Contacts of the helix formed by residues 182 - 194 (chain D) in PDB entry 1EJI
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 ASN 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D TYR* 5.7 0.3 - - - +
173D LYS* 2.9 24.2 + - + +
174D VAL 4.6 0.7 - - - -
175D TYR* 4.3 26.8 - - + +
180D TYR 3.3 2.7 + - - -
181D ILE* 1.3 72.4 - - - +
183D TYR* 1.3 58.3 - - - +
184D ASP* 3.0 11.3 + - - +
185D GLN* 2.8 43.8 + - + +
186D LEU* 3.3 10.1 + - - +
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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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180D TYR* 6.0 1.6 - + + -
181D ILE* 2.8 52.6 + - + +
182D ASN* 1.3 70.6 - - - +
184D ASP* 1.3 62.5 + - - +
186D LEU* 3.6 9.1 - - + +
187D GLU* 3.0 24.6 + - - +
205D TYR* 4.4 4.1 + - - -
208D ASN 4.2 3.5 + - - -
209D LEU* 3.6 18.4 - - - +
210D ASP* 3.0 47.0 + - + -
213D ARG* 3.7 32.0 + - + +
214D LEU* 3.8 36.3 - - + -
217D ILE* 3.7 5.1 - - + +
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Residues in contact with ASP 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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182D ASN* 3.0 8.8 + - - +
183D TYR* 1.3 79.1 - - - +
185D GLN* 1.3 62.5 + - - +
187D GLU* 3.4 3.5 + - - +
188D GLU* 3.1 23.5 + - - +
213D ARG* 2.7 27.0 + - - +
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Residues in contact with GLN 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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188B GLU* 3.0 27.5 + - - -
189B ASN* 5.4 0.8 + - - -
192B LEU* 4.3 6.8 - - - +
172D TYR* 4.9 2.5 - - + -
173D LYS* 3.9 32.0 + - - +
182D ASN* 2.8 31.9 + - - +
184D ASP* 1.3 74.4 - - - +
186D LEU* 1.3 60.8 + - - +
188D GLU* 3.1 7.9 + - + +
189D ASN* 2.8 51.2 + - - +
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Residues in contact with LEU 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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139D MSE 3.8 25.6 - - + -
172D TYR* 3.7 51.7 - - + +
181D ILE* 5.5 1.1 - - + -
182D ASN 3.3 9.9 + - - +
183D TYR* 3.6 11.7 - - + +
184D ASP 3.3 0.4 - - - -
185D GLN* 1.3 79.9 + - - +
187D GLU* 1.3 64.0 + - - +
188D GLU 3.1 0.2 + - - -
189D ASN* 3.7 3.2 - - - +
190D ALA* 2.8 27.4 + - + +
198D ILE* 4.8 9.4 - - + -
214D LEU* 3.5 31.9 - - + -
217D ILE* 4.0 15.7 - - + -
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Residues in contact with GLU 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 3.0 9.6 + - - +
184D ASP* 3.8 5.7 - - - +
186D LEU* 1.3 79.6 - - - +
188D GLU* 1.3 62.3 + - - +
190D ALA* 3.7 2.6 + - - +
191D SER* 3.6 16.3 + - - -
213D ARG* 2.7 33.3 + - - +
216D LYS* 2.9 31.2 + - - +
217D ILE* 3.5 32.7 - - + +
220D ASP* 3.6 9.2 - - + +
221D ASN* 4.9 2.0 + - - +
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Residues in contact with GLU 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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185B GLN* 2.8 31.7 + - - -
184D ASP 3.1 14.5 + - - +
185D GLN* 3.2 13.7 - - + +
186D LEU 3.1 0.2 - - - -
187D GLU* 1.3 76.0 - - - +
189D ASN* 1.3 63.6 + - - +
191D SER* 2.7 31.7 + - - -
192D LEU* 3.8 9.6 + - - +
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Residues in contact with ASN 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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170B MSE 6.2 0.7 - - - -
185B GLN* 5.1 0.9 + - - -
189B ASN* 2.8 36.1 + - - +
192B LEU* 3.7 18.8 - - - +
139D MSE 4.2 5.3 - - + +
170D MSE 3.6 23.9 - - + +
171D PRO 5.0 3.0 + - - -
172D TYR* 5.8 2.0 - - - +
185D GLN* 2.8 41.4 + - - +
186D LEU* 4.0 2.4 - - - +
188D GLU* 1.3 75.8 - - - +
190D ALA* 1.3 65.3 + - - +
192D LEU* 2.8 20.9 + - - +
193D PHE* 2.9 14.2 + - - +
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Residues in contact with ALA 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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139D MSE 4.0 10.2 - - - -
186D LEU* 2.8 23.6 + - + +
187D GLU 3.9 3.4 - - - +
188D GLU 3.3 0.2 - - - -
189D ASN* 1.3 73.1 - - - +
191D SER* 1.3 57.5 + - - +
194D HIS* 2.9 23.6 + - - -
195D PRO* 3.2 24.4 - - + +
198D ILE* 4.9 0.9 - - + -
217D ILE* 4.0 11.0 - - + -
221D ASN* 3.1 30.8 - - - +
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Residues in contact with SER 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 GLU 3.6 8.3 + - - -
188D GLU* 2.7 24.9 + - - -
189D ASN 3.1 0.2 - - - -
190D ALA* 1.3 78.9 - - - +
192D LEU* 1.3 66.7 + - - +
194D HIS* 3.1 24.1 + - - -
221D ASN* 3.3 13.4 + - - -
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Residues in contact with LEU 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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142B ASP* 6.0 0.2 - - - -
169B SER 5.1 0.2 - - - +
170B MSE 3.5 11.8 - - + +
171B PRO* 3.4 44.5 - - + +
172B TYR* 5.8 0.2 - - - -
173B LYS* 3.7 35.7 - - + +
185B GLN* 4.0 18.6 - - - +
189B ASN* 3.6 27.4 - - - +
137D ARG* 4.6 0.7 + - - -
188D GLU* 3.9 11.9 - - - +
189D ASN* 2.8 12.5 + - - +
191D SER* 1.3 90.2 - - - +
193D PHE* 1.3 60.2 + - - +
194D HIS* 3.6 10.1 + - - -
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Residues in contact with PHE 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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137B ARG* 4.7 2.0 - - - -
170B MSE 4.2 5.6 - - - -
193B PHE* 3.7 28.0 - + - -
137D ARG* 2.8 72.7 + - + +
138D ILE 3.9 14.4 - - - -
139D MSE 3.8 20.2 - - + -
168D GLU* 3.7 17.0 - - + -
169D SER 4.1 2.2 - - - -
170D MSE 3.6 47.8 - - + -
189D ASN 2.9 14.4 + - - +
190D ALA 4.5 0.2 - - - +
192D LEU* 1.3 77.8 - - - +
194D HIS* 1.3 71.0 + - - +
195D PRO* 4.1 9.2 - - + -
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Residues in contact with HIS 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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154B MSE 3.9 45.3 + - + +
155B THR* 3.9 24.0 - - - +
156B ASP* 4.2 22.6 + - - +
171B PRO* 5.4 5.8 - - + -
137D ARG* 3.8 10.8 + - - +
190D ALA 2.9 11.2 + - - -
191D SER 3.1 20.9 + - - -
192D LEU* 3.6 17.6 + - - -
193D PHE* 1.3 88.9 + - - +
195D PRO* 1.3 73.5 - - - +
196D LYS* 3.6 1.2 + - - +
221D ASN* 5.0 8.3 - - + +
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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