Contacts of the helix formed by residues 179 - 195 (chain D) in PDB entry 7CE1
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 ASP 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D ARG* 3.7 19.7 + - - +
177D ASP 4.1 1.2 + - - -
178D PHE* 1.3 80.1 - - - +
180D ASN* 1.3 55.3 + - - +
181D GLU* 3.3 14.0 + - - +
182D ALA* 3.1 32.9 + - + +
183D TYR* 3.1 24.3 + - - +
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Residues in contact with ASN 180 (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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166D ARG* 4.7 1.4 - - - +
177D ASP* 3.8 2.9 - - - +
178D PHE* 2.7 53.8 + - - +
179D ASP* 1.3 70.5 + - - +
181D GLU* 1.3 59.4 + - - +
183D TYR* 3.5 15.2 - - + +
184D ALA* 2.8 31.9 + - - +
210D PHE* 3.2 38.8 + - - +
213D HIS* 4.4 14.0 - - + +
214D ALA* 4.1 14.3 - - + +
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Residues in contact with GLU 181 (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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166D ARG* 5.9 0.2 - - - +
179D ASP* 3.1 9.8 + - - +
180D ASN* 1.3 78.3 - - - +
182D ALA* 1.3 64.8 + - - +
185D TYR* 3.2 23.7 + - - +
213D HIS* 3.1 35.3 + - + +
216D LYS* 3.5 17.0 - - - +
217D GLY* 3.4 8.3 - - - -
220D ARG* 3.4 34.6 + - - +
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Residues in contact with ALA 182 (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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179D ASP* 3.1 35.2 + - + +
181D GLU* 1.3 77.8 - - - +
183D TYR* 1.3 56.1 + - - +
185D TYR* 3.4 5.6 + - - +
186D GLU* 2.8 51.0 + - + +
220D ARG* 5.5 1.6 - - - +
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Residues in contact with TYR 183 (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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178D PHE* 3.8 26.2 - + + -
179D ASP 3.1 13.8 + - - +
180D ASN* 3.5 16.2 - - + +
182D ALA* 1.3 75.7 - - - +
184D ALA* 1.3 63.8 + - + +
186D GLU* 3.2 6.7 + - + +
187D ALA* 2.6 54.5 + - + +
201D ILE* 5.7 10.2 - - + +
214D ALA* 6.2 1.1 - - + -
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Residues in contact with ALA 184 (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 ASN 2.8 19.3 + - - +
183D TYR* 1.3 81.7 - - + +
185D TYR* 1.3 62.2 + - - +
187D ALA* 3.3 6.3 + - - +
188D VAL* 3.2 29.6 + - - +
201D ILE* 5.8 6.3 - - + -
214D ALA* 3.2 33.9 - - + +
217D GLY* 3.8 4.5 - - - -
218D PHE* 3.6 13.8 - - + +
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Residues in contact with TYR 185 (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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181D GLU 3.2 16.8 + - - +
182D ALA* 3.6 7.4 - - - +
184D ALA* 1.3 79.6 - - - +
186D GLU* 1.3 70.2 + - + +
188D VAL* 3.7 3.1 + - - +
189D GLU* 3.4 29.1 + - - +
217D GLY 3.3 12.4 + - - +
220D ARG* 3.4 34.3 - - - +
221D GLY* 3.4 27.1 - - - -
224D ASP* 3.7 22.1 + - - +
225D PHE* 4.3 18.8 - + - -
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Residues in contact with GLU 186 (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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182D ALA* 2.8 42.0 + - - +
183D TYR* 3.8 6.5 - - + +
185D TYR* 1.3 81.8 - - + +
187D ALA* 1.3 64.5 + - - +
189D GLU* 3.5 11.9 + - + +
190D ARG* 3.1 21.7 + - - +
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Residues in contact with ALA 187 (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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183D TYR* 2.6 43.5 + - + +
184D ALA* 3.4 10.1 - - - +
186D GLU* 1.3 73.9 - - - +
188D VAL* 1.3 59.2 + - + +
190D ARG* 3.0 7.7 + - - +
191D LEU* 2.9 38.6 + - + +
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Residues in contact with VAL 188 (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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184D ALA 3.2 17.3 + - - +
185D TYR 4.1 4.5 - - - +
186D GLU 3.4 0.2 - - - -
187D ALA* 1.3 73.5 - - + +
189D GLU* 1.3 61.0 + - - +
191D LEU* 3.2 8.9 + - + +
192D ALA* 2.8 26.5 + - - +
199D ILE* 4.6 11.7 - - + -
218D PHE* 3.6 35.9 - - + +
221D GLY* 4.1 19.1 - - - +
222D ILE* 4.1 21.5 - - + +
225D PHE* 4.8 4.4 - - + -
227D VAL* 4.2 14.4 - - + -
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Residues in contact with GLU 189 (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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185D TYR* 3.4 19.7 + - - +
186D GLU* 3.6 13.7 - - - +
187D ALA 3.2 0.2 - - - -
188D VAL* 1.3 79.9 - - - +
190D ARG* 1.3 61.1 + - - +
192D ALA* 3.3 4.0 + - - +
193D GLN* 3.3 21.0 + - - +
225D PHE* 3.2 42.5 - - + -
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Residues in contact with ARG 190 (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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186D GLU 3.1 12.5 + - - +
187D ALA* 3.0 12.6 + - - +
189D GLU* 1.3 78.1 - - - +
191D LEU* 1.3 61.6 + - + +
193D GLN* 3.5 11.3 + - - +
194D CYS* 3.1 34.4 + - - -
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Residues in contact with LEU 191 (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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187D ALA* 2.9 30.7 + - + +
188D VAL* 3.2 13.2 + - + +
190D ARG* 1.3 82.2 - - + +
192D ALA* 1.3 61.9 + - - +
194D CYS* 3.4 12.7 + - - +
195D GLY 3.3 2.3 + - - -
196D ARG* 3.2 38.6 + - + +
198D ARG 5.4 0.7 - - - +
199D ILE* 3.5 44.9 - - + -
200D ALA 5.6 1.3 - - - +
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Residues in contact with ALA 192 (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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188D VAL 2.8 14.8 + - - +
189D GLU 3.3 9.4 + - - +
191D LEU* 1.3 68.2 - - - +
193D GLN* 1.3 59.6 + - - +
194D CYS 3.1 1.1 - - - -
195D GLY* 2.7 26.1 + - - +
196D ARG 4.8 5.2 - - - -
225D PHE* 4.1 29.2 - - + -
227D VAL* 5.6 7.0 - - + -
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Residues in contact with GLN 193 (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 GLU 3.3 10.6 + - - +
190D ARG* 3.7 15.9 - - - +
192D ALA* 1.3 78.7 - - - +
194D CYS* 1.3 61.8 + - - +
195D GLY* 3.5 0.3 + - - -
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Residues in contact with CYS 194 (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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190D ARG* 3.1 30.6 + - - -
191D LEU* 3.5 17.5 - - - +
192D ALA 3.1 0.8 - - - -
193D GLN* 1.3 78.0 - - - +
195D GLY* 1.3 55.9 + - - +
196D ARG* 3.2 28.6 + - + +
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Residues in contact with GLY 195 (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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191D LEU 3.3 0.6 + - - -
192D ALA 2.7 22.7 + - - -
193D GLN 3.2 0.9 - - - -
194D CYS* 1.3 72.8 - - - +
196D ARG* 1.3 65.1 + - - +
197D LYS* 3.4 6.4 + - - +
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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