Contacts of the helix formed by residues 198 - 214 (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 SER 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLY* 3.6 12.8 - - - -
123C SER* 3.4 10.2 + - - -
197C ASP* 1.3 73.3 - - - +
199C SER* 1.3 71.0 + - - -
201C GLY* 2.9 11.8 + - - -
202C ASN 3.3 0.9 + - - -
224C LEU 3.0 12.3 + - - -
225C ASN* 3.1 16.1 + - - +
227C MET* 3.0 27.9 + - - +
251C ARG* 4.9 0.2 + - - -
329C TYR* 4.7 0.4 + - - -
401C GA4 2.9 42.9 + - - -
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Residues in contact with SER 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C HIS 3.8 2.1 + - - -
121C GLY 3.9 1.4 - - - -
123C SER* 3.4 10.7 + - - -
124C PHE* 3.0 52.4 + - - -
154C TYR* 2.8 25.1 + - - -
198C SER* 1.3 80.5 + - - +
200C GLY* 1.3 55.4 + - - +
202C ASN* 3.1 5.0 + - - +
203C ILE* 2.9 32.0 + - - +
227C MET* 3.6 11.5 - - - +
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Residues in contact with GLY 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.2 38.6 - - - +
120C HIS 3.5 5.6 + - - -
196C GLY* 3.4 7.6 - - - -
197C ASP 2.8 12.7 + - - -
199C SER* 1.3 76.5 + - - +
201C GLY* 1.3 50.5 + - - -
203C ILE* 3.4 4.6 + - - -
204C ALA* 2.8 34.0 + - - +
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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
----------------------------------------------------------
196C GLY* 3.3 26.2 - - - -
198C SER 2.9 9.8 + - - -
200C GLY* 1.3 72.8 - - - +
202C ASN* 1.3 64.1 + - - +
204C ALA* 3.4 2.3 + - - +
205C HIS* 3.1 23.0 + - - +
223C LEU* 3.7 14.1 - - - +
226C ALA* 3.8 18.2 - - - -
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 3.5 13.6 - - + -
166C TYR* 2.5 31.6 + - - -
198C SER 3.3 4.4 + - - +
199C SER* 3.1 10.7 + - - +
201C GLY* 1.3 73.8 - - - +
203C ILE* 1.3 65.6 + - - +
205C HIS* 3.2 4.2 + - - +
206C HIS* 3.1 25.2 + - - -
226C ALA* 4.1 1.6 - - - +
227C MET 2.9 30.8 + - - +
228C PHE* 3.5 21.4 - - - -
255C TRP* 3.8 7.5 - - - -
269C ALA 2.8 23.2 + - - -
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Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.6 29.4 - - + -
124C PHE* 3.9 8.7 - - + -
154C TYR* 3.5 46.0 - - + -
165C ALA* 3.7 24.9 - - + +
166C TYR* 3.8 25.8 - - + -
199C SER 2.9 18.0 + - - +
200C GLY* 3.6 7.6 - - - +
202C ASN* 1.3 74.8 + - - +
204C ALA* 1.3 63.0 + - - +
206C HIS* 3.1 3.6 + - - +
207C VAL* 2.9 32.5 + - + +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 4.2 11.9 - - + -
194C LEU* 3.6 12.7 - - + +
195C SER 4.0 26.9 - - - +
200C GLY 2.8 20.7 + - - +
201C GLY 3.6 6.1 - - - +
202C ASN 3.3 0.2 - - - -
203C ILE* 1.3 72.5 - - - +
205C HIS* 1.3 56.5 + - - +
207C VAL* 3.5 0.8 + - - -
208C ALA* 2.9 31.9 + - - +
221C ASN* 5.0 2.2 - - - -
223C LEU* 3.9 16.6 - - + -
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Residues in contact with HIS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLY 3.1 12.3 + - - +
202C ASN 3.4 8.5 - - - +
204C ALA* 1.3 77.2 - - - +
206C HIS* 1.3 84.7 + + - +
208C ALA* 3.3 6.4 + - - +
209C VAL* 3.0 52.5 + - + +
221C ASN* 4.6 3.8 - - - +
223C LEU* 4.6 2.6 - - + +
228C PHE* 4.3 10.5 - + + -
272C PRO* 3.9 18.9 - - + +
273C PHE* 4.6 3.6 - + - -
280C LEU* 3.9 16.9 - - + +
285C PHE* 3.9 7.8 - + - -
305C TYR* 2.8 44.0 + + + +
309C LEU* 5.1 0.2 - - + -
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Residues in contact with HIS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TYR* 3.2 46.1 + + + -
202C ASN* 3.1 24.6 + - - -
203C ILE 3.1 6.6 + - - +
205C HIS* 1.3 102.3 + + - +
207C VAL* 1.3 61.4 + - - +
209C VAL* 3.5 8.2 + - - +
210C ARG* 3.1 23.4 + - - +
268C PRO* 3.5 21.7 + - + -
269C ALA* 3.1 26.1 + - - -
272C PRO* 4.4 4.1 - - + +
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 4.4 3.8 - - + -
166C TYR* 4.0 10.3 - - + +
169C GLY* 3.7 42.0 - - - +
170C TRP* 3.9 10.1 - - + +
173C LEU* 4.0 16.8 - - + -
194C LEU* 3.7 21.1 - - + -
203C ILE* 2.9 28.9 + - + +
204C ALA* 3.8 4.7 - - - +
206C HIS* 1.3 74.6 - - - +
208C ALA* 1.3 59.3 + - - +
210C ARG* 3.4 7.0 + - - +
211C ALA* 2.9 27.0 + - - +
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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
----------------------------------------------------------
194C LEU* 3.5 9.3 - - + +
204C ALA 2.9 15.6 + - - +
205C HIS 3.4 4.7 - - - +
207C VAL* 1.3 76.7 - - - +
209C VAL* 1.3 55.2 + - - +
211C ALA* 3.3 6.6 + - - +
212C ALA* 3.0 27.4 + - - +
218C VAL* 4.8 3.5 - - + +
221C ASN* 3.2 38.8 - - - +
285C PHE* 3.5 11.8 - - + -
286C ALA* 5.0 5.3 + - + -
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C HIS* 3.0 44.6 + - + +
206C HIS* 3.6 12.1 - - - +
208C ALA* 1.3 73.0 - - - +
210C ARG* 1.3 61.2 + - - +
212C ALA* 3.2 5.1 + - - +
213C ASP* 2.9 29.6 + - - +
278C ARG* 3.9 25.6 - - - +
280C LEU* 3.8 17.5 - - + -
283C LEU* 4.2 7.1 - - + +
285C PHE* 3.7 15.2 - - + -
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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
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166C TYR 5.4 0.6 + - - -
167C ASP* 4.3 17.6 + - - +
170C TRP* 3.2 59.1 - - + +
206C HIS 3.1 15.0 + - - +
207C VAL* 3.8 5.4 - - - +
209C VAL* 1.3 82.0 - - - +
211C ALA* 1.3 61.9 + - - +
213C ASP* 3.5 7.8 + - + +
214C GLU* 3.2 48.4 + - + +
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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
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170C TRP* 3.6 10.9 - - - -
173C LEU* 3.7 23.8 - - + -
207C VAL 2.9 17.4 + - - +
208C ALA 3.6 4.9 - - - +
209C VAL 3.2 0.4 - - - -
210C ARG* 1.3 74.8 - - - +
212C ALA* 1.3 58.0 + - - +
214C GLU 3.6 0.3 + - - -
215C GLY 3.1 6.6 + - - -
216C VAL* 2.7 46.6 + - + +
218C VAL* 3.8 13.9 - - + -
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Residues in contact with ALA 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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208C ALA 3.0 13.6 + - - +
209C VAL* 3.2 9.8 + - - +
211C ALA* 1.3 75.4 - - - +
213C ASP* 1.3 65.0 + - - +
214C GLU 3.1 1.3 + - - -
215C GLY* 3.2 9.2 + - - -
216C VAL 4.1 1.8 + - - -
283C LEU* 3.7 28.4 - - + +
284C PRO* 3.5 43.9 - - - +
285C PHE* 4.1 6.7 - - + +
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Residues in contact with ASP 213 (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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209C VAL* 2.9 18.3 + - - +
210C ARG* 3.7 10.1 - - + +
212C ALA* 1.3 74.8 - - - +
214C GLU* 1.3 63.2 - - + +
215C GLY 3.5 0.4 + - - -
278C ARG* 2.8 42.3 + - - -
283C LEU* 3.2 15.4 - - - +
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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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170C TRP* 3.5 29.7 + - + -
210C ARG* 3.2 44.9 + - + +
211C ALA 4.4 0.4 - - - +
212C ALA 3.1 0.8 - - - -
213C ASP* 1.3 83.9 - - + +
215C GLY* 1.3 62.4 + - - +
216C VAL* 3.4 6.6 + - + +
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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