Contacts of the helix formed by residues 182 - 194 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C TYR* 5.7 0.2 - - - +
173C LYS* 2.9 24.4 + - + +
174C VAL 4.6 0.6 - - - -
175C TYR* 3.3 44.0 + - + +
180C TYR 3.3 2.2 + - - -
181C ILE* 1.3 72.0 - - - +
183C TYR* 1.3 58.9 - - - +
184C ASP* 3.2 10.4 + - - +
185C GLN* 2.8 45.1 + - + +
186C LEU* 3.2 10.0 + - - +
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Residues in contact with TYR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 6.0 1.6 - + + -
181C ILE* 2.8 53.4 + - + +
182C ASN* 1.3 71.5 - - - +
184C ASP* 1.3 61.6 + - - +
186C LEU* 3.7 9.5 - - + +
187C GLU* 3.1 23.9 + - - +
205C TYR* 4.5 3.5 + - - -
208C ASN 4.1 3.5 + - - -
209C LEU* 3.5 19.1 - - - +
210C ASP* 2.9 45.8 + - + +
213C ARG* 3.7 34.0 + - + +
214C LEU* 3.8 33.9 - - + -
217C ILE* 3.8 4.2 - - + +
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C TYR* 5.5 5.8 + - + +
182C ASN* 3.0 8.7 + - - +
183C TYR* 1.3 80.5 - - - +
185C GLN* 1.3 61.2 + - - +
187C GLU* 3.5 3.3 + - - +
188C GLU* 3.1 24.2 + - - +
213C ARG* 2.7 27.2 + - - +
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Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 2.8 30.7 + - - +
189A ASN* 5.3 0.8 + - - -
192A LEU* 4.2 8.9 - - - +
172C TYR* 4.8 1.8 - - - -
173C LYS* 3.8 32.7 + - - +
182C ASN* 2.8 32.8 + - - +
184C ASP* 1.3 73.2 - - - +
186C LEU* 1.3 61.6 + - - +
188C GLU* 3.0 9.9 + - + +
189C ASN* 2.8 47.0 + - - +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MSE 3.9 23.3 - - + -
172C TYR* 3.7 50.8 - - + +
181C ILE* 5.5 1.3 - - + -
182C ASN 3.2 9.6 + - - +
183C TYR* 3.7 12.6 - - + +
185C GLN* 1.3 79.8 + - - +
187C GLU* 1.3 64.4 + - - +
188C GLU 3.1 0.3 + - - -
189C ASN* 3.8 3.5 - - - +
190C ALA* 2.8 28.2 + - + +
198C ILE* 4.8 13.0 - - + -
214C LEU* 3.5 32.3 - - + -
217C ILE* 4.0 13.9 - - + -
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C TYR 3.1 9.0 + - - +
184C ASP* 3.8 4.6 - - - +
185C GLN 3.3 0.2 - - - -
186C LEU* 1.3 80.0 - - - +
188C GLU* 1.3 64.2 + - - +
190C ALA* 3.7 2.9 + - - +
191C SER* 3.6 15.9 + - - -
213C ARG* 2.8 32.5 + - - -
216C LYS* 2.8 32.5 + - - +
217C ILE* 3.5 33.1 - - + +
220C ASP* 3.7 8.7 - - + +
221C ASN* 4.9 2.1 + - - +
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLN* 2.9 30.3 + - - -
184C ASP 3.1 14.3 + - - +
185C GLN* 3.0 14.1 + - + +
187C GLU* 1.3 77.1 - - - +
189C ASN* 1.3 64.1 + - - +
191C SER* 2.6 32.3 + - - -
192C LEU* 3.7 9.6 + - - +
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Residues in contact with ASN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MSE 6.1 1.3 - - - -
185A GLN* 5.2 0.9 + - - -
189A ASN* 2.8 35.5 + - - +
192A LEU* 3.7 18.2 - - - +
139C MSE 4.2 5.3 - - + +
170C MSE 3.6 24.0 - - + +
171C PRO 5.0 3.0 + - - -
172C TYR* 5.7 2.0 - - - +
185C GLN* 2.8 40.6 + - - +
186C LEU* 4.0 2.6 - - - +
188C GLU* 1.3 74.9 - - - +
190C ALA* 1.3 66.1 + - - +
192C LEU* 2.8 22.8 + - - +
193C PHE* 2.9 15.3 + - - +
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MSE 4.0 10.4 - - - -
186C LEU* 2.8 23.6 + - + +
187C GLU 3.9 3.8 - - - +
188C GLU 3.3 0.2 - - - -
189C ASN* 1.3 72.2 - - - +
191C SER* 1.3 56.9 + - - +
194C HIS* 2.9 23.6 + - - -
195C PRO* 3.2 23.6 - - + +
198C ILE* 4.7 0.9 - - + -
217C ILE* 4.0 10.8 - - + -
221C ASN* 3.1 32.1 - - - +
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLU 3.6 7.8 + - - -
188C GLU* 2.6 26.6 + - - -
189C ASN 3.0 0.2 - - - -
190C ALA* 1.3 78.8 - - - +
192C LEU* 1.3 66.9 + - - +
194C HIS* 3.1 24.1 + - - -
221C ASN* 3.4 12.7 + - - -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MSE 5.9 0.2 - - - +
169A SER 5.2 0.2 - - - +
170A MSE 3.6 17.4 - - + +
171A PRO* 3.6 39.0 - - + +
173A LYS* 4.0 32.8 - - + -
185A GLN* 4.0 17.9 - - - +
189A ASN* 3.7 26.7 - - - +
137C ARG* 4.6 1.4 + - - -
188C GLU* 4.1 11.9 - - - +
189C ASN* 2.8 12.8 + - - +
191C SER* 1.3 89.8 - - - +
193C PHE* 1.3 60.5 + - - +
194C HIS* 3.6 10.6 + - - -
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Residues in contact with PHE 193 (chain C).
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* 4.7 1.6 - - - -
170A MSE 4.2 6.7 - - - -
193A PHE* 3.6 33.0 - + - -
137C ARG* 2.8 75.1 + - + +
138C ILE 3.9 14.1 - - - -
139C MSE 3.8 22.0 - - + -
168C GLU* 3.7 17.3 - - + -
169C SER 4.1 2.9 - - - -
170C MSE 3.6 41.3 - - + -
189C ASN 2.9 13.7 + - - +
190C ALA 4.6 0.2 - - - +
192C LEU* 1.3 78.7 - - - +
194C HIS* 1.3 69.5 + - - +
195C PRO 4.2 4.0 - - - -
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Residues in contact with HIS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MSE 4.3 28.5 - - + -
155A THR* 4.0 17.8 + - - +
156A ASP* 3.4 47.4 + - + +
171A PRO* 5.7 3.8 - - + -
137C ARG* 3.8 10.1 - - - +
190C ALA 2.9 11.0 + - - -
191C SER 3.1 19.9 + - - -
192C LEU* 3.6 17.4 + - - -
193C PHE* 1.3 84.0 + - - +
195C PRO* 1.3 73.1 - - - +
196C LYS* 3.6 0.9 + - - +
221C ASN* 5.0 7.0 - - - +
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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