Contacts of the helix formed by residues 168 - 186 (chain L) in PDB entry 5U0A
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 168 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F GLU* 5.6 3.8 + - - +
166L ARG 3.7 0.4 + - - -
167L GLN* 1.3 81.9 + - - +
169L LEU* 1.3 62.6 + - - +
170L ASP* 2.8 32.5 + - - +
171L GLY* 3.8 4.0 + - - -
172L VAL* 3.0 28.1 + - - +
174L ARG* 4.8 2.1 + - - -
202L TRP* 3.3 8.1 - - - +
206L PRO* 5.9 2.2 - - - -
207L ARG* 5.6 3.1 - - - +
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Residues in contact with LEU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L ALA* 3.4 26.9 - - + +
79L ARG* 3.3 29.6 + - - +
168L ASN* 1.3 78.3 - - - +
170L ASP* 1.3 59.5 + - - +
172L VAL* 3.3 4.3 - - + +
173L HIS* 2.9 42.9 - - + +
199L LEU 4.0 8.5 - - - +
202L TRP* 3.3 34.9 - - + +
203L GLY* 3.7 19.1 - - - +
206L PRO* 6.1 0.4 - - - +
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Residues in contact with ASP 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F THR* 5.3 3.6 + - - -
79L ARG* 4.1 20.1 - - - +
168L ASN* 2.8 32.2 + - - +
169L LEU* 1.3 78.2 - - - +
171L GLY* 1.3 69.1 + - - +
173L HIS* 3.8 7.0 + - - +
174L ARG* 3.3 32.5 + - - +
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Residues in contact with GLY 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L GLN* 3.7 15.9 - - - -
168L ASN* 3.4 3.2 + - - -
169L LEU 3.3 0.4 - - - -
170L ASP* 1.3 83.4 + - - +
172L VAL* 1.3 57.1 + - - +
173L HIS 3.0 2.5 - - - -
174L ARG* 2.7 49.3 + - - +
175L HIS* 3.0 16.5 + - - -
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Residues in contact with VAL 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L ILE* 3.8 29.7 - - + +
167L GLN* 3.6 7.9 - - + +
168L ASN 3.0 16.7 + - - +
169L LEU* 3.3 21.5 - - + +
171L GLY* 1.3 75.7 - - - +
173L HIS* 1.3 70.0 + - + +
175L HIS* 3.8 0.8 - - - +
176L LEU* 2.9 39.7 + - + +
199L LEU* 4.5 20.0 - - + -
202L TRP* 4.3 28.5 - - + +
213L TRP* 5.1 2.7 - - + -
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Residues in contact with HIS 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L ALA 5.3 0.2 + - - -
79L ARG* 3.7 47.0 - - + +
80L ALA* 4.2 2.9 + - - -
83L ALA* 3.4 21.1 - - + +
169L LEU* 2.9 40.9 - - + +
170L ASP* 3.8 9.8 + - - +
171L GLY 3.0 0.4 - - - -
172L VAL* 1.3 87.0 - - + +
174L ARG* 1.3 62.2 - - - +
176L LEU* 4.6 6.3 - - - +
177L PRO* 3.4 19.6 - - - +
199L LEU* 4.0 23.5 + - + +
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Residues in contact with ARG 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F GLU* 5.9 0.8 + - - -
198F THR* 4.4 13.0 + - - -
199F VAL* 4.0 35.6 + - - +
201F VAL* 4.2 16.7 - - + +
167L GLN* 3.4 23.6 - - - +
168L ASN* 4.8 1.6 + - - -
170L ASP* 3.3 22.6 + - - +
171L GLY* 2.7 26.0 + - - +
173L HIS* 1.3 81.4 - - - +
175L HIS* 1.3 77.2 + - + +
176L LEU 3.7 0.4 - - - -
177L PRO* 4.3 5.0 - - - +
178L ARG* 4.2 14.4 + - - -
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Residues in contact with HIS 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F VAL* 5.8 1.0 - - - +
201F VAL* 3.8 21.5 - - + -
225F GLN* 3.4 30.3 + - + +
163L LEU* 3.5 19.7 - - + +
164L ILE* 4.0 28.8 - - + +
167L GLN* 3.7 27.1 + - + -
171L GLY 3.0 24.1 + - - +
172L VAL* 4.5 1.8 - - - +
174L ARG* 1.3 93.3 + - - +
176L LEU* 1.3 65.0 + - - +
177L PRO 3.7 1.3 - - - -
178L ARG* 4.0 20.2 + - - +
179L LEU* 3.9 11.8 + - - +
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Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L ALA* 6.3 0.9 - - + -
84L VAL* 5.5 1.6 - - + -
87L ILE* 6.2 4.3 - - + -
139L LEU* 4.5 13.5 - - + -
164L ILE* 4.6 18.6 - - + -
172L VAL* 2.9 22.1 + - + +
173L HIS* 4.6 4.3 - - - +
175L HIS* 1.3 76.5 - - - +
177L PRO* 1.3 72.1 - - + +
178L ARG 3.0 0.7 + - - -
179L LEU* 3.2 5.4 + - + +
180L VAL* 2.9 39.8 + - + +
195L LEU* 4.2 16.6 - - + -
199L LEU* 3.7 37.2 - - + -
213L TRP* 4.9 11.9 - - + -
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Residues in contact with PRO 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L VAL* 4.1 26.9 - - + +
83L ALA* 6.5 1.3 - - + -
87L ILE* 3.5 29.8 - - + -
173L HIS* 3.4 23.6 - - - +
174L ARG 4.3 4.9 - - - +
175L HIS 3.7 1.8 - - - -
176L LEU* 1.3 93.6 - - + +
178L ARG* 1.3 58.1 + - - +
180L VAL* 4.6 0.4 - - + +
181L LEU* 2.9 37.3 + - + +
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Residues in contact with ARG 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 5.3 12.3 - - - +
201F VAL* 3.5 23.2 - - - +
203F PHE* 3.9 26.6 - - + +
222F ASN* 5.0 2.7 - - - +
223F ALA* 3.5 29.3 - - - +
160L ARG* 6.4 2.5 - - - +
174L ARG 4.2 17.7 + - - +
175L HIS* 4.3 20.4 + - - +
176L LEU 3.0 1.2 + - - -
177L PRO* 1.3 79.3 - - - +
179L LEU* 1.3 60.1 + - - +
181L LEU* 3.9 3.9 - - - +
182L TYR* 3.0 29.1 + - - +
31M A 4.6 20.3 + - + +
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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
----------------------------------------------------------
139L LEU* 4.5 6.5 - - + -
143L LEU* 3.8 42.4 - - + -
157L THR* 4.5 1.8 - - - +
160L ARG* 3.9 41.3 - - + +
164L ILE* 4.0 22.7 - - + -
175L HIS 3.9 9.5 + - - +
176L LEU* 3.2 6.1 + - + +
178L ARG* 1.3 78.7 - - - +
180L VAL* 1.3 76.0 + - + +
182L TYR* 3.2 11.7 + - + +
183L LEU* 2.9 32.7 + - + +
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Residues in contact with VAL 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L ILE* 4.0 15.9 - - + -
139L LEU* 4.2 18.2 - - + -
176L LEU* 2.9 43.2 + - + +
177L PRO 4.2 1.6 - - - +
179L LEU* 1.3 81.5 - - + +
181L LEU* 1.3 59.7 + - - +
183L LEU* 2.8 22.6 + - - +
184L ARG* 2.9 13.7 + - + +
190L ILE* 3.7 11.2 - - + -
192L TRP* 3.7 33.2 - - + -
195L LEU* 4.5 6.1 - - + -
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Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 5.6 5.6 - - - +
22E LEU* 5.8 8.1 - - + -
35L VAL* 5.9 3.1 - - + -
87L ILE* 3.5 27.4 - - + +
90L ALA* 3.5 40.6 - - + +
91L GLN* 4.1 10.8 - - + +
92L PRO* 4.8 4.2 - - + +
177L PRO* 2.9 23.4 + - + +
178L ARG* 4.1 4.0 - - - +
180L VAL* 1.3 76.3 - - - +
182L TYR* 1.3 58.0 + - - +
184L ARG* 3.9 5.5 - - + +
185L SER* 2.9 32.0 + - - +
31M A 5.4 1.3 - - - -
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Residues in contact with TYR 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L LEU* 3.2 45.0 - - + +
160L ARG* 4.0 18.6 - - - -
178L ARG 3.0 20.6 + - - +
179L LEU* 3.5 9.9 - - + +
180L VAL 3.1 0.4 - - - -
181L LEU* 1.3 79.0 - - - +
183L LEU* 1.3 64.4 + - + +
185L SER* 3.5 7.8 + - - -
186L ASP* 3.5 32.9 + - - +
31M A 3.2 82.2 + + + +
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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
----------------------------------------------------------
139L LEU* 5.0 3.4 - - + -
142L SER* 4.6 7.9 - - - -
143L LEU* 3.6 34.1 - - + -
146L ALA* 3.6 31.6 - - + -
152L LEU* 4.4 12.8 - - + -
179L LEU* 2.9 24.0 + - + +
180L VAL* 2.8 9.6 + - - +
182L TYR* 1.3 76.8 - - + +
184L ARG* 1.3 66.1 + - - +
186L ASP* 2.9 14.3 + - - +
187L GLN 3.1 8.3 + - - -
188L VAL* 3.3 17.4 + - + +
190L ILE* 3.7 29.2 - - + -
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Residues in contact with ARG 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L GLN* 3.4 35.9 + - + +
92L PRO* 4.5 4.7 - - + -
95L ALA* 2.8 64.7 + - + +
98L GLN* 3.8 22.6 - - - +
180L VAL* 2.9 18.6 + - + +
181L LEU* 3.9 8.5 - - + +
183L LEU* 1.3 76.7 - - - +
185L SER* 1.3 57.3 + - - +
187L GLN* 2.8 18.7 + - - +
188L VAL 3.2 21.3 + - - +
189L HIS* 4.4 3.0 - - - +
190L ILE* 4.0 19.4 - - + +
192L TRP* 3.7 29.9 - - + +
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Residues in contact with SER 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L PRO* 3.6 24.3 - - - +
94L SER* 5.9 1.9 - - - -
181L LEU* 2.9 21.3 + - - +
182L TYR* 3.6 16.8 - - - -
183L LEU 3.2 0.4 - - - -
184L ARG* 1.3 76.0 - - - +
186L ASP* 1.3 62.9 + - - +
187L GLN* 3.7 5.5 + - - +
30M C 4.8 15.8 + - - -
31M A 4.9 3.8 + - - -
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Residues in contact with ASP 186 (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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150L LYS* 3.0 46.0 - - + +
152L LEU* 4.2 13.5 - - + +
182L TYR* 3.5 34.9 + - - +
183L LEU* 2.9 9.5 + - - +
185L SER* 1.3 80.0 - - - +
187L GLN* 1.3 69.6 + - - +
188L VAL* 3.1 7.9 + - + +
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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