ARG* 1.3 95.4 - - + +
168C LEU* 1.3 62.7 + - + +
170C ILE* 3.3 2.8 + - + +
171C SER* 2.9 26.2 + - - -
205C VAL* 4.4 0.5 - - - +
208C VAL* 3.6 13.0 - - + -
209C VAL* 3.6 7.3 - - + +
212C LEU* 3.7 12.3 - - + -
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TYR 3.4 24.2 - - - +
165C SER* 3.0 9.1 + - - +
167C PRO* 1.3 76.1 - - - +
169C HIS* 1.3 67.7 + - + +
171C SER* 3.5 3.2 + - - -
172C THR* 3.3 25.3 + - - -
209C VAL* 3.4 30.7 - - + -
212C LEU* 4.1 9.6 - - + -
217C PHE* 3.5 34.5 - - + +
160D THR* 5.2 1.8 - - + -
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Residues in contact with HIS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR* 3.9 6.8 + - - +
111C GLU* 3.1 31.0 - - - +
165C SER* 3.1 29.4 + - - -
166C ARG* 3.0 10.8 + - - +
168C LEU* 1.3 78.8 - - + +
170C ILE* 1.3 65.9 + - - +
172C THR* 3.3 6.8 + - - -
173C PHE* 3.0 22.7 + - - +
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR* 3.5 22.2 - - + +
151C LEU* 3.7 35.9 - - + +
154C LEU* 4.0 11.2 - - + -
155C SER* 3.6 29.4 - - - +
166C ARG* 2.9 47.3 + - + +
167C PRO* 3.7 4.7 - - + +
169C HIS* 1.3 75.9 - - - +
171C SER* 1.3 64.3 + - - +
173C PHE* 3.2 3.4 + - - +
174C ILE* 2.9 30.8 + - + +
205C VAL* 3.9 13.7 - - + -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PRO 2.9 17.6 + - - -
168C LEU 3.7 5.2 - - - -
169C HIS 3.3 0.2 - - - -
170C ILE* 1.3 76.9 - - - +
172C THR* 1.3 63.7 + - - +
174C ILE* 3.3 2.2 + - - +
175C ASN* 3.1 39.3 + - - +
205C VAL* 3.3 21.0 - - - +
206C GLU* 4.0 13.0 - - - +
209C VAL* 3.7 15.4 - - - +
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Residues in contact with THR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU 3.3 12.8 + - - -
169C HIS* 3.7 9.5 - - - -
170C ILE 3.3 0.2 - - - -
171C SER* 1.3 77.7 + - - +
173C PHE* 1.3 65.9 + - - +
175C ASN* 3.2 8.6 + - - +
176C GLU* 3.0 44.5 + - + +
47D GLN* 4.9 8.0 + - + +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR* 3.5 33.0 - + + +
111C GLU 4.4 6.5 - - - -
112C THR* 4.0 4.3 - - - -
113C LEU* 3.7 43.7 - - + -
147C LEU* 3.9 13.0 - - + -
151C LEU* 3.3 33.9 - - + -
169C HIS 3.0 14.1 + - - +
170C ILE 3.2 8.0 + - - +
172C THR* 1.3 77.0 - - - +
174C ILE* 1.3 61.6 + - - +
176C GLU* 3.1 28.8 + - + +
177C LEU* 3.2 37.6 + - + +
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ALA* 4.1 16.4 - - + +
151C LEU* 3.2 43.7 - - + -
170C ILE* 2.9 29.5 + - + +
171C SER* 3.7 5.6 - - - +
173C PHE* 1.3 75.9 - - + +
175C ASN* 1.3 58.4 + - - +
177C LEU* 3.2 9.7 + - + +
178C ASP* 2.9 24.8 + - - +
198C LEU* 4.4 12.0 - - + +
201C ASP* 4.7 2.2 - - + -
202C VAL* 3.6 38.1 - - + +
205C VAL* 4.1 12.1 - - + -
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C SER* 3.1 33.4 + - - +
172C THR* 3.7 3.1 - - - +
174C ILE* 1.3 77.6 - - - +
176C GLU* 1.3 60.4 + - - +
178C ASP* 3.3 10.4 + - - +
179C SER* 3.0 30.5 + - - -
202C VAL* 3.6 9.1 - - - +
206C GLU* 3.3 19.9 + - - +
46D HIS* 5.3 0.2 - - - +
47D GLN* 3.0 39.6 + - - +
153D ARG* 3.1 25.1 + - - -
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C THR* 3.0 31.6 + - + +
173C PHE* 3.1 21.3 + - + +
175C ASN* 1.3 74.3 - - + +
177C LEU* 1.3 63.4 + - + +
179C SER* 3.2 8.7 + - - -
180C GLY* 2.8 25.5 + - - -
47D GLN* 5.5 3.4 - - - +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.9 28.0 - - + -
144C VAL* 4.1 23.8 - - + +
147C LEU* 5.2 0.9 - - + -
148C ALA* 4.4 22.0 - - + +
151C LEU* 5.0 0.2 - - + -
173C PHE* 3.2 46.3 + - + +
174C ILE* 3.4 13.5 - - + +
176C GLU* 1.3 79.1 - - + +
178C ASP* 1.3 63.0 + - - +
180C GLY* 3.0 12.1 + - - -
181C PHE* 3.0 26.8 + - + -
198C LEU* 4.3 9.0 - - + -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE 2.9 13.3 + - - +
175C ASN* 3.3 17.6 - - - +
176C GLU 3.2 0.2 - - - -
177C LEU* 1.3 77.9 - - - +
179C SER* 1.3 62.7 + - - +
181C PHE* 3.5 2.6 + - - +
182C ARG* 3.1 44.2 + - - +
195C TYR* 4.2 1.9 + - - -
198C LEU* 3.8 13.1 - - - +
199C LYS* 3.6 27.1 - - - +
202C VAL* 4.0 27.6 - - + +
43D GLN* 3.9 6.4 - - - +
153D ARG* 4.7 5.0 + - - -
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ASN 3.0 14.9 + - - -
176C GLU* 3.5 9.6 - - - -
177C LEU 3.2 0.2 - - - -
178C ASP* 1.3 74.1 - - - +
180C GLY* 1.3 68.0 + - - +
182C ARG* 3.2 25.7 + - - +
183C LEU* 3.3 13.0 + - - +
40D THR* 4.8 18.8 + - - +
47D GLN* 5.5 2.1 + - - -
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU 2.8 14.7 + - - -
177C LEU* 3.0 4.9 + - - -
179C SER* 1.3 76.9 - - - +
181C PHE* 1.3 62.5 + - - +
183C LEU* 3.0 27.4 + - - +
184C LEU* 3.6 9.5 + - - +
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Residues in contact with PHE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.8 39.0 - - + -
144C VAL* 4.4 17.5 - - + -
145C LEU* 3.5 41.5 - - + -
177C LEU* 3.0 33.9 + - + +
178C ASP 4.0 1.1 - - - +
180C GLY* 1.3 75.1 - - - +
182C ARG* 1.3 57.8 + - - +
184C LEU* 2.9 40.3 + - + +
186C LEU* 3.9 26.3 - - + +
191C LEU* 5.3 0.4 - - + -
195C TYR* 3.4 33.3 + + + -
198C LEU* 4.0 12.3 - - + -
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASP* 3.1 37.6 + - - +
179C SER* 3.2 18.9 + - - +
181C PHE* 1.3 77.4 - - - +
183C LEU* 1.3 58.8 + - + +
184C LEU 3.4 0.9 + - - +
195C TYR* 3.7 15.7 + - - -
199C LYS* 5.1 4.8 - - - +
36D ARG* 3.3 49.5 + - + +
39D LEU* 3.9 23.6 - - - +
40D THR* 3.1 41.5 + - - +
43D GLN* 2.7 31.2 + - - +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C SER 3.8 12.1 - - - +
180C GLY* 3.0 15.2 + - - +
182C ARG* 1.3 79.4 - - - +
184C LEU* 1.3 65.4 + - + +
185C ASN 3.9 1.0 + - - -
36D ARG* 5.0 4.7 + - - -
37D GLU* 6.2 4.3 - - + -
40D THR* 5.3 10.8 - - + +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.8 34.3 - - + -
180C GLY 3.8 13.7 - - - +
181C PHE* 2.9 33.3 + - + +
182C ARG 3.5 6.6 - - - +
183C LEU* 1.3 87.4 - - + +
185C ASN* 1.3 62.0 + - - +
186C LEU* 3.9 22.2 - - + +
36D ARG* 3.9 9.5 + - - -
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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
------------------------------------------------------------
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