Contacts of the helix formed by residues 196 - 213 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D GLU* 3.9 24.0 + - + +
154D ARG* 3.4 50.9 - - + +
192D GLY* 5.6 1.1 - - - -
193D SER* 3.2 32.1 + - - +
195D GLY* 1.3 80.0 - - - +
197D MET* 1.3 66.2 + - - +
198D THR* 3.8 13.2 - - - +
199D SER* 3.5 15.5 - - - +
200D ARG* 3.0 21.3 + - - -
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN 3.4 24.9 - - - +
154D ARG* 4.3 15.7 - - + +
155D GLU* 3.6 49.4 - - + +
165D LEU* 3.9 15.0 - - + -
168D ASN* 3.7 12.8 - - - +
196D LEU* 1.3 72.2 - - - +
198D THR* 1.3 57.8 + - - +
200D ARG* 3.2 24.2 + - - +
201D GLU* 2.9 69.6 + - + +
325D ARG* 4.0 6.3 - - - +
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Residues in contact with THR 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 3.3 44.0 - - - +
154D ARG* 4.1 10.4 + - + +
168D ASN* 4.1 13.7 - - - +
196D LEU* 3.8 16.6 - - - +
197D MET* 1.3 72.7 - - + +
199D SER* 1.3 69.9 + - - +
201D GLU* 3.3 0.9 + - - +
202D ARG* 2.9 59.9 + - - +
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Residues in contact with SER 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 4.1 21.7 - - - +
192D GLY* 3.5 21.4 + - - +
193D SER 2.6 29.2 + - - -
194D ALA* 4.4 5.6 - - - -
196D LEU* 3.5 15.1 + - - +
198D THR* 1.3 78.2 + - - +
200D ARG* 1.3 63.1 + - - +
202D ARG* 3.5 1.4 + - - -
203D LEU* 3.0 25.7 + - - +
252D SER* 5.3 3.1 - - - -
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLU* 5.5 2.4 + - - -
157D ARG* 4.7 14.8 - - - +
194D ALA 3.9 13.5 - - - +
195D GLY* 2.5 31.2 + - - -
196D LEU 3.0 6.5 + - - +
197D MET* 3.5 27.8 - - - +
199D SER* 1.3 80.3 - - - +
201D GLU* 1.3 59.8 + - + +
203D LEU* 3.3 7.5 + - - +
204D LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASN* 2.9 26.7 + - + +
169D VAL* 3.5 28.2 + - + -
197D MET* 2.9 35.9 + - + +
198D THR 4.1 0.2 - - - +
200D ARG* 1.3 77.1 - - + +
202D ARG* 1.3 65.8 + - - +
204D LYS* 3.5 10.0 + - + +
205D GLY 3.1 18.2 + - - -
325D ARG* 2.7 48.2 + - - -
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 4.5 4.9 - - - +
166D SER* 4.9 0.2 - - - -
168D ASN* 2.7 34.8 + - + -
172D ALA* 3.3 14.5 - - + +
191D VAL* 4.9 2.5 - - + -
198D THR* 2.9 41.8 + - - +
199D SER 4.1 2.2 - - - +
201D GLU* 1.3 76.3 - - - +
203D LEU* 1.3 62.9 - - - +
206D PHE 3.2 16.3 + - - -
250D LEU* 3.8 11.9 - - + +
252D SER* 2.6 51.3 + - - -
253D SER* 4.6 5.1 - - - -
280D PHE* 3.3 44.9 - - + +
298D GLN* 3.4 27.5 + - - +
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ALA* 3.7 25.1 - - + -
191D VAL* 3.9 21.2 - - + +
199D SER 3.0 18.4 + - - +
200D ARG* 3.6 6.3 - - - +
202D ARG* 1.3 77.1 - - - +
204D LYS* 1.3 56.2 + - - +
206D PHE* 3.1 9.0 + - + +
207D ARG* 2.9 52.6 + - - +
222D ILE* 3.7 38.8 - - + -
250D LEU* 5.5 0.2 - - - -
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Residues in contact with LYS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.2 28.1 - - + +
200D ARG 3.0 18.0 + - - +
201D GLU* 3.6 9.0 - - + +
202D ARG 3.5 0.2 - - - -
203D LEU* 1.3 71.3 - - - +
205D GLY* 1.3 59.3 + - - +
207D ARG* 3.4 11.5 + - - +
208D ALA* 3.0 28.5 + - + +
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Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.6 32.3 - - - +
172D ALA* 4.2 0.2 - - - -
173D ARG* 3.4 23.6 - - - +
201D GLU 3.1 12.0 + - - -
202D ARG 3.6 2.7 + - - -
204D LYS* 1.3 72.3 - - - +
206D PHE* 1.3 64.6 + - - +
208D ALA* 3.4 2.1 + - - +
209D ALA* 3.1 17.7 + - - +
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Residues in contact with PHE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ALA* 4.2 1.4 - - - +
176D VAL* 3.7 24.9 - - + -
187D ILE* 3.3 46.0 - - + -
188D GLY* 4.1 10.8 - - - -
189D ALA* 4.1 11.2 - - + -
202D ARG 3.2 12.6 + - - +
203D LEU* 3.1 15.8 + - + +
205D GLY* 1.3 74.5 - - - +
207D ARG* 1.3 69.9 + - + +
209D ALA* 3.2 3.8 + - - +
210D MET* 3.1 46.1 + - + +
217D VAL* 3.9 17.7 - - + -
222D ILE* 3.5 29.6 - - + -
250D LEU* 3.9 12.6 - - + -
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Residues in contact with ARG 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 2.9 37.5 + - - +
204D LYS* 3.4 10.9 + - - +
206D PHE* 1.3 87.5 - - + +
208D ALA* 1.3 57.1 + - - +
210D MET* 3.8 5.5 - - - +
211D SER* 3.0 30.1 + - - -
217D VAL* 4.1 28.6 + - + +
219D GLN* 2.7 30.9 + - - +
222D ILE* 4.4 13.4 - - - +
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Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 5.5 4.9 - - + -
173D ARG* 4.3 25.9 - - - +
204D LYS* 3.0 19.1 + - + +
205D GLY* 3.8 7.2 - - - +
206D PHE 3.2 0.2 - - - -
207D ARG* 1.3 74.4 - - - +
209D ALA* 1.3 65.1 + - - +
211D SER* 3.8 5.8 - - - -
212D ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ARG* 3.7 24.0 - - + +
176D VAL* 3.5 27.6 - - + -
177D GLU* 3.9 11.3 - - + +
180D ILE* 3.7 5.8 - - + +
205D GLY 3.1 16.6 + - - +
206D PHE 3.5 4.7 - - - +
208D ALA* 1.3 79.8 - - - +
210D MET* 1.3 62.2 - - - +
212D ALA* 3.6 4.4 + - - +
213D ALA* 3.3 21.8 + - - +
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Residues in contact with MET 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D VAL* 4.2 2.2 - - + -
180D ILE* 4.1 20.9 - - - -
185D THR 3.8 17.5 - - - +
187D ILE* 4.1 37.7 - - + +
206D PHE* 3.1 40.1 + - + +
207D ARG* 3.8 6.3 - - - +
209D ALA* 1.3 73.9 - - - +
211D SER* 1.3 66.1 + - - +
213D ALA* 3.1 3.1 + - - -
214D GLY 3.1 4.0 + - - -
215D LEU* 2.9 55.4 + - + +
216D PRO 3.9 13.9 - - - +
217D VAL* 4.8 9.2 - - + -
221D TRP* 4.7 1.8 - - + -
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Residues in contact with SER 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ARG 3.0 19.8 + - - -
208D ALA* 3.8 7.4 - - - -
210D MET* 1.3 77.4 - - - +
212D ALA* 1.3 57.6 + - - +
214D GLY* 2.9 20.5 + - - -
215D LEU 4.6 3.6 - - - +
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Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ARG* 3.8 22.2 - - - +
177D GLU* 5.3 3.4 - - - +
208D ALA 3.1 15.4 + - - +
209D ALA* 3.9 5.6 - - - +
210D MET 3.3 0.2 - - - -
211D SER* 1.3 80.2 - - - +
213D ALA* 1.3 58.6 + - - +
214D GLY 3.3 0.7 + - - -
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Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ILE* 4.0 29.8 - - + -
209D ALA 3.3 14.0 + - - +
210D MET 3.1 5.8 + - - +
212D ALA* 1.3 78.3 - - - +
214D GLY* 1.3 61.4 + - - +
215D LEU* 3.1 14.5 + - + +
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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
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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