Contacts of the helix formed by residues 163 - 179 (chain C) in PDB entry 3EBL
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 PRO 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ARG 4.3 0.2 - - - +
162C TYR* 1.3 117.6 - - + +
164C CYS* 1.3 70.7 + - - +
165C ALA 3.4 2.2 - - - -
166C TYR* 3.1 12.8 + - + +
167C ASP* 2.9 38.0 + - - +
258C TYR* 3.8 3.6 - - - +
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Residues in contact with CYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG* 3.6 35.2 - - + +
160C HIS* 4.0 27.8 - - + +
161C ARG 3.1 20.3 + - - +
163C PRO* 1.3 82.0 - - - +
165C ALA* 1.3 57.4 + - - +
167C ASP* 3.2 9.1 + - - +
168C ASP* 2.9 34.4 + - - +
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 4.6 1.6 - - + -
154C TYR* 3.7 16.5 - - + +
155C ARG 3.7 21.1 + - - +
160C HIS 5.6 0.2 + - - -
163C PRO 3.4 1.0 - - - -
164C CYS* 1.3 75.9 - - - +
166C TYR* 1.3 63.1 + - - +
168C ASP* 3.3 3.8 + - - +
169C GLY* 3.0 19.6 + - - -
203C ILE* 3.7 32.1 - - + +
258C TYR* 3.9 24.0 + - + +
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Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 4.3 0.8 - + - -
162C TYR* 3.6 31.2 - + - -
163C PRO* 3.1 11.5 + - + +
165C ALA* 1.3 74.7 - - - +
167C ASP* 1.3 65.8 + - - +
169C GLY* 3.1 2.3 + - - -
170C TRP* 3.0 23.6 + - - +
202C ASN* 2.5 29.7 + - - -
203C ILE* 3.8 33.4 - - + -
206C HIS* 3.2 37.4 - + + -
207C VAL* 4.0 6.8 - - + +
210C ARG* 5.8 0.7 - - - -
258C TYR* 3.3 27.7 - + - -
269C ALA* 3.2 22.1 + - + +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG* 4.1 11.6 + - - +
163C PRO* 2.9 40.5 + - - +
164C CYS* 3.2 12.3 + - - +
166C TYR* 1.3 72.0 - - - +
168C ASP* 1.3 59.0 + - - +
170C TRP* 3.4 8.7 + - - +
171C THR* 3.0 32.4 + - - +
210C ARG* 4.3 13.8 + - - +
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Residues in contact with ASP 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 4.2 4.5 - - - +
76C LEU* 3.5 39.7 - - + +
152C VAL* 4.2 2.4 - - + +
154C TYR* 3.7 9.9 - - + -
155C ARG* 2.6 67.9 + - - +
164C CYS 2.9 15.9 + - - +
165C ALA 3.6 4.9 - - - +
166C TYR 3.2 0.2 - - - -
167C ASP* 1.3 73.1 - - - +
169C GLY* 1.3 60.7 + - - +
171C THR* 3.5 1.8 + - - -
172C ALA* 3.0 27.4 + - - +
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Residues in contact with GLY 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.5 34.5 - - - -
165C ALA 3.0 12.5 + - - -
166C TYR 3.1 3.5 + - - -
168C ASP* 1.3 74.8 - - - +
170C TRP* 1.3 58.2 + - - +
172C ALA* 3.3 3.5 + - - +
173C LEU* 3.0 27.0 + - - +
207C VAL* 3.7 16.4 - - - +
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Residues in contact with TRP 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TYR 3.0 13.2 + - - +
167C ASP 3.6 8.1 - - - +
169C GLY* 1.3 73.2 - - - +
171C THR* 1.3 68.9 + - - +
173C LEU* 3.1 25.3 + - + +
174C LYS* 3.1 44.3 + - + +
207C VAL* 3.9 11.0 - - + +
210C ARG* 3.2 68.1 - - + +
211C ALA* 3.6 29.4 - - - -
214C GLU* 3.5 25.3 + - + -
216C VAL* 4.1 17.9 - - + -
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Residues in contact with THR 171 (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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70C ILE* 4.2 11.9 - - + +
71C ASP* 4.2 22.8 + - + +
76C LEU* 3.8 20.0 - - + +
167C ASP* 3.0 19.2 + - - +
168C ASP* 3.6 7.4 + - - -
170C TRP* 1.3 78.7 - - - +
172C ALA* 1.3 57.5 + - - +
174C LYS* 3.6 6.3 + - - +
175C TRP* 2.9 27.7 + - + +
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.6 20.4 - - + +
78C VAL* 4.7 2.2 - - + -
117C ILE* 4.4 7.2 - - + -
150C VAL* 5.5 2.2 - - + -
152C VAL* 3.5 33.7 - - + -
168C ASP 3.0 17.1 + - - +
169C GLY* 3.6 6.3 - - - +
170C TRP 3.1 0.2 - - - -
171C THR* 1.3 71.0 - - - +
173C LEU* 1.3 66.7 + - - +
175C TRP* 3.3 3.2 + - - +
176C VAL* 2.9 27.4 + - - +
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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
----------------------------------------------------------
117C ILE* 3.7 23.0 - - + +
169C GLY 3.0 13.3 + - - +
170C TRP* 3.1 23.3 + - + +
172C ALA* 1.3 75.8 - - - +
174C LYS* 1.3 60.6 + - + +
176C VAL* 2.9 21.7 + - + +
177C MET* 3.0 32.1 + - + +
192C VAL* 4.0 21.3 - - + -
194C LEU* 4.4 5.4 - - + -
207C VAL* 4.0 16.2 - - + -
211C ALA* 3.7 30.3 - - + -
216C VAL* 4.1 11.7 - - + -
218C VAL* 4.5 5.6 - - + -
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Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C TRP* 3.1 49.5 + - + +
171C THR* 3.8 6.3 - - - +
173C LEU* 1.3 78.8 - - + +
175C TRP* 1.3 63.4 + - - +
177C MET* 3.4 10.6 + - - +
178C SER* 3.0 27.7 + - - +
216C VAL* 6.0 2.7 - - + -
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Residues in contact with TRP 175 (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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68C HIS* 3.6 28.3 + + - -
70C ILE* 3.6 43.2 - - + +
78C VAL* 4.6 1.6 - - + -
80C ILE* 3.8 22.9 - - + -
150C VAL* 4.4 14.6 - - + -
171C THR* 2.9 19.3 + - + +
172C ALA* 3.6 4.3 - - - +
174C LYS* 1.3 75.8 - - - +
176C VAL* 1.3 94.7 + - + +
178C SER* 3.2 11.6 + - - -
179C GLN* 3.1 61.0 + - + +
182C MET* 4.1 18.6 - - + -
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C VAL* 3.7 26.2 - - + -
117C ILE* 3.6 28.0 - - + -
150C VAL* 4.0 17.0 - - + -
172C ALA 2.9 15.8 + - - +
173C LEU 2.9 9.4 + - - +
175C TRP* 1.3 97.6 - - + +
177C MET* 1.3 67.4 + - - +
179C GLN* 3.1 9.7 + - - -
182C MET* 3.6 24.6 - - + +
190C ALA* 4.5 8.2 - - + +
192C VAL* 5.0 6.1 - - + -
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Residues in contact with MET 177 (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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173C LEU* 3.0 24.0 + - + +
174C LYS* 3.5 10.8 - - - +
176C VAL* 1.3 78.7 - - - +
178C SER* 1.3 58.6 + - - +
179C GLN 2.9 12.1 + - - +
183C ARG* 4.5 10.4 - - - +
190C ALA* 4.8 18.5 + - - +
192C VAL* 4.1 19.7 - - + -
216C VAL* 3.0 39.7 - - + -
217C LYS* 3.8 19.1 - - + +
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Residues in contact with SER 178 (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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174C LYS 3.0 12.8 + - - -
175C TRP* 3.4 12.6 - - - -
177C MET* 1.3 76.5 - - - +
179C GLN* 1.3 69.7 + - - +
180C PRO* 3.3 12.5 - - - +
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Residues in contact with GLN 179 (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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175C TRP* 3.1 71.3 + - + +
176C VAL 3.7 6.1 - - - +
177C MET 2.9 5.9 + - - +
178C SER* 1.3 92.3 + - - +
180C PRO* 1.4 71.8 - - + +
181C PHE* 4.4 6.7 - - + +
182C MET* 3.2 27.9 + - + +
183C ARG* 3.6 12.2 + - - +
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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
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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