Contacts of the helix formed by residues 196 - 213 (chain C) in PDB entry 3EGC
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 LEU 196 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 4.0 6.3 - - - +
133C GLU* 3.8 24.2 - - + +
154C ARG* 3.4 50.5 - - + +
192C GLY* 5.2 1.3 - - - -
193C SER* 3.3 31.1 + - - +
194C ALA 3.4 0.4 - - - -
195C GLY* 1.3 77.2 - - - +
197C MET* 1.3 59.3 + - - +
198C THR* 3.3 18.8 - - - +
199C SER* 3.8 10.3 - - - +
200C ARG* 2.9 32.1 + - - +
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Residues in contact with MET 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 4.4 6.8 + - - +
153C ASN 3.5 23.6 - - - +
154C ARG* 4.5 14.2 - - + +
155C GLU* 3.5 52.0 - - + +
165C LEU* 3.9 12.6 - - + -
168C ASN* 3.8 10.5 - - - +
196C LEU* 1.3 72.8 - - - +
198C THR* 1.3 56.5 + - - +
200C ARG* 3.6 20.6 - - - +
201C GLU* 2.9 70.4 + - + +
325C ARG* 4.1 6.5 - - - +
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Residues in contact with THR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN* 3.4 46.4 - - - +
154C ARG* 4.1 8.1 + - + +
168C ASN* 4.3 13.7 - - - +
196C LEU* 3.7 18.9 - - - +
197C MET* 1.3 73.1 - - + +
199C SER* 1.3 65.3 + - - -
201C GLU* 3.5 0.3 + - - +
202C ARG* 2.9 65.5 + - - +
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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
----------------------------------------------------------
191C VAL* 4.1 21.3 - - - +
192C GLY* 3.4 19.9 + - - -
193C SER 2.6 29.2 + - - -
194C ALA* 4.3 6.3 - - - -
196C LEU* 3.5 13.6 + - - +
197C MET 3.5 0.2 - - - -
198C THR* 1.3 79.6 + - - +
200C ARG* 1.3 64.1 + - - +
202C ARG* 3.9 2.3 - - - +
203C LEU* 3.0 26.6 + - - +
252C SER* 5.3 3.1 + - - -
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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
----------------------------------------------------------
135B GLU* 3.7 4.8 + - - -
137B ASP* 3.5 26.7 + - - +
138B TYR* 4.0 7.9 - - - +
141B THR* 2.9 35.4 + - - +
142B GLU* 3.1 36.1 - - - +
155C GLU* 5.7 1.6 + - - -
157C ARG* 4.7 0.4 - - - +
194C ALA 3.9 12.1 - - - +
195C GLY 2.9 26.8 + - - -
196C LEU 2.9 9.4 + - - +
197C MET* 3.6 26.6 - - - +
199C SER* 1.3 79.2 - - - +
201C GLU* 1.3 59.7 + - + +
203C LEU* 3.3 5.8 + - - +
204C LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU* 5.4 0.3 - - - +
168C ASN* 2.8 32.8 + - + +
169C VAL* 3.6 28.2 + - + +
197C MET* 2.9 36.0 + - + +
200C ARG* 1.3 77.2 - - + +
202C ARG* 1.3 62.8 + - - +
204C LYS* 3.6 10.1 + - + +
205C GLY 3.2 16.1 + - - -
325C ARG* 2.7 48.2 + - - -
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Residues in contact with ARG 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN* 4.3 4.9 - - - +
168C ASN* 2.9 32.9 + - + -
172C ALA* 3.3 17.2 - - + +
191C VAL* 4.9 2.9 - - + -
198C THR* 2.9 47.7 + - - +
199C SER 4.1 1.8 - - - +
201C GLU* 1.3 74.4 - - - +
203C LEU* 1.3 66.8 + - - +
205C GLY 3.4 0.2 + - - -
206C PHE* 3.0 21.1 + - - +
250C LEU* 3.9 7.1 - - + +
252C SER* 2.7 53.0 + - - -
253C SER* 4.6 5.3 - - - -
280C PHE* 3.4 37.8 - - + -
298C GLN* 3.6 26.3 + - - +
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ALA* 3.8 23.3 - - + -
191C VAL* 3.8 29.7 - - + +
199C SER 3.0 15.7 + - - +
200C ARG* 3.6 5.6 - - - +
202C ARG* 1.3 75.0 - - - +
204C LYS* 1.3 65.5 + - - +
206C PHE* 3.1 9.4 + - + +
207C ARG* 2.9 46.6 + - - +
222C ILE* 3.8 34.3 - - + -
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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
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169C VAL* 4.2 26.8 - - + +
200C ARG 2.9 17.6 + - - +
201C GLU* 3.6 10.1 - - + +
203C LEU* 1.3 75.0 - - - +
205C GLY* 1.3 63.7 + - - +
207C ARG* 3.2 12.2 + - - +
208C ALA* 2.9 24.8 + - + +
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Residues in contact with GLY 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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169C VAL* 3.5 33.4 - - - +
172C ALA* 4.1 0.4 - - - -
173C ARG* 3.6 19.3 - - - -
201C GLU 3.2 10.0 + - - -
202C ARG 3.4 2.7 + - - -
203C LEU 3.3 0.2 - - - -
204C LYS* 1.3 78.0 - - - +
206C PHE* 1.3 62.6 + - - +
208C ALA* 3.3 4.1 + - - +
209C ALA* 3.0 18.9 + - - +
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Residues in contact with PHE 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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172C ALA* 4.1 2.0 - - - +
176C VAL* 3.7 26.0 - - + -
187C ILE* 3.3 45.8 - - + -
188C GLY* 3.9 12.1 - - - -
189C ALA* 4.2 11.2 - - + -
202C ARG 3.0 13.3 + - - +
203C LEU* 3.1 14.1 - - + +
205C GLY* 1.3 73.7 - - - +
207C ARG* 1.3 67.9 + - + +
209C ALA* 3.2 5.4 + - - +
210C MET* 3.0 48.1 + - + +
217C VAL* 3.8 18.4 - - + -
222C ILE* 3.5 27.4 - - + -
250C LEU* 4.0 11.7 - - + -
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 2.9 38.5 + - - +
204C LYS* 3.5 12.6 - - - +
206C PHE* 1.3 82.6 - - + +
208C ALA* 1.3 60.8 + - - +
210C MET* 3.7 5.4 - - - +
211C SER* 2.8 32.4 + - - -
217C VAL* 4.0 30.2 + - + +
219C GLN* 2.8 30.7 + - - +
222C ILE* 4.5 10.7 - - - +
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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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169C VAL* 5.5 4.7 - - + -
173C ARG* 4.1 27.0 - - - +
204C LYS* 2.9 18.7 + - + +
205C GLY* 3.3 7.4 + - - +
207C ARG* 1.3 75.4 - - - +
209C ALA* 1.3 63.6 + - - +
211C SER* 3.6 6.3 - - - -
212C ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 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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173C ARG* 3.6 36.3 - - + +
176C VAL* 3.7 18.4 - - + -
177C GLU* 3.9 11.6 - - + +
180C ILE* 3.8 5.1 - - + +
205C GLY 3.0 11.5 + - - +
206C PHE 3.6 8.3 - - - +
208C ALA* 1.3 74.2 - - - +
210C MET* 1.3 65.4 + - - +
212C ALA* 3.5 4.4 + - - +
213C ALA* 3.2 23.0 + - - +
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Residues in contact with MET 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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176C VAL* 4.0 9.4 - - + -
180C ILE* 4.0 20.9 - - - -
185C THR 3.9 17.0 - - - +
187C ILE* 4.0 31.2 - - + +
206C PHE* 3.0 39.8 + - + +
207C ARG* 3.2 6.3 + - - +
209C ALA* 1.3 77.1 - - - +
211C SER* 1.3 61.5 + - - +
213C ALA* 3.3 2.6 + - - -
214C GLY 3.2 2.9 + - - -
215C LEU* 2.9 58.8 + - + +
216C PRO 4.0 13.0 - - - +
217C VAL* 4.9 9.9 - - + -
221C TRP* 4.7 1.3 - - + -
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Residues in contact with SER 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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207C ARG 2.8 19.1 + - - -
208C ALA* 3.6 7.9 - - - -
210C MET* 1.3 78.3 - - - +
212C ALA* 1.3 57.9 + - - +
214C GLY* 2.8 22.8 + - - -
215C LEU 4.7 2.2 - - - -
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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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173C ARG* 3.6 23.1 - - - +
177C GLU* 5.4 2.9 - - - +
208C ALA 3.0 15.5 + - - +
209C ALA* 4.0 4.5 - - - +
210C MET 3.4 0.2 - - - -
211C SER* 1.3 79.0 - - - +
213C ALA* 1.3 57.9 + - - +
214C GLY 3.3 0.7 + - - -
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Residues in contact with ALA 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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180C ILE* 3.9 30.1 - - + -
209C ALA 3.2 16.7 + - - +
210C MET 3.9 3.4 - - - +
211C SER 3.0 1.4 - - - -
212C ALA* 1.3 75.2 - - - +
214C GLY* 1.3 62.5 + - - +
215C LEU* 3.3 14.0 + - + +
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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