Contacts of the helix formed by residues 170 - 185 (chain L) in PDB entry 2ONM
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 PHE 170 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L GLU* 4.5 0.2 - - - -
112L LYS* 3.1 26.5 - - - +
120L VAL* 6.1 0.7 - - + -
121L ASP* 3.5 15.7 - - - +
168L TRP 4.7 0.4 - - - -
169L ASN* 1.3 111.9 + - - +
171L PRO* 1.3 59.3 - - - +
172L LEU 3.4 2.0 + - - -
173L LEU* 4.0 26.7 - - + -
174L MET* 2.8 49.6 + - + +
296L PHE* 3.9 18.6 - + - -
297L ASN* 3.5 27.1 - - + -
300L GLN 3.8 0.2 - - - -
301L CYS* 3.7 29.2 - - - -
302L CYS* 5.4 1.8 - - - -
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Residues in contact with PRO 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L GLU* 3.2 31.9 - - - +
110L ASN* 4.0 6.3 - - + +
112L LYS* 4.3 1.8 - - - +
166L ILE* 3.8 9.6 - - + +
167L PRO 4.5 8.5 - - - +
168L TRP 3.3 11.8 - - - +
169L ASN 3.7 3.1 - - - +
170L PHE* 1.3 89.0 - - - +
172L LEU* 1.3 61.6 + - - +
174L MET* 4.8 0.4 - - + -
175L GLN* 3.2 20.6 + - - +
197L THR* 3.2 41.7 - - + +
200L THR* 3.6 10.1 - - - +
201L ALA* 5.2 5.0 - - + +
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Residues in contact with LEU 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L ILE* 6.0 1.1 - - + -
102L LEU* 4.2 18.4 - - + +
106L GLU* 3.0 24.5 + - + +
121L ASP* 5.3 4.3 - - + +
122L LEU* 3.9 39.3 - - + +
125L VAL* 3.8 17.9 - - + +
171L PRO* 1.3 73.8 - - - +
173L LEU* 1.3 66.7 + - - +
175L GLN* 3.1 13.3 + - - +
176L ALA* 3.0 22.9 + - - +
200L THR* 3.5 26.7 - - - +
204L VAL* 3.6 28.7 - - + -
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Residues in contact with LEU 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ASP* 4.4 12.2 + - - +
124L MET* 3.4 62.4 - - + +
125L VAL* 3.6 12.7 - - + +
170L PHE* 3.5 33.0 + - + -
172L LEU* 1.3 78.1 - - - +
174L MET* 1.3 57.8 + - + +
176L ALA* 3.2 2.1 + - + +
177L TRP* 2.8 75.4 + - + +
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Residues in contact with MET 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ILE* 4.0 18.8 - - + -
167L PRO* 3.7 32.1 - - + +
169L ASN* 4.4 3.1 - - - +
170L PHE* 2.8 50.0 + - + +
171L PRO* 3.9 4.0 - - + +
173L LEU* 1.3 75.6 - - + +
175L GLN* 1.3 62.4 + - - +
177L TRP* 3.4 45.0 + - + +
178L LYS* 3.3 33.2 + - - +
244L THR* 3.9 19.1 - - + -
268L GLU* 5.2 3.6 - - - +
302L CYS* 6.0 4.3 - - - -
476L GLU* 5.6 0.7 - - - +
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Residues in contact with GLN 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L VAL* 6.3 0.8 - - - +
166L ILE* 3.9 7.4 - - + +
171L PRO 3.2 11.0 + - - +
172L LEU* 3.1 16.2 + - - +
174L MET* 1.3 79.1 - - - +
176L ALA* 1.3 57.4 + - - +
178L LYS* 3.1 4.0 + - - +
179L LEU* 2.8 44.5 + - + +
191L MET* 3.6 25.1 - - - +
201L ALA* 3.2 34.2 - - + +
204L VAL* 3.4 40.3 - - - +
220L ILE* 3.5 16.8 - - - +
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Residues in contact with ALA 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L VAL* 3.7 37.7 - - + +
128L CYS* 3.6 13.8 - - + -
129L LEU* 4.3 14.6 - - + +
172L LEU 3.0 13.6 + - - +
173L LEU 3.6 7.0 - - - +
175L GLN* 1.3 77.8 - - - +
177L TRP* 1.3 57.1 + - + +
178L LYS 3.0 0.2 - - - -
179L LEU* 4.5 2.7 - - - +
180L GLY* 2.9 30.3 + - - -
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Residues in contact with TRP 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L MET* 4.5 9.7 + - + +
128L CYS* 3.6 25.8 - - - +
132L TYR* 5.1 1.6 + - - -
173L LEU* 2.8 54.9 + - + +
174L MET* 3.4 36.1 - - + +
176L ALA* 1.3 76.8 - - - +
178L LYS* 1.3 59.1 + - + +
181L PRO* 3.2 21.2 - - - +
268L GLU* 5.2 1.8 - - - -
459L PHE* 4.2 30.5 - + + -
461L ALA* 5.9 0.4 - - - +
465L PHE* 4.2 20.6 - + - -
476L GLU* 4.1 33.1 - - + +
477L LEU* 3.6 39.2 + - + +
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Residues in contact with LYS 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L GLN* 3.1 35.0 + - + +
165L ILE 4.9 0.2 - - - -
166L ILE* 3.8 19.6 - - + +
174L MET* 3.3 18.7 + - - +
175L GLN 3.1 7.5 + - - +
176L ALA 3.0 0.4 - - - -
177L TRP* 1.3 80.4 - - - +
179L LEU* 1.3 63.2 + - - +
180L GLY 3.3 0.2 - - - -
181L PRO* 3.4 4.3 - - - +
182L ALA* 3.2 13.5 + - - +
191L MET* 3.7 5.2 - - + -
242L ALA* 3.7 30.1 - - + -
243L PHE 4.9 0.2 - - - +
244L THR* 2.8 31.3 + - - +
476L GLU* 2.9 29.1 + - - +
485L TYR* 3.6 17.3 - - - +
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Residues in contact with LEU 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L LEU* 5.1 5.2 - - + -
129L LEU* 5.0 7.2 - - + -
164L GLN* 4.0 13.9 - - - +
175L GLN* 2.8 45.3 + - + +
176L ALA* 4.4 3.6 - - - +
178L LYS* 1.3 70.3 - - - +
180L GLY* 1.3 60.4 + - - +
182L ALA* 4.5 1.3 - - - -
183L LEU* 2.8 47.8 + - + +
189L VAL* 4.1 15.7 - - + -
191L MET* 4.0 10.1 - - + -
204L VAL* 4.9 3.1 - - + -
208L ILE* 3.8 26.9 - - + -
218L VAL* 4.1 25.1 - - + -
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Residues in contact with GLY 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L LEU* 4.1 5.6 - - - +
128L CYS* 5.1 0.4 - - - -
129L LEU* 4.5 11.8 - - - +
132L TYR* 3.5 24.7 - - - +
176L ALA 2.9 16.8 + - - -
179L LEU* 1.3 80.9 - - - +
181L PRO* 1.3 60.8 - - - +
184L ALA* 3.0 27.2 + - - +
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Residues in contact with PRO 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L TYR* 3.7 35.4 - - + +
177L TRP 3.2 25.8 - - - +
178L LYS 3.4 7.0 - - - +
180L GLY* 1.3 86.9 - - - +
182L ALA* 1.3 67.0 + - - +
184L ALA* 3.9 0.4 - - + +
185L THR* 2.7 33.5 + - - +
476L GLU* 6.6 0.2 - - - -
477L LEU 6.1 0.9 - - - +
481L GLY* 3.8 23.8 - - - +
482L LEU* 4.2 3.1 - - + -
485L TYR* 3.6 18.2 - - + -
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Residues in contact with ALA 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L CYS* 5.0 0.4 - - - -
164L GLN* 3.4 19.3 - - - +
178L LYS 3.2 16.8 + - - +
179L LEU 3.9 1.3 - - - +
180L GLY 3.4 0.2 - - - -
181L PRO* 1.3 83.4 - - - +
183L LEU* 1.3 59.3 + - - +
185L THR* 3.2 3.3 + - - -
187L ASN* 2.9 36.9 + - + -
189L VAL* 4.0 16.2 - - + -
485L TYR* 3.8 20.6 - - + -
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Residues in contact with LEU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L TRP* 3.5 21.1 - - + -
84L ARG* 3.7 6.6 - - - +
88L LEU* 4.2 20.0 - - + -
91L LEU* 5.2 4.0 - - + -
179L LEU* 2.8 42.3 + - + +
182L ALA* 1.3 71.3 - - + +
184L ALA* 1.3 66.2 + - - +
185L THR 3.1 2.0 - - - -
186L GLY* 3.0 11.3 + - - -
187L ASN 3.8 11.2 - - - +
189L VAL* 4.5 6.7 - - + -
208L ILE* 5.4 0.7 - - + -
213L PHE* 3.9 24.0 - - + -
217L VAL* 3.6 30.7 - - + +
218L VAL* 3.9 21.8 - - + -
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Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L ARG* 3.1 23.2 + - - +
88L LEU* 3.8 10.0 - - + +
132L TYR* 3.3 31.6 - - + +
135L TRP* 4.7 0.9 - - + -
136L ALA* 3.5 23.0 - - - +
180L GLY 3.0 20.2 + - - +
181L PRO* 3.9 6.3 - - + +
183L LEU* 1.3 76.8 - - - +
185L THR* 1.3 58.8 - - - +
482L LEU* 4.6 7.0 - - + -
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Residues in contact with THR 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500I SER* 4.9 0.2 - - - -
84L ARG* 4.0 9.8 + - - +
139L TYR* 4.7 9.4 - - + -
156L HIS 5.7 0.5 - - - +
157L GLU 5.0 0.7 - - - -
158L PRO* 3.1 23.7 - - - +
181L PRO 2.7 20.2 + - - +
184L ALA* 1.3 77.4 - - - +
186L GLY* 1.3 57.0 + - - +
187L ASN* 2.6 26.0 + - - -
482L LEU* 3.8 31.9 - - + +
485L TYR* 3.4 11.4 - - + +
486L THR* 3.9 17.3 - - - +
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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