Contacts of the helix formed by residues 171 - 183 (chain D) in PDB entry 2EHO
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 MSE 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C HIS* 3.0 43.6 - - + +
170C LEU* 5.3 0.7 - - - -
13D LEU* 3.9 24.7 - - + -
117D TYR* 3.4 29.8 - - + -
142D PHE* 3.7 31.0 - - + -
169D ASP* 3.1 21.0 + - - +
170D GLU* 1.3 76.7 - - - +
172D GLU* 1.3 64.7 + - + +
174D GLY* 3.6 3.4 + - - +
175D LEU* 3.3 26.5 + - + +
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Residues in contact with GLU 172 (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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109D LEU* 3.9 0.2 - - - +
117D TYR* 2.8 33.2 + - + -
142D PHE* 4.7 1.9 - - + -
145D ARG* 2.5 38.8 + - - +
149D ILE* 3.5 19.1 - - + +
168D LEU* 3.1 26.5 - - + +
169D ASP* 2.7 29.5 + - - +
171D MSE 1.3 87.1 - - + +
173D ARG* 1.3 53.9 + - - +
174D GLY 2.8 4.7 - - - -
175D LEU* 2.8 6.0 + - - +
176D PHE* 2.7 35.3 + - - +
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Residues in contact with ARG 173 (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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110D HIS* 3.5 31.6 + - - -
165D VAL* 2.8 35.7 + - + +
166D ALA* 3.9 7.5 - - - +
168D LEU* 3.4 23.4 + - + +
169D ASP 2.8 17.9 + - - +
170D GLU* 3.2 30.7 + - - +
172D GLU* 1.3 77.4 - - - +
174D GLY* 1.3 56.4 + - - +
176D PHE* 3.3 9.7 - - - +
177D GLN* 3.1 33.3 + - - +
104F PHE* 3.2 70.5 + - + +
105F HIS* 6.0 0.2 - - - -
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Residues in contact with GLY 174 (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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162C GLN* 4.6 2.9 - - - -
170D GLU 3.6 9.9 + - - -
171D MSE 3.6 7.1 + - - -
172D GLU 2.8 2.4 - - - -
173D ARG* 1.3 76.6 - - - +
175D LEU* 1.3 63.6 + - - -
176D PHE 3.1 0.7 - - - -
177D GLN* 3.1 14.4 + - - +
178D THR* 3.1 24.9 + - - -
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Residues in contact with LEU 175 (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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159C PHE* 3.8 38.4 - - + +
162C GLN* 3.9 32.7 + - + +
163C ALA* 4.1 13.7 - - + +
166C HIS* 4.8 4.2 - - + +
142D PHE* 3.9 33.0 - - + -
146D PHE* 4.9 4.3 - - + -
149D ILE* 4.2 20.9 - - + -
171D MSE 3.3 21.0 + - + +
172D GLU* 2.8 11.5 + - - +
174D GLY* 1.3 71.0 - - - +
176D PHE* 1.3 64.1 + - - +
178D THR* 3.2 4.0 + - - -
179D GLY 3.0 20.4 + - - -
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Residues in contact with PHE 176 (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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149D ILE* 4.4 6.2 - - - +
152D SER* 3.3 37.9 - - - -
153D SER* 3.5 18.0 - - - -
161D THR* 4.4 9.6 - - - -
165D VAL* 3.4 32.5 - - + -
168D LEU* 4.1 12.3 - - + -
172D GLU 2.7 10.6 + - - +
173D ARG* 3.3 14.4 - - - +
175D LEU* 1.3 77.3 - - - +
177D GLN* 1.3 66.9 - - - +
179D GLY 3.4 0.3 + - - -
180D GLN* 2.9 36.4 + - + +
100F ASN* 4.0 24.9 - - - -
103F ARG* 4.4 7.2 - - - -
104F PHE* 4.2 15.3 - + - -
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Residues in contact with GLN 177 (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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173D ARG 3.1 14.6 + - - +
174D GLY* 3.1 13.7 + - - +
176D PHE* 1.3 80.2 - - - +
178D THR* 1.3 51.5 + - - +
180D GLN* 2.7 30.0 + - - +
181D LYS* 2.7 18.4 + - - +
100F ASN* 4.2 12.1 - - + +
101F ALA* 4.7 6.4 + - - +
104F PHE* 3.1 36.5 - - + -
1005F SO4 3.6 25.8 + - - +
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Residues in contact with THR 178 (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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158C THR* 4.1 14.3 + - - -
159C PHE* 3.8 30.9 - - - +
162C GLN* 3.0 35.1 + - + +
174D GLY 3.1 6.6 + - - -
175D LEU* 3.5 7.6 - - - -
177D GLN* 1.3 76.8 - - - +
179D GLY* 1.3 60.4 + - - +
181D LYS* 3.0 34.4 + - + +
182D GLY* 3.3 5.9 + - - -
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Residues in contact with GLY 179 (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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159C PHE* 3.4 28.4 - - - -
153D SER* 3.6 15.4 - - - +
154D GLN* 3.4 12.0 - - - +
175D LEU 3.0 11.3 + - - -
178D THR* 1.3 78.9 - - - +
180D GLN* 1.3 58.2 + - - +
181D LYS 3.1 0.2 - - - -
182D GLY* 4.4 0.8 - - - -
183D LEU* 3.4 24.1 + - - +
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Residues in contact with GLN 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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152D SER 4.3 1.8 + - - -
153D SER* 3.1 24.4 + - - +
155D ASN 3.9 12.2 + - - +
156D ALA* 5.7 0.5 - - - -
157D TYR* 5.0 13.0 + - - +
176D PHE* 2.9 27.8 + - + +
177D GLN* 2.7 13.6 + - - +
179D GLY* 1.3 77.0 - - - +
181D LYS* 1.3 58.0 + - - +
183D LEU* 4.1 4.6 - - - +
184D ASN* 3.0 50.6 + - - +
100F ASN* 3.3 26.7 + - - +
1005F SO4 5.5 2.9 - - - +
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Residues in contact with LYS 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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158C THR* 5.9 8.5 - - - +
3D GLU 6.0 2.0 - - - +
177D GLN 2.7 8.1 + - - +
178D THR* 3.1 21.1 - - + +
180D GLN* 1.3 76.8 - - - +
182D GLY* 1.3 60.6 + - - +
183D LEU 3.2 1.1 - - - -
184D ASN* 3.0 6.0 + - - +
185D ASP* 2.8 31.0 + - + +
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Residues in contact with GLY 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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154C ASN 5.5 0.9 - - - -
155C THR* 4.0 26.1 - - - +
158C THR* 5.5 6.3 + - - -
178D THR 3.3 8.4 + - - -
179D GLY 3.8 1.1 + - - -
181D LYS* 1.3 75.7 - - - +
183D LEU* 1.3 56.3 + - - +
184D ASN 3.0 5.2 - - - -
185D ASP* 3.7 8.6 - - - +
186D PHE* 3.0 32.4 + - - +
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Residues in contact with LEU 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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155C THR 5.2 0.9 - - - +
153D SER 3.8 6.1 - - - +
154D GLN* 3.5 45.4 + - - +
155D ASN* 4.5 14.1 - - - +
156D ALA* 4.7 2.9 - - - +
179D GLY 3.4 18.6 + - - +
180D GLN* 4.3 6.5 - - - +
181D LYS 3.2 0.4 - - - -
182D GLY* 1.3 77.0 - - - +
184D ASN* 1.3 60.4 + - - +
185D ASP 3.5 0.2 - - - -
186D PHE* 4.4 7.6 - - + -
187D GLN* 2.9 47.5 + - + +
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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