Contacts of the helix formed by residues 186 - 202 (chain C) in PDB entry 4BL5
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 HIS 186 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 6.0 1.8 - - + +
73C VAL* 3.9 26.6 - - + +
74C GLY* 3.2 21.1 + - - -
75C GLY* 3.4 17.7 - - - -
76C LEU 4.9 0.9 - - - -
172C ASN* 5.2 13.7 - - + +
173C VAL 4.9 13.7 + - - +
178C ASP* 4.8 9.1 + - - -
179C ASN 4.5 0.4 + - - -
182C ILE 5.4 0.3 - - - +
185C GLY* 1.3 76.8 - - - -
187C VAL* 1.3 65.2 + - + +
188C LEU 3.5 0.7 - - - +
189C PRO* 3.7 18.7 - - + +
190C GLY* 2.9 26.0 + - - -
217C PHE* 6.5 0.2 - - + -
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Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN* 5.3 5.8 - - - +
186C HIS* 1.3 73.3 - - + +
188C LEU* 1.3 61.8 + - + +
190C GLY* 2.8 6.1 + - - -
191C LEU* 2.5 61.4 + - + +
207C VAL* 5.7 0.4 - - + -
215C ARG* 5.8 1.1 - - + -
217C PHE* 3.8 31.4 - - + -
252C ILE* 4.1 31.4 - - + -
255C ALA* 5.5 1.3 - - + -
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 3.4 47.1 - - + -
187C VAL* 1.3 81.7 - - + +
189C PRO* 1.3 65.7 - - + +
191C LEU* 3.7 5.9 - - + +
192C ILE* 2.7 41.7 + - + +
217C PHE* 3.8 28.9 - - + -
255C ALA* 3.8 27.8 - - + +
259C VAL* 3.9 22.9 - - + -
301C PHE* 4.2 13.0 - - + -
305C VAL* 4.8 4.3 - - + -
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Residues in contact with PRO 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 5.0 2.9 - - + -
178C ASP* 3.4 32.3 - - - +
179C ASN 3.7 17.0 - - - +
180C PHE* 3.2 45.7 - - + +
186C HIS* 3.5 24.2 - - + +
188C LEU* 1.3 94.6 - - + +
190C GLY* 1.3 61.4 + - - +
192C ILE* 4.0 1.3 - - + -
193C HIS* 3.2 21.1 + - - +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE 5.2 0.2 - - - -
181C ASN 5.0 2.2 + - - -
182C ILE* 3.8 28.0 - - - +
186C HIS 2.9 13.8 + - - -
187C VAL* 2.8 8.1 + - - -
189C PRO* 1.3 75.9 - - - +
191C LEU* 1.3 58.8 + - - +
193C HIS 3.5 0.7 + - - -
194C LYS* 3.0 37.3 + - - +
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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 VAL* 2.5 41.4 + - + +
188C LEU* 3.7 6.5 - - + +
190C GLY* 1.3 69.1 - - - +
192C ILE* 1.3 67.8 + - - +
194C LYS* 3.1 19.7 + - + +
195C VAL* 2.9 27.6 + - + +
205C LEU* 4.4 7.0 - - + -
207C VAL* 3.9 36.6 - - + -
208C TRP 5.4 0.2 - - - +
252C ILE 4.9 1.6 - - - +
255C ALA* 4.3 7.4 - - + +
256C ALA* 3.6 37.2 - - + +
259C VAL* 4.3 14.1 - - + -
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 5.9 1.1 - - + -
180C PHE* 4.0 9.2 - - + -
188C LEU* 2.7 40.4 + - + +
189C PRO* 3.9 4.0 - - + +
191C LEU* 1.3 73.1 - - - +
193C HIS* 1.3 61.6 + - - +
195C VAL 3.4 0.5 + - - -
196C HIS* 3.1 21.5 + - - +
259C VAL* 3.9 17.7 - - + -
263C MET* 3.8 14.3 - - - +
305C VAL* 5.7 1.8 - - + -
308C THR* 3.6 32.3 - - + -
309C CYS* 3.9 22.7 - - - -
312C PHE* 3.4 37.0 - - + -
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Residues in contact with HIS 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B SER 5.2 1.0 + - - -
202B GLY* 6.0 0.4 - - - -
180C PHE* 2.9 24.2 + - + +
182C ILE* 3.9 14.4 - - + +
189C PRO 3.2 16.3 + - - +
190C GLY 3.9 3.8 - - - +
192C ILE* 1.3 78.9 - - - +
194C LYS* 1.3 56.4 + - - +
196C HIS* 3.2 1.6 + - - +
197C LEU* 2.9 48.9 + - + +
312C PHE* 3.9 21.8 - + + -
316C TYR* 3.2 25.5 + + - -
321C LYS* 3.3 37.0 - - + +
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 3.6 37.0 - - + +
190C GLY* 3.0 19.2 + - - +
191C LEU* 3.4 17.0 - - + +
193C HIS* 1.3 78.1 - - - +
195C VAL* 1.3 57.9 + - - +
197C LEU* 3.3 4.3 + - - +
198C ALA* 2.8 31.2 + - - +
205C LEU* 3.5 16.7 - - + +
206C THR* 2.8 30.9 + - - +
207C VAL* 4.3 1.2 - - - +
208C TRP* 3.2 45.0 - - - +
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LEU* 2.9 19.0 + - + +
192C ILE 3.8 3.8 - - - +
194C LYS* 1.3 74.8 - - - +
196C HIS* 1.3 58.4 + - - +
198C ALA* 3.5 5.8 - - - +
199C LYS* 3.0 31.6 + - + +
205C LEU* 3.4 32.3 - - + -
259C VAL* 3.7 18.4 - - + +
260C VAL* 5.0 3.1 - - - +
263C MET* 3.9 26.0 - - + -
265C PHE* 3.5 33.2 - - + -
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Residues in contact with HIS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER 5.6 2.9 - - - -
192C ILE 3.1 13.9 + - - +
193C HIS 3.2 7.6 + - - +
195C VAL* 1.3 77.6 - - - +
197C LEU* 1.3 65.4 + - + +
199C LYS* 3.8 9.2 + - + +
200C SER* 3.6 19.3 + - - -
263C MET* 3.8 13.2 - - + +
312C PHE* 3.9 14.1 - + + -
313C THR* 4.3 23.0 + - + +
316C TYR* 3.2 58.1 + + - +
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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
----------------------------------------------------------
200B SER 6.0 0.4 - - - +
201B SER* 4.3 13.9 - - - +
182C ILE* 3.8 21.5 - - + -
193C HIS* 2.9 37.4 + - + +
194C LYS* 3.9 4.0 - - - +
196C HIS* 1.3 77.1 - - + +
198C ALA* 1.3 54.0 + - - +
200C SER* 3.1 9.0 + - - -
201C SER* 2.7 40.3 + - - -
316C TYR* 3.6 21.1 - - - +
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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
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194C LYS 2.8 18.6 + - - +
195C VAL* 3.5 7.4 - - - +
197C LEU* 1.3 71.7 - - - +
199C LYS* 1.3 68.7 + - - +
201C SER 2.8 1.3 + - - +
202C GLY* 2.6 27.0 + - - -
203C SER* 3.6 30.7 - - - +
204C ALA 4.0 12.8 - - - +
205C LEU* 4.6 2.2 - - - +
265C PHE* 3.8 15.5 - - + -
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Residues in contact with LYS 199 (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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195C VAL* 3.0 27.2 + - + +
196C HIS* 3.9 11.2 - - + +
197C LEU 3.4 0.2 - - - -
198C ALA* 1.3 74.4 - - - +
200C SER* 1.3 62.1 + - - +
202C GLY* 3.4 7.8 + - - -
263C MET* 3.9 26.2 - - + +
264C ASP 4.6 6.3 - - - +
265C PHE* 3.7 27.5 - - + -
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Residues in contact with SER 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER 5.3 8.7 - - - -
196C HIS* 3.6 12.8 + - - -
197C LEU* 3.1 12.3 + - - -
199C LYS* 1.3 79.2 - - - +
201C SER* 1.3 58.8 + - - +
202C GLY 3.5 0.6 + - - -
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Residues in contact with SER 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 2.7 24.9 + - - -
198C ALA 2.8 3.2 + - - -
200C SER* 1.3 71.7 - - - +
202C GLY* 1.3 57.0 + - - +
203C SER* 2.8 22.6 + - - -
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Residues in contact with GLY 202 (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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198C ALA 2.6 12.0 + - - -
199C LYS* 3.4 8.2 + - - -
200C SER 3.5 1.0 + - - -
201C SER* 1.3 70.7 - - - +
203C SER* 1.3 65.4 + - - +
265C PHE* 6.0 0.4 - - - -
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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