Contacts of the helix formed by residues 179 - 197 (chain C) in PDB entry 4G1U
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 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ALA 3.4 11.8 + - - +
178C LEU* 1.3 81.0 - - - +
180C LEU* 1.3 66.3 + - - +
181C TYR* 3.3 10.9 - - + +
182C HIS* 3.7 25.8 + - + +
183C GLN* 3.6 18.7 + - - +
46D ASN* 4.8 17.7 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP* 1.3 73.1 - - - +
181C TYR* 1.3 68.0 + - - +
183C GLN* 3.4 5.1 + - + +
184C GLN* 2.9 27.1 + - - +
207C ASP* 4.7 9.2 - - - +
210C LEU* 3.8 29.8 - - + -
247D ALA* 4.4 12.3 - - + -
249D LEU* 4.7 9.9 - - + -
264D LEU* 3.5 39.3 - - + -
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ARG* 6.3 0.2 - - - -
179C ASP* 3.3 8.8 - - + +
180C LEU* 1.3 79.6 - - - +
182C HIS* 1.3 83.9 + + + +
184C GLN* 3.6 11.0 - - - +
185C HIS* 2.9 50.9 + + + +
188C ARG* 5.8 5.8 - - - -
246D GLN* 4.1 41.5 - - + -
247D ALA* 4.4 17.7 - - + +
248D ASP 5.5 0.2 - - - -
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Residues in contact with HIS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLY* 3.6 35.3 - - - -
148C GLN* 4.4 8.2 - - + +
149C ARG* 4.6 14.6 + - + -
178C LEU* 4.0 27.1 - - + +
179C ASP* 3.7 29.2 + - + +
180C LEU 3.2 0.6 - - - -
181C TYR* 1.3 102.0 - + - +
183C GLN* 1.3 65.8 + - - +
185C HIS* 3.7 8.1 - - + +
186C THR* 2.9 29.5 + - - -
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLN* 5.6 1.9 - - - +
148C GLN* 5.0 1.3 - - - +
174C PRO* 3.4 36.2 - - + +
178C LEU* 4.1 23.2 - - + +
179C ASP 3.6 14.0 + - - +
180C LEU* 3.4 10.2 + - - +
182C HIS* 1.3 77.2 - - - +
184C GLN* 1.3 64.3 + - - +
186C THR* 3.8 4.3 - - - -
187C LEU* 2.9 41.6 + - - +
205C LEU* 4.3 11.1 - - - +
207C ASP* 5.3 3.9 - - - +
210C LEU* 3.7 28.0 - - + +
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Residues in contact with GLN 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU 2.9 17.3 + - - +
181C TYR* 3.6 9.2 - - - +
183C GLN* 1.3 77.9 - - - +
185C HIS* 1.3 57.0 + - - +
187C LEU* 3.3 2.3 + - - +
188C ARG* 2.9 49.6 + - - +
210C LEU* 4.6 9.1 - - + +
214C TYR* 3.2 28.9 + - + +
247D ALA* 4.3 7.3 - - - +
248D ASP* 3.6 28.8 + - - +
264D LEU* 3.6 25.9 - - + +
265D ARG 3.1 26.9 + - - -
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Residues in contact with HIS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN 6.1 0.4 - - - -
129C THR 5.6 1.6 - - - -
130C ASP* 5.5 7.4 - - + -
149C ARG* 4.8 21.7 - - - +
181C TYR* 2.9 43.0 + + + +
182C HIS* 3.7 11.0 - - - +
183C GLN 3.3 0.2 - - - -
184C GLN* 1.3 76.7 - - - +
186C THR* 1.3 64.0 + - - +
188C ARG* 3.2 18.3 + - + +
189C LEU* 3.0 38.1 + - + +
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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
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90C MET* 5.2 0.2 - - + -
148C GLN* 2.7 40.4 + - - +
152C LEU* 4.0 26.5 - - + +
171C LEU* 4.5 13.2 - - + -
182C HIS 2.9 14.3 + - - -
183C GLN* 3.8 3.4 - - - -
185C HIS* 1.3 76.2 + - - +
187C LEU* 1.3 60.0 + - + +
189C LEU* 3.2 7.4 + - - +
190C LEU* 2.9 48.5 + - + +
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Residues in contact with LEU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 3.5 30.2 - - + +
171C LEU* 4.3 17.0 - - + -
183C GLN* 2.9 34.7 + - - +
184C GLN 3.8 3.1 - - - +
186C THR* 1.3 78.2 - - - +
188C ARG* 1.3 57.1 + - - +
190C LEU* 4.7 0.9 - - + -
191C ARG* 2.9 29.9 + - - +
203C CYS* 4.1 9.9 - - - -
205C LEU* 3.5 33.7 - - + -
210C LEU* 4.0 17.7 - - + +
214C TYR* 3.9 24.3 - - + +
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Residues in contact with ARG 188 (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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181C TYR* 5.8 5.3 - - - -
184C GLN* 2.9 33.5 + - - +
185C HIS* 3.5 18.8 - - + +
186C THR 3.2 0.2 - - - -
187C LEU* 1.3 74.5 - - - +
189C LEU* 1.3 66.0 + - - +
191C ARG* 3.1 9.4 + - - +
192C GLN* 3.0 29.4 + - - +
214C TYR* 3.4 30.6 + - + -
248D ASP* 3.4 26.3 + - - +
265D ARG 3.9 4.9 + - - -
266D GLN 3.0 30.2 + - - -
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN* 3.6 34.3 - - + +
129C THR* 4.4 7.4 - - + -
152C LEU* 3.8 24.2 - - + -
156C LEU* 4.4 8.3 - - + -
185C HIS* 3.0 30.2 + - + +
186C THR* 3.5 9.4 - - - +
188C ARG* 1.3 76.9 - - - +
190C LEU* 1.3 64.7 + - + +
192C GLN* 3.2 15.8 - - + +
193C LEU* 3.0 48.5 + - + +
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 4.1 6.7 - - + -
152C LEU* 4.1 16.6 - - + -
156C LEU* 4.8 0.2 - - + -
169C LEU* 3.5 37.5 - - + -
171C LEU* 4.0 20.4 - - + -
186C THR* 2.9 39.9 + - + +
187C LEU* 4.1 4.7 - - - +
189C LEU* 1.3 76.4 - - + +
191C ARG* 1.3 63.6 + - - +
193C LEU* 3.2 18.8 + - + +
194C THR* 2.9 28.0 + - - -
199C LEU* 4.9 0.7 - - + -
201C VAL* 3.8 26.9 - - + +
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Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 3.8 12.6 - - - +
187C LEU 2.9 21.4 + - - +
188C ARG* 3.1 10.5 - - - +
190C LEU* 1.3 76.0 - - - +
192C GLN* 1.3 61.0 + - + +
194C THR* 3.1 22.5 - - - -
195C ARG* 3.1 38.9 + - + +
213C LEU 4.3 8.3 + - - -
214C TYR* 3.5 42.3 + - + +
215C ALA 3.6 8.9 + - - +
216C ASP* 3.0 23.2 + - - -
259C LEU* 6.2 0.2 - - - +
266D GLN* 4.4 16.3 - - - +
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Residues in contact with GLN 192 (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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188C ARG* 3.0 18.2 + - - +
189C LEU* 3.2 22.6 - - + +
191C ARG* 1.3 73.6 - - + +
193C LEU* 1.3 68.5 + - + +
194C THR 3.1 1.3 - - - -
195C ARG* 2.9 22.8 + - + +
196C GLN* 3.0 41.4 + - + +
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Residues in contact with LEU 193 (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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128C GLN* 3.8 15.0 - - - +
156C LEU* 3.9 29.6 - - + -
189C LEU* 3.0 39.1 + - + +
190C LEU* 3.5 15.7 - - + +
192C GLN* 1.3 77.9 - - + +
194C THR* 1.3 61.6 + - - +
195C ARG 3.2 0.2 + - - -
196C GLN* 4.1 18.4 - - - +
197C GLU* 3.2 54.0 + - - +
199C LEU* 3.9 18.7 - - + +
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Residues in contact with THR 194 (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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37C GLY* 3.3 42.1 - - - +
38C GLU* 3.3 12.7 + - - +
39C MET* 4.1 10.7 - - + +
190C LEU 2.9 16.2 + - - -
191C ARG* 3.1 14.6 - - - -
192C GLN 3.1 0.2 - - - -
193C LEU* 1.3 77.4 - - - +
195C ARG* 1.3 70.1 + - - +
197C GLU 3.5 9.4 - - - +
199C LEU* 3.9 14.7 + - - +
201C VAL* 4.1 13.7 - - - +
216C ASP* 4.5 2.9 - - - +
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Residues in contact with ARG 195 (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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37C GLY 5.7 1.1 - - - -
39C MET* 5.2 0.2 - - - +
191C ARG* 3.1 49.3 + - + +
192C GLN* 2.9 12.7 + - + +
194C THR* 1.3 88.4 - - - +
196C GLN* 1.3 69.4 + - + +
216C ASP* 2.8 41.5 + - - -
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLN* 3.0 43.4 + - - +
193C LEU* 4.0 18.1 - - - +
195C ARG* 1.3 81.8 - - + +
197C GLU* 1.3 65.4 + - + +
198C PRO* 4.6 1.4 - - - +
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Residues in contact with GLU 197 (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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37C GLY* 5.0 0.2 - - - -
124C GLN* 6.0 0.2 + - - -
128C GLN* 5.2 1.2 + - - +
156C LEU* 5.8 1.9 - - - +
167C ARG* 2.1 40.7 + - - +
193C LEU* 3.2 50.7 + - + +
194C THR 3.5 9.7 - - - +
196C GLN* 1.3 82.3 - - + +
198C PRO* 1.3 69.8 - - + +
199C LEU* 3.0 17.5 + - + -
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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
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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