Contacts of the helix formed by residues 183 - 200 (chain C) in PDB entry 4YC6
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 THR 183 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C HIS* 3.2 53.0 - - + +
125C LEU* 3.6 23.2 - - + +
182C SER* 1.3 85.6 + - - +
184C PRO* 1.3 71.6 - - - +
185C VAL 3.0 1.7 + - - -
186C ASP 3.0 12.0 + - - +
187C ILE* 3.5 7.7 + - - +
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Residues in contact with PRO 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLU* 4.3 1.8 - - - +
182C SER* 2.8 17.0 - - - +
183C THR* 1.3 97.6 - - - +
185C VAL* 1.3 60.3 + - - +
187C ILE* 3.2 11.6 + - + +
188C TRP 3.0 13.2 + - - -
272C PRO* 3.4 41.5 - - + +
275C ARG* 2.7 35.8 + - + +
276C ILE 5.6 1.6 - - - +
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Residues in contact with VAL 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 5.0 2.0 - - + -
127C ARG* 4.2 20.2 - - + +
171C SER* 3.6 20.1 + - - +
173C GLU* 3.2 21.3 - - - +
174C VAL* 4.0 7.4 - - + -
181C TYR* 3.8 30.5 - - + -
182C SER 3.0 17.4 + - - +
183C THR 3.0 0.4 + - - -
184C PRO* 1.3 76.6 - - - +
186C ASP* 1.3 81.1 + - - +
188C TRP* 3.3 4.0 + - - +
189C SER* 3.1 26.2 + - - +
275C ARG* 4.2 2.2 - - - +
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Residues in contact with ASP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 3.5 14.4 - - + +
120C HIS* 3.1 32.5 + - + +
125C LEU* 3.6 4.7 - - - +
126C HIS* 2.7 32.4 + - - +
127C ARG* 2.7 30.9 + - - -
129C LEU* 4.0 5.1 - - + +
183C THR 3.0 2.9 + - - +
185C VAL* 1.3 85.8 - - - +
187C ILE* 1.3 58.2 + - - +
189C SER* 3.5 6.9 + - - -
190C ILE* 3.0 33.0 + - - +
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Residues in contact with ILE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 4.8 3.6 - - + -
116C ILE* 4.4 11.7 - - + -
120C HIS* 4.2 16.4 - - + -
183C THR* 3.7 12.3 - - - +
184C PRO* 3.2 9.3 + - + +
186C ASP* 1.3 76.9 - - - +
188C TRP* 1.3 65.1 + - - +
190C ILE* 3.2 8.8 + - + +
191C GLY* 2.9 19.9 + - - -
267C MET* 3.7 19.8 - - + +
275C ARG* 4.3 5.2 - - - -
276C ILE* 3.5 45.8 - - + +
277C SER* 4.5 1.6 - - - -
278C GLY* 3.7 28.9 - - - +
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Residues in contact with TRP 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TRP 5.3 0.2 + - - -
169C TYR 3.9 4.7 - - - -
170C ARG 3.4 15.0 + - - +
171C SER* 3.6 22.2 - - - -
172C PRO* 3.6 31.2 - - + -
184C PRO 3.0 5.3 + - - -
185C VAL 3.4 9.0 - - - +
187C ILE* 1.3 73.8 - - - +
189C SER* 1.3 69.3 + - - +
191C GLY* 2.9 11.6 + - - -
192C THR* 3.1 23.8 + - + +
204C PHE* 4.2 10.5 - + - -
216C ILE* 4.1 21.4 - - + +
220C LEU* 3.9 22.0 - - + -
267C MET 3.7 8.9 + - - -
268C LEU* 3.5 42.9 - - + +
269C ILE 3.8 6.3 - - - -
270C TYR* 4.7 2.2 - + - -
275C ARG* 3.6 34.3 - - - +
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ARG 4.6 7.6 + - - -
129C LEU* 3.8 34.1 + - - +
169C TYR* 2.6 24.2 + - - -
170C ARG* 4.9 0.2 - - - -
171C SER 5.2 0.3 + - - -
185C VAL* 3.1 13.6 + - - +
186C ASP* 3.7 8.6 + - - -
188C TRP* 1.3 76.9 - - - +
190C ILE* 1.3 61.4 + - - +
192C THR* 2.5 24.3 + - - -
193C ILE* 2.9 15.9 + - - +
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.6 25.4 - - + -
112C ILE* 4.0 22.4 - - + -
113C LEU* 4.3 9.4 - - + -
116C ILE* 3.7 35.9 - - + -
129C LEU* 3.6 18.8 - - + -
186C ASP 3.0 26.5 + - - +
187C ILE* 3.7 9.2 - - + +
188C TRP 3.1 0.2 - - - -
189C SER* 1.3 76.9 - - - +
191C GLY* 1.3 58.3 + - - +
193C ILE* 3.4 9.8 + - + +
194C PHE* 2.9 26.2 + - - +
267C MET* 3.7 13.0 - - + -
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Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE 2.9 10.5 + - - -
188C TRP 2.9 7.9 + - - -
190C ILE* 1.3 76.9 - - - +
192C THR* 1.3 63.0 + - - +
194C PHE* 3.1 2.4 + - - +
195C ALA* 3.1 18.7 + - - +
264C LEU* 3.1 21.0 - - - +
267C MET* 3.8 26.9 - - - -
268C LEU* 4.3 4.9 - - - -
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TRP 4.0 10.5 - - - +
169C TYR* 3.5 23.2 - - - -
188C TRP* 3.1 30.5 + - - +
189C SER* 2.5 29.1 + - - -
191C GLY* 1.3 74.5 - - - +
193C ILE* 1.3 61.6 + - - +
195C ALA* 3.3 6.1 + - - +
196C GLU* 3.3 21.5 + - - +
203C LEU* 4.3 15.6 + - + +
204C PHE* 3.7 30.3 - - + -
268C LEU* 4.2 3.8 - - + -
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.3 14.8 - - + -
91C LEU* 6.4 0.2 - - + -
112C ILE* 5.1 3.1 - - + -
129C LEU* 4.1 18.2 - - + +
130C LYS* 4.0 24.0 - - - -
131C PRO* 4.2 10.5 - - + -
134C LEU* 4.0 25.1 - - + -
169C TYR* 3.9 19.3 - - + -
189C SER 2.9 27.8 + - - +
190C ILE* 3.7 9.6 - - + +
192C THR* 1.3 75.2 - - - +
194C PHE* 1.3 65.9 + - - +
196C GLU* 3.2 8.2 + - + +
197C LEU* 3.0 28.5 + - + +
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Residues in contact with PHE 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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105C VAL* 3.7 17.0 - - + -
109C LEU* 3.6 37.5 - - + -
190C ILE 2.9 14.6 + - - +
191C GLY* 3.2 9.9 - - - +
193C ILE* 1.3 75.5 - - - +
195C ALA* 1.3 63.9 + - - +
197C LEU* 3.1 19.9 + - + +
198C ALA* 3.3 9.9 + - - +
256C LEU* 3.7 21.1 - - + -
260C GLY* 3.5 23.1 - - - -
263C LEU* 4.4 4.9 - - + -
264C LEU* 4.0 26.5 - - + -
267C MET* 4.4 6.3 - - - -
286C TYR* 3.5 38.6 - + - -
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLY 3.1 8.6 + - - +
192C THR 3.6 9.2 - - - +
193C ILE 3.2 0.4 - - - -
194C PHE* 1.3 78.1 - - - +
196C GLU* 1.3 57.9 + - - +
198C ALA* 3.3 6.6 + - - +
199C THR* 3.0 35.3 + - + +
201C LYS 4.5 0.9 - - - -
203C LEU* 3.8 37.0 - - + -
253C VAL* 4.8 9.6 - - + -
256C LEU* 5.5 0.9 - - - -
264C LEU* 4.3 15.5 - - + +
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Residues in contact with GLU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.8 20.5 - - + +
131C PRO* 4.1 9.3 - - + +
168C TRP* 5.6 0.2 - - - -
169C TYR* 2.8 40.8 + - - -
192C THR 3.3 7.8 + - - +
193C ILE* 3.2 11.0 + - + +
194C PHE 3.1 0.2 - - - -
195C ALA* 1.3 74.6 - - - +
197C LEU* 1.3 61.3 + - - +
198C ALA 3.1 1.6 - - - -
200C LYS* 2.7 41.4 + - - +
201C LYS 3.4 22.9 + - - +
202C PRO* 3.4 28.6 - - + +
203C LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 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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87C LEU* 3.7 32.5 - - + -
91C LEU* 4.3 8.7 - - + +
100C MET* 3.5 54.3 - - + +
105C VAL* 3.8 30.2 - - + +
108C TYR* 4.2 13.5 - - + -
109C LEU* 4.7 4.9 - - + +
112C ILE* 4.6 14.6 - - + -
193C ILE* 3.0 21.9 + - + +
194C PHE* 3.1 17.2 + - + +
196C GLU* 1.3 78.5 - - - +
198C ALA* 1.3 61.7 + - - +
200C LYS* 4.4 1.6 + - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 3.4 25.5 - - - +
100C MET 4.8 1.8 + - - +
105C VAL* 4.5 9.8 - - + +
194C PHE 3.3 7.4 + - - +
195C ALA 3.3 9.3 + - - +
196C GLU 3.1 0.6 - - - -
197C LEU* 1.3 82.9 - - - +
199C THR* 1.3 60.8 + - + +
200C LYS* 3.7 0.9 + - - +
253C VAL* 4.4 3.1 - - + -
254C LYS 3.6 19.5 - - - +
255C ASN* 3.6 20.8 - - - +
256C LEU* 4.2 17.0 - - + -
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 3.7 17.0 - - - -
195C ALA* 3.0 19.2 + - + +
198C ALA* 1.3 75.1 - - - +
200C LYS* 1.3 69.8 + - - +
201C LYS* 3.0 51.8 + - - +
203C LEU* 6.5 0.2 - - + -
252C HIS 4.6 3.8 - - - +
253C VAL* 3.7 30.1 - - + -
254C LYS* 3.9 15.9 - - + +
255C ASN* 4.9 0.2 - - - -
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Residues in contact with LYS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.1 26.8 - - + +
94C ILE* 3.6 30.0 + - + +
95C PRO 3.3 16.8 + - - -
96C PRO* 3.7 5.5 - - - +
97C GLY 3.6 13.9 - - - +
98C GLN 2.8 28.3 + - - +
99C TYR* 4.1 23.2 - - + -
100C MET 5.2 1.1 - - - +
196C GLU* 2.7 31.0 + - - +
197C LEU 5.3 1.1 - - - +
198C ALA 3.5 2.8 - - - +
199C THR* 1.3 72.7 - - - +
201C LYS* 1.3 58.9 + - + -
202C PRO* 4.1 3.8 - - - +
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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