Contacts of the helix formed by residues 182 - 194 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A TYR* 5.6 0.3 - - - +
173A LYS* 2.9 24.9 + - + +
174A VAL 4.6 0.7 - - - -
175A TYR* 3.4 45.6 + - + +
180A TYR 3.3 1.8 + - - -
181A ILE* 1.3 71.3 - - - +
183A TYR* 1.3 59.5 + - - +
184A ASP* 3.0 11.6 + - - +
185A GLN* 2.8 45.1 + - + +
186A LEU* 3.2 10.6 + - - +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 4.9 1.0 + - - -
180A TYR* 6.1 0.9 - + + -
181A ILE* 2.9 52.7 + - + +
182A ASN* 1.3 71.4 - - - +
184A ASP* 1.3 61.6 + - - +
186A LEU* 3.7 9.4 - - + +
187A GLU* 3.1 20.1 + - - +
205A TYR* 4.5 3.2 + - - -
208A ASN 4.2 3.1 + - - -
209A LEU* 3.5 19.1 - - - +
210A ASP* 2.9 47.0 + - + +
213A ARG* 3.6 37.7 + - + +
214A LEU* 3.8 33.2 - - + -
217A ILE* 3.8 4.3 - - + +
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 3.6 15.6 + - - +
182A ASN* 3.0 8.6 + - - +
183A TYR* 1.3 79.6 - - - +
185A GLN* 1.3 61.5 + - - +
187A GLU* 3.4 3.3 + - - +
188A GLU* 3.2 23.1 + - - +
213A ARG* 2.9 25.1 + - - +
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Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 4.9 1.7 - - - -
173A LYS* 3.8 33.1 + - - +
182A ASN* 2.8 35.8 + - - +
184A ASP* 1.3 69.8 - - - +
186A LEU* 1.3 61.5 + - - +
188A GLU* 3.1 7.6 + - + +
189A ASN* 2.8 46.4 + - - +
188C GLU* 2.9 28.5 + - - -
189C ASN* 5.2 1.4 + - - -
192C LEU* 4.0 13.1 - - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MSE 3.7 26.7 - - + -
172A TYR* 3.7 52.6 - - + +
181A ILE* 5.5 0.9 - - + -
182A ASN 3.2 9.1 + - - +
183A TYR* 3.7 13.0 - - + +
184A ASP 3.2 0.4 - - - -
185A GLN* 1.3 79.3 + - - +
187A GLU* 1.3 64.3 + - - +
188A GLU 3.1 0.3 + - - -
189A ASN* 3.2 3.1 + - - -
190A ALA* 2.8 27.6 + - + +
198A ILE* 4.7 9.9 - - + -
214A LEU* 3.5 31.6 - - + -
217A ILE* 4.0 14.1 - - + -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR 3.1 10.2 + - - +
184A ASP 3.8 4.5 - - - +
186A LEU* 1.3 80.2 - - - +
188A GLU* 1.3 62.9 + - - +
190A ALA* 3.7 2.4 + - - +
191A SER* 3.6 15.9 + - - -
213A ARG* 2.8 32.9 + - - -
216A LYS* 2.9 31.2 + - - +
217A ILE* 3.5 32.2 - - + +
220A ASP* 3.7 9.4 - - + +
221A ASN* 4.9 2.5 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP 3.2 13.6 + - - +
185A GLN* 3.1 13.7 + - + +
187A GLU* 1.3 77.7 - - - +
189A ASN* 1.3 63.6 + - - +
191A SER* 2.6 32.4 + - - -
192A LEU* 3.7 8.2 + - - +
185C GLN* 2.8 31.4 + - - -
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Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MSE 4.2 5.1 - - + +
170A MSE 3.5 26.0 - - + +
171A PRO 5.1 3.4 + - - -
172A TYR* 5.8 1.8 - - - +
185A GLN* 2.8 41.3 + - - +
186A LEU* 4.0 2.4 - - - +
188A GLU* 1.3 74.3 - - - +
190A ALA* 1.3 65.9 + - - +
192A LEU* 2.8 21.8 + - - +
193A PHE* 2.9 13.9 + - - +
170C MSE 5.8 1.0 - - - +
185C GLN* 5.3 0.9 + - - -
189C ASN* 2.8 35.5 + - - +
192C LEU* 3.7 17.2 - - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MSE 3.9 13.6 - - - -
186A LEU* 2.8 23.2 + - + +
187A GLU 3.9 3.8 - - - +
189A ASN* 1.3 72.0 - - - +
191A SER* 1.3 57.8 + - - +
194A HIS* 2.9 24.6 + - - -
195A PRO* 3.2 24.6 - - + +
198A ILE* 4.8 0.7 - - + -
217A ILE* 4.0 10.8 - - + -
221A ASN* 3.3 27.0 - - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU 3.6 8.3 + - - -
188A GLU* 2.6 25.8 + - - -
189A ASN 3.0 0.2 - - - -
190A ALA* 1.3 80.6 - - - +
192A LEU* 1.3 66.4 + - - +
194A HIS* 3.2 24.8 + - - -
221A ASN* 3.4 14.3 + - - -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 4.6 1.0 + - - -
188A GLU* 3.9 12.1 - - - +
189A ASN* 2.8 13.1 + - - +
191A SER* 1.3 94.3 + - - +
193A PHE* 1.3 58.3 + - - +
194A HIS* 3.6 11.4 + - - -
142C ASP* 5.7 0.7 - - - +
169C SER 4.9 0.3 - - - +
170C MSE 3.5 18.7 - - + +
171C PRO* 3.4 41.0 - - + +
172C TYR* 5.8 0.2 - - - -
173C LYS* 3.9 32.5 - - + -
185C GLN* 4.2 16.8 - - - +
189C ASN* 3.7 26.9 - - - +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 2.7 71.2 + - + +
138A ILE 3.9 13.9 - - - -
139A MSE 3.8 21.1 - - + -
168A GLU* 3.7 19.7 - - + -
169A SER 4.1 2.0 - - - -
170A MSE 3.7 44.9 - - + -
189A ASN 2.9 13.7 + - - +
190A ALA 4.5 0.2 - - - +
192A LEU* 1.3 75.5 - - - +
194A HIS* 1.3 75.4 + - - +
195A PRO* 4.2 4.9 - - + -
137C ARG* 4.7 2.7 - - - -
170C MSE 4.3 5.2 - - - -
193C PHE* 3.6 31.4 - + - -
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.9 9.8 - - - +
190A ALA 2.9 11.4 + - - -
191A SER 3.2 24.9 + - - -
192A LEU* 3.6 12.4 + - - -
193A PHE* 1.3 84.8 + - - +
195A PRO* 1.3 72.9 - - - +
196A LYS* 3.6 1.9 + - - +
221A ASN* 5.1 8.7 - - - -
154C MSE 3.6 40.0 + - + +
155C THR* 4.6 2.0 - - - +
156C ASP* 3.9 41.6 + - + +
171C PRO* 5.5 5.2 - - + -
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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