Contacts of the helix formed by residues 175 - 191 (chain P) in PDB entry 6CNB
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 ILE 175 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527O LEU* 3.5 36.3 - - + -
169P GLU* 4.7 25.1 - - + -
170P LEU 4.6 1.8 - - - +
171P ASP 5.0 2.5 - - - +
172P ILE 3.0 29.6 - - - +
173P GLU* 3.5 18.6 + - - +
174P PHE* 1.3 77.7 - - - +
176P ASN* 1.3 61.3 + - - +
177P SER 3.0 0.9 - - - -
178P LEU* 2.7 43.8 + - + +
179P LEU* 2.9 27.3 + - + +
243P LEU* 4.9 6.7 - - + -
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Residues in contact with ASN 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P GLU* 4.5 11.4 + - - +
174P PHE* 4.3 7.4 + - - -
175P ILE* 1.3 82.7 + - - +
177P SER* 1.3 76.5 + - - +
179P LEU* 3.2 22.9 - - + +
180P THR* 2.9 25.8 + - - +
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Residues in contact with SER 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P PHE* 3.7 28.0 + - - +
175P ILE 3.5 4.1 + - - -
176P ASN* 1.3 84.3 + - - +
178P LEU* 1.3 69.3 + - - +
180P THR* 3.0 28.8 - - - +
181P ILE* 3.3 8.5 - - - +
230P VAL* 6.0 2.3 - - - +
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Residues in contact with LEU 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P GLU* 6.2 3.4 - - + -
174P PHE 4.9 4.5 - - - +
175P ILE* 2.7 28.6 + - + +
177P SER* 1.3 80.6 + - - +
179P LEU* 1.3 69.5 + - + +
181P ILE* 3.0 15.4 + - + +
182P VAL* 2.9 23.9 + - + +
225P ILE* 6.3 4.0 - - + -
230P VAL* 6.2 4.5 - - + -
232P ASN* 5.0 14.4 - - - +
235P LEU* 5.7 8.1 - - + -
243P LEU* 3.4 32.3 - - + -
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Residues in contact with LEU 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506O ARG* 5.3 5.8 - - - +
527O LEU* 5.3 5.8 - - + -
175P ILE* 2.9 40.7 + - + +
176P ASN* 3.1 23.5 + - + +
178P LEU* 1.3 83.5 - - + +
180P THR* 1.3 64.9 + - - +
181P ILE 2.9 0.5 + - - -
182P VAL* 2.9 12.8 + - + +
183P TRP* 2.9 23.3 + - - +
243P LEU* 4.1 14.1 - - + -
246P VAL* 5.0 11.0 - - + -
247P LEU* 3.7 32.7 - - + +
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Residues in contact with THR 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176P ASN 2.9 15.7 + - - +
177P SER* 3.0 24.7 - - - +
179P LEU* 1.3 71.5 - - - +
181P ILE* 1.3 64.5 + - + +
183P TRP* 3.7 13.8 - - - +
184P ARG* 2.9 48.4 + - + +
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Residues in contact with ILE 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P SER 3.3 17.7 - - - +
178P LEU* 3.1 17.0 - - + +
179P LEU 3.0 1.0 - - - -
180P THR* 1.3 81.3 - - + +
182P VAL* 1.3 66.0 + - - +
184P ARG* 3.0 23.4 + - + +
185P PHE* 3.1 12.1 + - - +
224P PHE* 4.0 23.7 - - + -
225P ILE* 6.3 2.2 - - + -
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Residues in contact with VAL 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P LEU* 2.9 16.9 + - + +
179P LEU* 2.9 28.7 + - + +
181P ILE* 1.3 77.4 - - - +
183P TRP* 1.3 57.3 + - - +
185P PHE* 3.2 6.0 + - - +
186P ILE* 2.9 50.9 + - + +
221P ILE* 3.7 30.1 - - + -
224P PHE* 4.9 1.8 - - - -
225P ILE* 5.6 5.4 - - + -
240P ILE* 6.4 1.3 - - + -
243P LEU* 5.6 7.9 - - + -
244P CYS* 6.5 1.1 - - + -
247P LEU* 4.6 11.9 - - + -
253P LEU* 5.9 0.4 - - + -
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Residues in contact with TRP 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P LEU 2.9 15.3 + - - +
180P THR* 3.7 13.9 - - - +
182P VAL* 1.3 77.4 - - - +
184P ARG* 1.3 79.5 + - - +
186P ILE* 4.7 3.8 - - - +
187P SER* 2.8 42.8 + - - -
247P LEU* 4.0 15.0 - - + -
252P LYS* 2.7 61.4 + - + +
253P LEU* 4.8 5.6 - - + -
263P VAL* 4.1 12.1 - - + +
266P GLU* 4.4 4.0 - - + -
267P SER* 3.9 34.8 - - - -
269P LEU* 6.3 0.9 - - + -
270P GLN* 3.1 34.8 - - + -
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Residues in contact with ARG 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P THR* 2.9 39.9 + - + +
181P ILE* 3.0 16.9 + - + +
183P TRP* 1.3 90.5 - - - +
185P PHE* 1.3 61.8 + - - +
187P SER* 2.2 27.5 + - - -
188P GLU* 2.9 10.0 + - - +
224P PHE* 6.1 1.1 - - + -
270P GLN* 4.5 17.4 - - - +
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Residues in contact with PHE 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P ILE 3.1 3.4 + - - -
182P VAL* 3.2 7.4 + - - +
184P ARG* 1.3 78.9 - - - +
186P ILE* 1.3 61.8 + - + +
188P GLU* 2.9 38.1 + - + +
189P ASN* 2.9 22.3 + - + -
216P SER 5.7 0.4 - - - -
217P THR* 3.3 21.5 - - + -
220P GLU* 3.1 41.1 - - - -
221P ILE* 4.3 5.4 - - + -
224P PHE* 3.5 54.2 - + + -
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Residues in contact with ILE 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P VAL* 2.9 39.2 + - + +
183P TRP* 4.6 2.7 - - + +
185P PHE* 1.3 72.6 - - + +
187P SER* 1.3 58.9 + - - +
189P ASN* 2.9 31.6 + - + +
190P THR* 3.5 5.5 - - + +
215P TYR* 5.9 0.7 - - + -
216P SER* 5.6 1.6 - - - +
217P THR* 3.7 33.4 - - + +
244P CYS* 4.9 9.6 - - - -
253P LEU* 4.3 20.6 - - + -
261P TYR* 5.0 15.3 - - + +
262P ARG* 4.2 12.3 - - - +
263P VAL* 3.4 22.9 - - + +
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Residues in contact with SER 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P TRP* 2.8 39.1 + - - -
184P ARG* 2.2 33.6 + - - -
186P ILE* 1.3 77.4 - - - +
188P GLU* 1.3 55.5 + - - +
190P THR* 3.0 23.6 + - - -
191P PHE* 4.5 6.6 - - - +
192P PRO 4.9 1.4 - - - +
193P ASN* 5.8 0.2 - - - -
263P VAL* 3.7 17.3 - - - +
267P SER* 5.9 3.4 - - - -
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Residues in contact with GLU 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ARG 3.7 6.5 - - - +
185P PHE* 2.9 27.9 + - + +
187P SER* 1.3 81.9 + - - +
189P ASN* 1.3 68.3 + - - +
190P THR 3.0 0.7 - - - -
191P PHE 2.6 27.1 - - - +
192P PRO* 5.0 5.1 - - - +
193P ASN* 5.0 21.3 - - + +
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Residues in contact with ASN 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P PHE* 2.9 22.7 + - + +
186P ILE* 2.9 22.8 + - + +
188P GLU* 1.3 86.2 + - - +
190P THR* 1.3 63.0 + - - +
191P PHE 4.3 0.2 - - - -
215P TYR* 3.1 30.1 - - + +
216P SER* 3.1 43.0 + - - +
217P THR* 5.2 0.8 - - - +
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Residues in contact with THR 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P ILE* 3.5 15.5 - - + +
187P SER 3.0 13.0 + - - -
188P GLU 3.0 1.6 + - - -
189P ASN* 1.3 81.8 - - - +
191P PHE* 1.3 84.5 + - - -
206P VAL* 4.7 10.9 - - - +
213P LYS* 5.6 1.2 - - - +
215P TYR* 3.2 44.2 - - + +
262P ARG* 4.6 0.9 - - - -
263P VAL* 3.6 32.9 - - + +
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Residues in contact with PHE 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187P SER 4.8 4.3 - - - -
188P GLU* 2.6 24.6 - - - +
190P THR* 1.3 107.1 + - - +
192P PRO* 1.3 100.2 - - + +
193P ASN 3.4 12.8 - - - -
194P GLY* 3.5 12.6 - - - -
196P LYS* 3.1 26.5 - - - -
201P GLY 4.6 2.0 - - - -
202P PRO* 4.1 12.3 - - + -
203P LYS* 3.5 39.5 - - + -
206P VAL* 5.2 6.3 - - + -
265P LEU* 5.9 7.9 - - + -
267P SER* 5.4 4.0 - - - -
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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
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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