Contacts of the helix formed by residues 199 - 215 (chain C) in PDB entry 3E3M
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 199 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C TYR* 4.7 5.6 - - + -
132C TYR* 5.8 1.6 - - - -
133C ASP* 3.5 29.8 - - + +
155C GLU* 5.3 0.4 - - - +
193C GLU* 4.4 0.5 + - - -
195C ASP 5.5 0.2 - - - +
196C ASP* 2.6 35.9 + - - +
197C ASP 3.5 9.2 - - - +
198C TRP* 1.3 81.3 - - - +
200C ARG* 1.3 65.6 + - - +
201C GLY* 3.6 4.2 + - - -
202C ALA* 3.2 17.0 + - - +
203C ALA* 3.3 10.4 + - - +
228C PRO* 4.3 21.8 - - + +
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Residues in contact with ARG 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 5.2 4.4 - - - +
82C HIS* 5.5 5.3 + - - -
83C PHE* 3.5 30.2 - - - -
108C TYR* 3.3 19.0 + - - -
131C SER* 5.8 0.4 - - - -
132C TYR* 3.3 19.3 + - + +
133C ASP* 3.0 36.6 + - - +
154C TRP* 3.5 38.0 + - - +
155C GLU* 3.8 19.7 - - + -
169C ASN* 3.9 15.3 - - - +
199C THR* 1.3 72.5 - - - +
201C GLY* 1.3 62.4 + - - +
203C ALA* 3.1 10.6 + - - +
204C ARG* 3.0 48.1 + - - +
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Residues in contact with GLY 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PHE* 4.9 1.2 - - - -
193C GLU* 3.7 14.1 + - - -
196C ASP* 3.8 6.0 - - - +
199C THR* 3.2 4.6 + - - -
200C ARG* 1.3 78.2 - - - +
202C ALA* 1.3 60.9 + - - +
204C ARG* 3.2 6.4 + - - +
205C ARG* 3.0 23.8 + - - +
255C VAL* 3.7 28.0 - - - +
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ASP* 3.3 42.3 + - - +
197C ASP* 4.7 1.6 - - - -
198C TRP* 4.3 6.1 - - - +
199C THR* 3.2 13.2 + - - +
201C GLY* 1.3 74.0 - - - +
203C ALA* 1.3 57.8 + - - +
205C ARG* 3.4 9.6 + - - +
206C ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU* 3.5 24.9 - - - +
169C ASN* 3.8 9.0 - - + -
170C GLU* 3.2 22.1 - - + +
199C THR 3.3 6.5 + - - +
200C ARG 3.1 10.8 + - - +
202C ALA* 1.3 77.3 - - - +
204C ARG* 1.3 64.5 + - - +
206C ALA* 3.2 8.0 + - - +
207C GLY 3.0 17.7 + - - -
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Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C HIS* 6.0 3.8 + - - -
154C TRP* 5.6 0.8 + - - -
167C PHE* 5.1 3.6 - - - -
169C ASN* 2.8 38.4 + - + +
173C ALA* 3.1 23.4 - - + +
190C PHE* 4.0 15.4 - - + -
200C ARG* 3.0 40.7 + - - +
201C GLY* 3.2 6.5 + - - +
203C ALA* 1.3 73.1 - - - +
205C ARG* 1.3 66.2 + - - +
207C GLY 3.1 0.5 + - - -
208C PHE* 3.0 21.1 + - - +
253C PHE* 6.0 0.2 - - + -
255C VAL* 2.8 45.2 + - - +
256C SER* 4.4 7.1 - - - -
283C PHE* 3.5 40.7 + - + +
286C PHE* 6.0 1.4 - - - -
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Residues in contact with ARG 205 (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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190C PHE* 4.0 20.4 - - + -
192C GLY* 3.6 4.4 - - - -
193C GLU 2.6 43.6 + - - +
196C ASP* 2.4 32.1 + - - -
201C GLY 3.0 10.1 + - - +
202C ALA* 3.5 15.3 + - - +
204C ARG* 1.3 76.3 - - - +
206C ALA* 1.3 58.3 + - - +
208C PHE* 3.3 4.8 + - + +
209C LYS* 2.9 49.7 + - + +
222C GLU* 2.8 31.5 + - - +
224C ARG* 3.1 22.9 - - - +
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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
----------------------------------------------------------
170C GLU* 3.8 12.8 - - + +
202C ALA 3.0 13.7 + - - +
203C ALA* 3.5 10.8 - - - +
204C ARG 3.2 0.2 - - - -
205C ARG* 1.3 77.4 - - - +
207C GLY* 1.3 57.1 + - - +
209C LYS* 3.3 11.1 + - - +
210C ARG* 2.9 30.0 + - - +
213C ARG* 5.0 1.4 + - - -
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Residues in contact with GLY 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 3.3 37.2 - - - +
174C TYR* 3.3 20.7 - - - +
203C ALA 3.0 10.9 + - - -
204C ARG 3.1 3.3 + - - -
206C ALA* 1.3 74.7 - - - +
208C PHE* 1.3 64.8 + - - +
210C ARG 3.4 0.3 + - - -
211C ALA* 3.1 18.2 + - - +
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Residues in contact with PHE 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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173C ALA* 4.1 2.6 - - + +
177C THR* 3.6 26.9 - - + +
188C ILE* 3.8 33.0 - - + -
190C PHE* 3.5 46.9 - + + -
204C ARG 3.0 8.1 + - - +
205C ARG* 3.5 7.9 - - + +
207C GLY* 1.3 75.7 - - - +
209C LYS* 1.3 68.3 + - + +
211C ALA* 3.2 4.2 + - - +
212C MET* 2.9 59.5 + - + +
219C PRO 4.0 14.8 - - - -
221C GLN* 3.4 28.7 - - + -
222C GLU* 4.7 2.2 - - + -
253C PHE* 4.5 3.8 - + + -
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Residues in contact with LYS 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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205C ARG* 2.9 42.4 + - + +
206C ALA* 3.6 8.1 - - - +
207C GLY 3.2 0.2 - - - -
208C PHE* 1.3 81.8 - - + +
210C ARG* 1.3 57.8 + - - +
212C MET* 3.2 1.9 + - - +
213C ARG* 2.9 44.0 + - - +
219C PRO* 3.0 49.8 + - + +
220C ASP* 4.5 7.3 + - - +
222C GLU* 2.9 30.7 + - - +
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Residues in contact with ARG 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 2.7 40.8 + - - +
171C ARG* 4.6 6.7 - - - +
174C TYR* 3.2 48.2 + - + +
206C ALA 2.9 17.9 + - - +
207C GLY 3.9 2.7 - - - +
209C LYS* 1.3 77.8 - - - +
211C ALA* 1.3 62.7 + - - +
213C ARG* 3.7 25.4 - - - +
214C GLU* 3.0 52.4 + - + +
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C TYR* 3.6 19.1 - - + +
177C THR* 3.5 27.8 - - + -
178C ASN* 3.5 21.6 - - - +
181C LEU* 4.1 4.3 - - + +
207C GLY 3.1 12.0 + - - +
208C PHE 3.5 7.6 - - - +
210C ARG* 1.3 75.3 - - - +
212C MET* 1.3 62.8 + - - +
214C GLU* 3.4 3.4 + - - +
215C ALA* 3.1 22.5 + - - +
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Residues in contact with MET 212 (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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177C THR* 4.2 11.4 - - + -
181C LEU* 4.5 9.0 - - - -
188C ILE* 3.8 17.3 - - + +
208C PHE* 2.9 46.2 + - + +
209C LYS 3.2 3.8 + - - +
211C ALA* 1.3 73.1 - - - +
213C ARG* 1.3 66.0 + - - +
215C ALA* 3.1 9.8 + - - +
217C LEU* 2.9 54.7 + - + +
218C ASN 3.8 22.9 - - - +
219C PRO* 4.1 6.5 - - + -
221C GLN* 3.5 28.5 - - - +
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Residues in contact with ARG 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA 5.0 1.2 + - - -
209C LYS* 2.9 37.0 + - - +
210C ARG* 3.7 32.3 - - - +
212C MET* 1.3 77.1 - - - +
214C GLU* 1.3 65.0 + - + +
216C GLY* 3.0 14.7 + - - -
217C LEU 4.1 8.0 + - - -
219C PRO* 4.8 15.3 - - + +
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Residues in contact with GLU 214 (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 TYR* 2.5 34.3 + - - -
178C ASN* 5.1 1.5 + - - +
210C ARG* 3.0 46.8 + - + +
211C ALA* 3.9 4.9 - - - +
213C ARG* 1.3 80.6 - - + +
215C ALA* 1.3 58.4 + - - +
216C GLY 3.3 1.4 + - - -
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Residues in contact with ALA 215 (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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181C LEU* 3.9 21.5 - - + -
211C ALA 3.1 15.6 + - - +
212C MET 3.1 7.2 + - - +
214C GLU* 1.3 75.2 - - - +
216C GLY* 1.3 61.9 + - - +
217C LEU* 3.6 18.8 + - + +
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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
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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