Contacts of the helix formed by residues 193 - 210 (chain C) in PDB entry 3DBI
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 SER 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C ARG* 4.7 3.6 - - - +
190C SER* 3.1 18.3 + - - -
192C ASP* 1.3 79.1 + - - +
194C PRO* 1.3 61.8 - - - +
195C THR 3.4 1.0 + - - -
196C SER* 3.2 19.2 + - - -
197C ILE* 3.0 32.2 + - - +
224C TRP* 3.3 20.0 - - - -
339C PO4 2.6 26.1 + - - -
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Residues in contact with PRO 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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128C ARG* 4.4 5.6 - - - +
151C ARG* 3.7 34.5 - - - +
192C ASP 3.4 9.0 - - - +
193C SER* 1.3 82.9 - - - +
195C THR* 1.3 55.9 + - - +
197C ILE* 3.3 12.1 + - + +
198C GLU* 3.0 41.7 + - - +
339C PO4 3.4 17.3 - - - +
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 5.7 0.7 - - + +
150C ASN* 3.8 14.4 + - - +
151C ARG* 4.1 1.9 + - - -
165C HIS* 3.8 23.9 - - + +
193C SER* 4.0 0.7 - - - -
194C PRO* 1.3 77.0 - - - +
196C SER* 1.3 57.8 + - - +
198C GLU* 3.4 6.0 + - - +
199C ARG* 3.0 66.9 + - - +
224C TRP* 4.5 4.9 - - + -
339C PO4 2.7 35.7 + - - +
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C PHE* 5.1 1.7 - - - -
188C THR* 4.0 5.4 - - - -
189C GLY* 3.0 26.6 + - - +
190C SER 3.2 25.8 + - - -
191C MSE 5.1 0.7 - - - -
193C SER* 3.1 14.8 + - - -
195C THR* 1.3 74.5 - - - +
197C ILE* 1.3 65.2 + - - +
199C ARG* 3.4 5.5 + - - +
200C LEU* 3.2 24.8 + - - +
224C TRP* 3.7 17.4 - - - -
249C SER* 5.3 1.2 + - - -
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Residues in contact with ILE 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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191C MSE 3.6 22.0 - - - +
192C ASP* 4.4 5.8 - - - +
193C SER 3.0 23.4 + - - +
194C PRO* 3.3 11.9 + - + +
196C SER* 1.3 77.0 - - - +
198C GLU* 1.3 61.8 + - + +
200C LEU* 3.4 6.6 + - - +
201C ALA* 3.0 28.9 + - + +
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C CYS 4.2 4.2 - - - +
164C ASP* 4.5 3.6 - - - +
165C HIS* 3.6 32.8 + - + +
166C LYS* 3.3 33.0 + - + +
194C PRO* 3.0 29.1 + - - +
195C THR* 3.8 5.5 + - - +
197C ILE* 1.3 81.8 - - + +
199C ARG* 1.3 56.6 + - - +
201C ALA* 3.4 6.5 + - - +
202C GLY 3.0 22.2 + - - -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 4.9 2.0 + - - -
165C HIS* 3.4 46.3 + - + +
169C SER* 2.7 33.3 + - - +
186C PHE* 3.4 18.4 - - + -
195C THR* 3.0 34.4 + - - +
196C SER* 4.0 3.8 - - - +
197C ILE 3.3 0.2 - - - -
198C GLU* 1.3 74.1 - - - +
200C LEU* 1.3 63.7 + - - +
203C TYR 3.2 7.8 + - - -
224C TRP* 4.0 13.1 - - - -
249C SER* 2.7 40.3 + - - +
250C ASN* 4.9 0.6 - - - +
277C PHE* 3.4 36.3 - - + +
278C ASP* 4.7 8.3 + - - -
295C ILE* 4.0 18.2 - - - +
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Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C PHE* 3.6 31.8 - - + -
188C THR* 4.2 14.1 - - + -
196C SER 3.2 17.2 + - - +
197C ILE* 3.8 6.7 - - - +
198C GLU 3.4 0.2 - - - -
199C ARG* 1.3 73.9 - - - +
201C ALA* 1.3 66.4 + - - +
203C TYR* 3.2 10.7 + - + +
204C LYS* 3.1 37.1 + - + +
219C ILE* 3.9 33.2 - - + -
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Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LYS* 3.7 25.4 + - + +
197C ILE* 3.0 20.4 + - + +
198C GLU* 3.5 8.7 - - - +
199C ARG 3.3 0.2 - - - -
200C LEU* 1.3 77.1 - - - +
202C GLY* 1.3 55.9 + - - +
204C LYS* 3.3 15.8 + - - +
205C ASP* 2.9 31.2 + - - +
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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
----------------------------------------------------------
166C LYS* 3.4 31.8 - - - +
169C SER* 4.0 0.4 - - - -
170C PHE* 3.4 24.3 - - - +
198C GLU 3.0 12.3 + - - -
199C ARG 3.6 2.7 + - - -
200C LEU 3.3 0.2 - - - -
201C ALA* 1.3 76.0 - - - +
203C TYR* 1.3 59.1 + - - +
205C ASP* 3.8 3.7 - - - +
206C ALA* 3.1 17.7 + - - +
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Residues in contact with TYR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C SER* 3.8 0.4 + - - -
173C VAL* 4.0 26.2 - - + -
184C ILE* 2.4 45.8 + - + -
185C ALA* 4.4 0.2 - - - -
186C PHE* 3.6 46.8 - + + +
199C ARG 3.2 8.6 + - - +
200C LEU* 3.2 20.2 + - + +
202C GLY* 1.3 75.1 - - - +
204C LYS* 1.3 70.8 + - + +
206C ALA* 3.3 4.0 + - - +
207C LEU* 3.1 52.6 + - + +
214C LEU* 5.0 2.9 - - + +
215C ASN 4.9 2.1 + - - -
218C LEU* 4.1 13.2 - - - +
219C ILE* 3.9 18.3 - - + +
247C VAL* 5.1 0.4 - - + -
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 3.1 41.0 + - + +
201C ALA* 3.5 13.0 - - - +
203C TYR* 1.3 84.9 - - + +
205C ASP* 1.3 63.3 + - - +
207C LEU* 3.2 8.5 + - - +
208C ALA* 3.0 24.8 + - - +
214C LEU* 4.0 37.1 - - + +
219C ILE* 5.2 1.8 - - + -
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Residues in contact with ASP 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 4.9 2.4 - - - +
328B ILE* 5.8 1.4 - - - +
330B ARG* 4.2 16.3 + - - -
166C LYS* 3.8 22.4 + - + +
170C PHE* 3.7 11.7 - - + -
201C ALA 2.9 16.7 + - - +
202C GLY* 3.8 8.5 - - - +
204C LYS* 1.3 77.8 - - - +
206C ALA* 1.3 57.6 + - - +
208C ALA* 3.5 4.8 + - - +
209C GLN* 3.2 57.4 + - - +
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Residues in contact with ALA 206 (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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170C PHE* 3.6 30.5 - - + +
173C VAL* 3.7 21.3 - - + -
174C ALA* 4.3 5.6 - - - +
177C ILE* 3.6 4.9 - - + +
202C GLY 3.1 18.2 + - - +
203C TYR 3.7 4.5 - - - +
204C LYS 3.2 0.2 - - - -
205C ASP* 1.3 75.6 - - - +
207C LEU* 1.3 63.4 + - - +
209C GLN 3.6 0.2 + - - -
210C HIS* 2.9 32.5 + - - +
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Residues in contact with LEU 207 (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 VAL* 4.4 5.4 - - + -
177C ILE* 4.2 10.5 - - + -
182C GLN 5.2 1.1 - - - +
184C ILE* 4.6 11.4 - - + +
203C TYR* 3.1 57.8 + - + +
204C LYS* 3.2 7.6 + - - +
206C ALA* 1.3 77.4 - - - +
208C ALA* 1.3 57.3 + - - +
210C HIS 3.4 1.2 + - - -
211C GLY 3.4 4.0 + - - -
212C ILE* 2.8 66.4 + - + +
213C ALA 4.4 15.7 - - - +
214C LEU* 4.5 15.9 - - + +
215C ASN 5.1 2.2 - - - +
218C LEU* 6.0 2.2 - - + -
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Residues in contact with ALA 208 (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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294B LYS* 6.4 1.6 - - - -
204C LYS 3.0 16.6 + - - +
205C ASP* 3.9 7.4 - - - +
206C ALA 3.3 0.2 - - - -
207C LEU* 1.3 76.0 - - - +
209C GLN* 1.3 63.3 + - + +
211C GLY* 3.5 11.3 + - - -
212C ILE 4.2 5.6 - - - -
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Residues in contact with GLN 209 (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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281B ALA* 5.4 3.1 - - - +
284B PRO* 3.4 27.6 - - + +
285B TYR* 2.4 38.5 + - - -
330B ARG* 5.4 0.2 - - - +
170C PHE* 3.3 14.8 - - + -
205C ASP* 3.2 37.5 + - - +
207C LEU 3.3 0.2 - - - -
208C ALA* 1.3 79.0 - - + +
210C HIS* 1.3 71.1 + - + +
211C GLY 3.4 2.0 + - - -
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Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PHE* 4.5 16.8 - + - -
174C ALA* 4.1 27.4 - - + +
177C ILE* 3.7 37.5 - - + +
178C ASN* 3.9 19.0 + - - -
182C GLN* 5.4 2.1 + - - +
206C ALA 2.9 26.3 + - - +
207C LEU 3.4 1.5 + - - +
208C ALA 3.3 0.2 - - - -
209C GLN* 1.3 83.4 - - + +
211C GLY* 1.3 62.6 + - - +
212C ILE* 3.3 12.5 + - + +
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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
------------------------------------------------------------
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