Contacts of the helix formed by residues 172 - 190 (chain C) in PDB entry 1YI8
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 GLN 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C THR* 5.3 0.7 - - - -
167C PRO 5.3 0.4 - - - +
168C VAL* 3.1 22.5 - - + +
169C GLY* 2.6 33.2 + - - -
171C ASP* 1.3 113.9 + - - +
173C LEU* 1.3 59.9 + - - +
174C PRO* 3.2 3.4 - - - -
175C MET* 2.8 34.6 + - + +
176C LEU* 2.9 9.7 + - - +
3000C TRP 5.1 12.6 - - - +
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL* 3.5 26.0 - - + -
169C GLY 3.5 1.0 + - - -
170C ASP* 3.6 30.5 - - + +
172C GLN* 1.3 77.1 - - - +
174C PRO* 1.3 65.7 - - + +
176C LEU* 3.1 11.0 + - + +
177C GLU* 2.7 33.5 + - + +
199C ALA* 4.2 15.0 - - + -
201C LEU* 4.5 17.7 - - + -
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Residues in contact with PRO 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASN* 4.0 12.0 + - - +
128C PRO* 3.9 33.9 - - + -
129C THR* 3.5 27.4 - - + -
170C ASP 3.7 10.3 - - - +
171C ASP 3.9 2.7 - - - +
172C GLN 3.5 1.6 - - - -
173C LEU* 1.3 96.3 - - + +
175C MET* 1.3 59.3 + - - +
177C GLU* 4.4 5.8 - - + +
178C GLN* 3.2 23.9 + - - +
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Residues in contact with MET 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASN* 4.4 8.6 - - - +
129C THR* 4.8 5.1 - - + +
150C TYR* 5.3 2.2 - - + +
151C PRO* 4.6 15.5 - - + +
154C GLN* 3.3 54.1 - - + +
155C ALA 4.9 0.2 - - - -
158C ILE* 4.9 7.6 - - + -
166C VAL* 5.6 3.8 - - + -
168C VAL* 5.2 2.9 - - + -
172C GLN* 2.8 31.1 + - + +
174C PRO* 1.3 83.3 - - - +
176C LEU* 1.3 76.0 + - + +
178C GLN* 3.7 4.6 - - - +
179C THR* 3.0 31.5 + - - +
3000C TRP* 4.6 12.6 - - + -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ILE* 5.6 0.9 - - + -
166C VAL* 3.2 36.6 - - + -
168C VAL* 4.6 5.6 - - + -
172C GLN 2.9 9.6 + - - +
173C LEU* 3.1 16.6 + - + +
175C MET* 1.3 87.2 - - + +
177C GLU* 1.3 67.7 + - + +
179C THR* 3.0 11.4 + - + +
180C ARG* 3.0 46.0 + - + +
197C PRO* 4.1 24.2 - - + +
199C ALA* 4.1 25.8 - - + +
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Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 2.7 21.5 + - + +
174C PRO* 4.3 6.1 - - + +
176C LEU* 1.3 74.6 - - + +
178C GLN* 1.3 64.9 + - - +
180C ARG* 2.9 40.4 + - - +
181C GLU* 2.9 32.6 + - + +
184C ARG* 4.7 4.8 + - - -
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Residues in contact with GLN 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C VAL* 3.8 23.2 - - + +
123C HIS* 4.1 19.0 + - - +
124C LEU* 3.6 19.0 - - - +
127C ASN* 4.6 7.9 + - - +
151C PRO* 3.4 29.9 - - + +
152C VAL* 4.7 0.6 + - - -
174C PRO 3.2 19.4 + - - +
175C MET* 3.7 4.9 - - - +
176C LEU 3.2 0.2 - - - -
177C GLU* 1.3 77.3 - - - +
179C THR* 1.3 63.1 + - - +
181C GLU* 3.0 17.5 + - + +
182C ILE* 2.8 38.9 + - + +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ALA* 3.7 37.0 - - + +
158C ILE* 3.9 16.0 - - + +
175C MET* 3.0 29.2 + - - -
176C LEU* 3.0 11.9 + - - -
178C GLN* 1.3 77.7 - - - +
180C ARG* 1.3 57.2 + - - +
182C ILE* 3.1 3.5 + - - +
183C VAL* 2.9 35.3 + - + +
197C PRO* 3.6 26.0 - - + -
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Residues in contact with ARG 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.0 34.4 + - + +
177C GLU* 2.9 30.6 + - - +
179C THR* 1.3 76.7 - - - +
181C GLU* 1.3 61.4 + - - +
183C VAL* 4.0 4.4 - - - +
184C ARG* 3.1 44.4 + - - +
196C GLU* 2.9 44.5 + - - +
197C PRO* 2.6 33.8 + - - -
198C GLN* 5.7 2.2 - - - +
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C HIS* 5.2 12.0 + - - +
177C GLU* 2.9 26.4 + - + +
178C GLN* 3.0 18.6 + - + +
180C ARG* 1.3 76.0 - - - +
182C ILE* 1.3 59.4 + - + +
184C ARG* 3.5 20.0 - - - +
185C ARG* 2.9 29.3 + - - +
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PHE* 3.6 49.1 - - + +
118C LEU* 4.0 21.2 - - + +
119C VAL* 4.8 8.3 - - + -
152C VAL* 4.5 20.0 - - + -
155C ALA* 3.8 22.7 - - + -
178C GLN* 2.8 30.4 + - + +
179C THR* 3.5 7.2 - - - +
181C GLU* 1.3 75.8 - - + +
183C VAL* 1.3 55.1 + - + +
185C ARG* 3.0 8.0 + - - +
186C PHE* 2.7 33.3 + - - +
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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
----------------------------------------------------------
115C PHE* 5.2 2.9 - - + -
159C ALA* 4.3 16.8 - - + -
179C THR* 2.9 27.1 + - + +
180C ARG 4.0 3.6 - - - +
182C ILE* 1.3 73.6 - - + +
184C ARG* 1.3 58.6 + - - +
186C PHE* 3.2 7.2 + - - +
187C ASN* 2.8 49.0 + - - +
194C LEU* 3.5 20.4 - - + +
195C ALA 3.5 29.4 - - - +
196C GLU* 4.2 9.6 - - + -
197C PRO* 4.2 9.6 - - + -
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C GLU* 4.7 5.5 + - - -
180C ARG* 3.1 49.9 + - - +
181C GLU* 3.5 18.7 - - - +
183C VAL* 1.3 81.8 - - - +
185C ARG* 1.3 60.2 + - - +
187C ASN* 4.2 5.3 - - - +
188C ALA* 3.2 25.5 + - - +
196C GLU* 3.5 21.5 + - - +
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Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.6 27.5 - - - -
117C ASN 4.9 3.0 + - - -
118C LEU* 3.9 38.0 + - + +
181C GLU 2.9 18.8 + - - +
182C ILE* 3.3 8.1 - - - +
184C ARG* 1.3 75.7 - - - +
186C PHE* 1.3 57.7 + - - +
188C ALA* 4.0 4.0 - - - +
189C LEU* 3.0 69.3 + - - +
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Residues in contact with PHE 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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111C LEU* 5.2 0.7 - - + -
114C TYR* 5.5 1.3 - - + -
115C PHE* 4.0 19.5 - + + -
118C LEU* 3.7 14.1 - - + +
182C ILE 2.7 19.3 + - - +
183C VAL* 3.6 4.3 - - - +
185C ARG* 1.3 73.0 - - - +
187C ASN* 1.3 68.0 + - - +
189C LEU* 3.3 0.6 + - - -
190C TYR* 2.9 68.4 + + + +
191C ALA 4.0 13.0 - - - -
193C VAL* 4.8 2.7 - - + -
194C LEU* 3.5 29.2 - - + -
342C VAL* 3.8 38.8 - - + -
345C ALA* 4.4 6.3 - - + -
346C MET* 3.8 17.0 - - + -
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Residues in contact with ASN 187 (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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183C VAL* 2.8 29.6 + - - +
184C ARG* 4.2 5.4 - - - +
186C PHE* 1.3 75.9 - - - +
188C ALA* 1.3 61.8 + - - +
190C TYR 3.6 0.9 - - - +
191C ALA* 3.3 30.4 + - - +
192C PRO* 3.3 27.8 - - + +
193C VAL 2.9 18.8 + - - -
194C LEU* 2.9 36.4 + - - +
196C GLU* 6.1 0.4 - - - +
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Residues in contact with ALA 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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184C ARG 3.2 16.4 + - - +
185C ARG* 4.1 4.9 - - - +
187C ASN* 1.3 79.2 - - - +
189C LEU* 1.3 63.3 + - + +
190C TYR 4.6 1.9 - - - +
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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
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70B PHE* 3.7 33.2 - - + +
71B ASP* 4.4 18.0 - - + +
73B PRO* 5.3 5.4 - - - +
118C LEU* 3.7 15.7 - - + -
185C ARG* 3.0 51.3 + - - +
186C PHE 3.8 2.0 - - - +
188C ALA* 1.3 83.4 - - + +
190C TYR* 1.3 74.1 + - + +
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Residues in contact with TYR 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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66B LEU* 4.6 2.1 - - + +
70B PHE* 3.0 41.8 + - - +
73B PRO* 4.4 22.9 - - + -
114C TYR* 5.4 2.1 + - + -
117C ASN* 5.6 0.7 + - - +
118C LEU* 4.2 14.6 - - + +
186C PHE* 2.9 56.5 + + + +
187C ASN 3.6 3.4 - - - +
188C ALA 4.6 1.7 - - - +
189C LEU* 1.3 94.6 - - + +
191C ALA* 1.3 64.3 + - - +
345C ALA* 3.4 25.8 - - + +
346C MET* 3.7 35.8 - - + +
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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