Contacts of the helix formed by residues 175 - 193 (chain C) in PDB entry 4U1D
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 LEU 175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS* 4.4 8.7 - - - -
86C LEU* 3.5 32.5 - - + +
87C VAL* 5.6 0.2 - - - -
89C VAL* 4.0 17.7 - - + -
90C GLY* 3.8 21.5 - - - +
169C LEU* 4.1 27.4 - - + +
172C ASN* 2.9 40.1 + - + +
174C LEU* 1.3 84.7 - - + +
176C GLU* 1.3 64.4 + - - +
177C ILE 3.2 3.5 + - - -
178C THR* 3.3 8.9 + - - +
179C TYR* 2.9 25.0 + - - +
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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
----------------------------------------------------------
169C LEU 5.8 0.2 - - - -
172C ASN 3.0 18.5 + - - +
173C ALA* 3.4 24.5 - - - +
174C LEU 3.4 1.6 - - - -
175C LEU* 1.3 77.1 - - - +
177C ILE* 1.3 59.8 + - + +
179C TYR* 3.8 8.9 - - - +
180C SER* 2.9 31.0 + - - -
225C VAL* 3.3 33.5 - - + +
226C ASP 4.2 1.2 + - - -
232C THR* 2.8 35.9 + - - +
235C ARG* 3.0 26.7 + - - +
236C TYR* 5.0 8.2 - - + +
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA 5.3 0.2 + - - -
174C LEU 5.0 4.4 + - - +
175C LEU 3.2 0.6 - - - -
176C GLU* 1.3 79.1 - - + +
178C THR* 1.3 63.1 - - - +
180C SER* 3.4 2.6 + - - -
181C GLY* 3.0 19.4 + - - -
235C ARG* 3.9 31.6 - - - +
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Residues in contact with THR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLY* 3.8 18.9 - - - +
93C ALA* 4.5 2.5 - - + -
94C ARG* 3.6 47.0 + - + +
169C LEU* 3.6 21.1 - - + -
174C LEU 5.4 0.9 + - - -
175C LEU* 3.3 10.9 + - - +
177C ILE* 1.3 77.1 - - - +
179C TYR* 1.3 62.1 + - - +
181C GLY* 3.1 3.8 + - - -
182C VAL* 2.9 37.7 + - + +
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 3.6 39.6 - - + +
169C LEU* 3.6 29.9 - - + +
170C ARG* 4.1 7.4 - - - -
171C ASN 5.3 1.8 - - - -
175C LEU 2.9 18.6 + - - +
176C GLU* 3.8 7.0 - - - +
178C THR* 1.3 76.1 - - - +
180C SER* 1.3 58.9 + - - +
182C VAL* 3.1 4.0 + - - -
183C VAL* 2.9 49.1 + - + +
206C LEU* 3.8 16.5 + - + +
209C HIS* 2.8 36.3 + + + +
236C TYR* 4.0 21.2 - + - -
239C GLN* 3.8 19.0 + - - -
240C ARG* 5.1 2.3 + - - -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU 2.9 19.0 + - - -
177C ILE 3.8 3.4 - - - -
179C TYR* 1.3 77.3 - - - +
181C GLY* 1.3 61.3 + - - +
183C VAL* 3.8 2.3 - - - +
184C LYS* 3.3 20.8 + - - +
235C ARG* 3.5 31.5 + - - +
238C ASP* 5.9 0.5 - - - +
239C GLN* 3.1 32.9 + - - +
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Residues in contact with GLY 181 (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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177C ILE 3.0 14.1 + - - -
178C THR* 3.1 5.1 + - - -
180C SER* 1.3 78.1 - - - +
182C VAL* 1.3 56.1 + - - +
184C LYS* 3.2 22.3 + - - +
185C LYS* 3.0 29.5 + - - +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA* 5.9 0.9 - - + -
94C ARG* 6.0 2.5 - - + -
97C ILE* 4.3 13.5 - - + -
162C TYR* 3.9 18.6 - - + +
165C VAL* 3.8 28.9 - - + -
166C LEU* 3.6 25.1 - - + -
169C LEU* 4.4 3.1 - - + -
178C THR* 2.9 23.9 + - + +
179C TYR 3.7 1.1 - - - +
181C GLY* 1.3 73.6 - - - +
183C VAL* 1.3 61.3 + - - +
185C LYS* 3.3 8.1 + - + +
186C THR* 2.8 43.5 + - - +
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 3.5 26.9 - - + -
179C TYR* 2.9 46.1 + - + +
180C SER 3.8 5.2 - - - +
181C GLY 3.3 0.2 - - - -
182C VAL* 1.3 76.7 - - - +
184C LYS* 1.3 59.0 + - - +
186C THR* 3.2 2.6 + - - -
187C MET* 2.9 39.9 + - + +
202C LEU* 5.0 1.3 - - + +
206C LEU* 3.7 25.4 - - + -
239C GLN* 3.9 26.2 - - + +
242C GLN* 5.6 0.2 - - - +
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Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C SER 3.3 9.8 + - - +
181C GLY* 3.2 24.4 + - - +
183C VAL* 1.3 77.7 - - - +
185C LYS* 1.3 79.8 + - - +
187C MET 3.4 0.5 + - - -
188C HIS* 3.0 28.5 + - + +
239C GLN* 5.8 0.2 - - - +
242C GLN* 3.5 33.0 + - - +
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 4.1 13.7 - - + -
98C ASP* 4.7 7.4 - - - -
101C GLU* 3.1 35.3 - - - +
162C TYR* 3.9 16.8 + - + +
181C GLY 3.0 19.7 + - - +
182C VAL* 3.7 7.9 - - + +
183C VAL 3.3 0.2 - - - -
184C LYS* 1.3 94.6 - - - +
186C THR* 1.3 56.5 + - - +
188C HIS* 3.4 7.2 + - - +
189C PHE* 3.0 27.7 + - - +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TRP* 3.8 23.8 - - + -
162C TYR* 3.2 34.8 - - + +
163C ARG 5.5 0.2 - - - +
166C LEU* 4.0 6.8 - - + +
182C VAL* 2.8 31.2 + - - +
183C VAL* 3.2 6.5 + - - -
185C LYS* 1.3 74.9 - - - +
187C MET* 1.3 61.4 + - - +
189C PHE* 3.2 7.8 + - + +
190C CYS* 3.1 21.8 + - - -
202C LEU* 3.6 27.4 - - + -
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Residues in contact with MET 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 2.9 22.9 + - + +
186C THR* 1.3 74.3 - - - +
188C HIS* 1.3 65.2 + - - +
190C CYS* 3.4 5.6 + - - +
191C LEU* 3.2 22.3 + - - +
199C PHE* 4.5 9.6 - - + -
202C LEU* 3.7 20.2 - - + -
203C ALA* 5.8 0.4 - - - -
206C LEU* 3.7 30.1 - - + -
239C GLN 3.7 9.2 - - - +
242C GLN* 3.4 29.2 - - - +
243C GLN* 3.5 51.1 - - + +
246C VAL* 3.8 13.5 - - + +
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Residues in contact with HIS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LYS* 3.0 19.4 + - + +
185C LYS* 3.7 8.0 + - - +
187C MET* 1.3 76.0 - - - +
189C PHE* 1.3 59.1 + - - +
191C LEU* 3.6 8.3 + - + +
192C LYS* 3.0 56.5 + - + +
242C GLN* 4.2 5.1 - - - +
246C VAL* 5.7 0.7 - - - -
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Residues in contact with PHE 189 (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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104C ILE* 5.1 3.6 - - + -
155C LEU* 3.9 42.0 - - + -
158C THR* 3.8 17.0 - - + -
159C TRP* 4.3 15.0 - + + -
162C TYR* 3.7 27.4 - + + +
185C LYS 3.0 14.0 + - - +
186C THR 3.4 10.5 - - - +
187C MET 3.2 0.2 - - - -
188C HIS* 1.3 78.2 + - - +
190C CYS* 1.3 73.8 + - - +
192C LYS* 4.3 3.6 - - - -
193C TYR* 3.1 45.4 + + - +
195C ARG* 4.2 17.3 - - + -
198C GLU* 3.9 19.7 - - - -
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Residues in contact with CYS 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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159C TRP* 4.1 20.4 - - - -
186C THR 3.1 20.8 + - - +
187C MET 3.9 4.5 - - - +
188C HIS 3.4 0.2 - - - -
189C PHE* 1.3 86.1 - - - +
191C LEU* 1.3 57.5 + - - +
194C GLN* 2.9 24.4 + - - -
195C ARG* 3.0 22.9 + - - +
198C GLU 4.5 0.2 - - - -
199C PHE* 3.9 50.0 - - + -
202C LEU* 4.6 2.9 - - - -
246C VAL* 4.9 0.2 - - + -
250C LEU* 4.2 5.5 - - + +
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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
----------------------------------------------------------
187C MET 3.2 15.3 + - - +
188C HIS* 4.0 8.3 - - + +
190C CYS* 1.3 78.8 - - - +
192C LYS* 1.3 63.6 + - - +
193C TYR 3.4 0.7 + - - -
194C GLN* 3.5 16.3 + - - +
246C VAL* 4.1 19.2 - - + +
249C LYS* 3.6 53.6 - - + +
250C LEU* 3.7 24.7 - - + -
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 6.0 1.6 - - - +
188C HIS* 3.0 43.8 + - + +
189C PHE* 4.3 0.4 - - - -
191C LEU* 1.3 76.7 - - - +
193C TYR* 1.3 92.5 + - + +
194C GLN* 3.6 1.1 - - - +
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Residues in contact with TYR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 3.5 31.6 + - + +
155C LEU* 3.8 32.0 - - + +
189C PHE* 3.1 40.6 + + + +
190C CYS 3.7 0.2 - - - -
192C LYS* 1.3 107.9 + - + +
194C GLN* 1.3 71.1 + - - +
195C ARG* 2.9 27.4 + - + +
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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