Contacts of the helix formed by residues 182 - 194 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B TYR* 5.6 1.0 - - - +
173B LYS* 2.9 24.4 + - + +
174B VAL 4.6 0.2 - - - -
175B TYR* 3.3 50.6 + - + +
180B TYR 3.3 1.6 + - - -
181B ILE* 1.3 69.6 - - - +
183B TYR* 1.3 61.0 + - - +
184B ASP* 3.0 7.6 + - - +
185B GLN* 2.8 43.9 + - + +
186B LEU* 3.2 10.3 + - - +
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 4.8 1.6 + - - -
180B TYR* 6.1 0.9 - + + -
181B ILE* 2.9 52.5 + - + +
182B ASN* 1.3 71.0 - - - +
184B ASP* 1.3 62.6 + - - +
186B LEU* 3.6 10.8 - - + +
187B GLU* 3.1 19.6 + - - +
205B TYR* 4.6 3.2 + - - -
208B ASN 4.2 3.5 + - - -
209B LEU* 3.5 18.5 - - - +
210B ASP* 2.8 50.1 + - + +
213B ARG* 3.6 36.8 + - + +
214B LEU* 3.8 30.7 - - + -
217B ILE* 3.8 4.2 - - + +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 3.5 15.6 + - - +
182B ASN* 3.0 8.3 + - - +
183B TYR* 1.3 79.6 - - - +
185B GLN* 1.3 62.9 + - - +
187B GLU* 3.5 3.7 + - - +
188B GLU* 3.2 23.0 + - - +
213B ARG* 2.8 26.3 + - - +
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Residues in contact with GLN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B TYR* 4.9 1.1 - - + -
173B LYS* 3.9 32.7 + - - +
182B ASN* 2.8 33.7 + - - +
184B ASP* 1.3 72.7 - - - +
186B LEU* 1.3 62.6 + - - +
188B GLU* 3.0 9.3 + - + +
189B ASN* 2.8 46.9 + - - +
188D GLU* 2.8 29.7 + - - -
189D ASN* 5.1 1.2 + - - -
192D LEU* 4.0 11.7 - - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MSE 3.8 23.6 - - + -
172B TYR* 3.6 52.4 - - + +
181B ILE* 5.5 0.7 - - + -
182B ASN 3.2 9.7 + - - +
183B TYR* 3.6 13.7 - - + +
184B ASP 3.3 0.2 - - - -
185B GLN* 1.3 79.6 - - - +
187B GLU* 1.3 64.6 + - - +
188B GLU 3.1 0.2 + - - -
189B ASN* 3.2 3.3 + - - +
190B ALA* 2.9 27.6 + - + +
198B ILE* 4.7 12.1 - - + -
214B LEU* 3.5 31.9 - - + -
217B ILE* 4.0 13.7 - - + -
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR 3.1 8.5 + - - +
184B ASP 3.8 4.7 - - - +
186B LEU* 1.3 81.6 - - - +
188B GLU* 1.3 64.0 + - - +
190B ALA* 3.7 2.4 + - - +
191B SER* 3.6 15.8 + - - -
213B ARG* 2.7 36.5 + - - +
216B LYS* 3.0 29.9 + - - +
217B ILE* 3.6 32.3 - - + +
220B ASP* 3.7 8.7 - - + +
221B ASN* 4.9 2.2 + - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ASP 3.2 11.2 + - - +
185B GLN* 3.0 14.5 + - + +
187B GLU* 1.3 79.3 - - - +
189B ASN* 1.3 64.0 + - - +
191B SER* 2.6 31.7 + - - -
192B LEU* 3.7 9.6 + - - +
185D GLN* 3.0 28.9 + - - -
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MSE 4.3 4.8 - - + +
170B MSE 3.6 24.3 - - + +
171B PRO 5.1 3.4 + - - -
172B TYR* 5.8 1.8 - - - +
185B GLN* 2.8 41.6 + - - +
186B LEU* 4.0 2.6 - - - +
188B GLU* 1.3 74.6 - - - +
190B ALA* 1.3 65.5 + - - +
192B LEU* 2.8 22.1 + - + +
193B PHE* 2.9 14.2 + - - +
170D MSE 5.5 0.8 - - - +
185D GLN* 5.4 0.5 + - - -
189D ASN* 2.8 30.4 + - - +
192D LEU* 3.6 24.0 - - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MSE 3.9 11.1 - - - -
186B LEU* 2.9 23.8 + - + +
187B GLU 3.9 3.8 - - - +
189B ASN* 1.3 71.9 - - - +
191B SER* 1.3 57.3 + - - +
193B PHE 4.5 0.2 - - - +
194B HIS* 2.9 24.1 + - - -
195B PRO* 3.2 27.0 - - + +
198B ILE* 4.8 0.4 - - + -
217B ILE* 4.0 11.7 - - + -
221B ASN* 3.3 27.0 - - - +
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B GLU 3.6 7.6 + - - -
188B GLU* 2.6 27.3 + - - -
189B ASN 3.0 0.2 - - - -
190B ALA* 1.3 78.7 - - - +
192B LEU* 1.3 68.3 + - - +
194B HIS* 3.1 23.6 + - - -
221B ASN* 3.4 14.1 + - - -
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Residues in contact with LEU 192 (chain B).
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* 4.6 1.0 + - - -
188B GLU* 3.9 21.5 - - - +
189B ASN* 2.8 13.5 + - - +
191B SER* 1.3 93.8 + - - +
193B PHE* 1.3 57.7 + - - +
194B HIS* 3.4 15.0 + - - -
154D MSE 6.0 0.2 - - - +
169D SER 5.0 0.3 - - - +
170D MSE 3.7 20.1 - - + +
171D PRO* 3.7 37.2 - - + +
172D TYR* 6.0 0.2 - - - -
173D LYS* 4.1 29.4 - - + +
185D GLN* 4.3 7.4 - - - +
189D ASN* 3.7 26.2 - - - +
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Residues in contact with PHE 193 (chain B).
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* 2.9 77.5 + - + +
138B ILE 3.9 13.9 - - - -
139B MSE 3.8 20.6 - - + -
168B GLU* 3.7 13.9 - - + -
169B SER 4.1 2.2 - - - -
170B MSE 3.6 44.0 - - + -
189B ASN 2.9 13.5 + - - +
190B ALA 4.5 0.2 - - - +
192B LEU* 1.3 77.0 - - - +
194B HIS* 1.3 73.7 + - - +
195B PRO* 4.2 7.2 - - + -
137D ARG* 4.7 3.1 - - - -
170D MSE 4.4 4.5 - - - -
193D PHE* 3.7 27.1 - + - -
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Residues in contact with HIS 194 (chain B).
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* 3.8 10.2 - - - +
190B ALA 2.9 10.8 + - - -
191B SER* 3.1 21.0 + - - -
192B LEU* 3.4 19.1 + - - -
193B PHE* 1.3 88.7 + - - +
195B PRO* 1.3 73.0 - - - +
196B LYS* 3.6 1.2 + - - +
221B ASN* 5.1 7.9 - - - +
154D MSE 4.3 34.2 - - + +
155D THR* 4.1 8.3 - - - +
156D ASP* 3.5 44.7 + - + +
171D PRO* 5.7 2.9 - - + -
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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