Contacts of the helix formed by residues 156 - 171 (chain C) 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 SER 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C ILE* 4.0 13.3 - - - +
128C LEU* 4.2 13.7 - - - +
152C GLU 3.6 11.8 + - - -
153C ILE* 5.4 0.4 - - - -
155C THR* 1.3 87.0 + - - +
157C GLY* 1.3 68.8 + - - +
158C THR* 3.6 2.0 - - - -
159C PHE* 3.2 10.7 + - - +
160C LEU* 3.1 31.4 + - - +
154D GLN* 2.9 28.4 + - - +
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Residues in contact with GLY 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 6.5 0.7 - - - -
0C MSE 3.6 5.6 - - - -
153C ILE* 3.0 29.3 + - - +
154C ASN* 3.5 2.9 + - - -
156C SER* 1.3 80.7 - - - +
158C THR* 1.3 66.1 + - - +
160C LEU* 2.9 7.7 + - - +
161C THR* 2.7 27.8 + - - -
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Residues in contact with THR 158 (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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0C MSE 3.1 42.8 - - + +
154C ASN 3.9 12.3 + - - +
155C THR 5.4 0.5 - - - -
156C SER 4.7 1.2 + - - -
157C GLY* 1.3 69.3 + - - -
159C PHE* 1.3 62.2 + - - +
161C THR* 3.1 4.5 - - - -
162C GLN* 2.9 26.6 + - - +
178D THR* 4.1 16.8 + - - +
181D LYS* 5.9 8.6 - - - +
182D GLY* 5.5 5.9 - - - -
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Residues in contact with PHE 159 (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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156C SER* 3.2 12.2 + - - +
157C GLY 2.8 4.4 + - - -
158C THR* 1.3 72.7 + - - +
160C LEU* 1.3 80.6 + - + +
162C GLN* 2.8 16.4 + - - +
163C ALA* 3.0 10.9 + - - +
146D PHE* 3.8 27.4 - + - -
149D ILE 4.8 1.3 - - - -
150D MSE 3.4 38.4 - - + -
153D SER* 3.3 19.5 - - - -
154D GLN* 5.7 6.1 - - + +
175D LEU* 3.8 37.3 - - + +
178D THR* 3.8 11.5 - - + +
179D GLY* 3.4 33.9 - - - -
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Residues in contact with LEU 160 (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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205A LEU* 5.2 19.1 - - + -
128C LEU* 5.0 16.8 - - + +
129C ARG* 6.3 0.2 - - - -
132C ALA* 4.1 28.3 - - + -
153C ILE* 6.6 0.2 - - - -
156C SER* 3.3 27.8 - - - +
157C GLY* 2.9 10.5 + - - +
159C PHE* 1.3 94.5 - - + +
161C THR* 1.3 61.0 + - - +
163C ALA* 3.5 4.2 + - - -
164C LEU* 2.8 38.3 + - + +
146D PHE* 4.5 4.0 - - + -
150D MSE 4.1 10.8 - - - -
154D GLN* 6.1 1.3 - - - +
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Residues in contact with THR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 3.1 34.7 - - - +
171A VAL* 5.1 3.0 + - - -
205A LEU* 6.1 1.7 - - - +
0C MSE 2.9 25.2 - - + +
157C GLY* 2.7 21.2 + - - -
158C THR* 3.1 12.6 - - - -
159C PHE 2.9 0.2 + - - -
160C LEU* 1.3 78.7 - - - +
162C GLN* 1.3 62.8 + - + +
164C LEU* 3.4 4.0 + - - +
165C ASN* 3.1 34.4 + - - +
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Residues in contact with GLN 162 (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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158C THR* 2.9 17.5 + - - +
159C PHE 2.8 11.9 + - - +
161C THR* 1.3 68.9 - - + +
163C ALA* 1.3 57.9 + - - +
165C ASN* 2.5 36.7 + - - +
166C HIS* 3.0 28.0 + - - +
174D GLY 4.3 1.7 - - - +
175D LEU* 3.9 20.7 + - + +
178D THR* 3.0 34.4 + - + +
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Residues in contact with ALA 163 (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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159C PHE* 3.0 8.6 + - + +
160C LEU* 3.7 9.0 - - - +
162C GLN* 1.3 77.5 - - - +
164C LEU* 1.3 60.1 + - + +
166C HIS* 3.0 11.2 + - - +
167C MSE 3.0 39.1 + - + +
142D PHE* 4.2 5.1 - - + -
146D PHE* 3.4 35.4 - - + -
175D LEU* 4.1 14.2 - - + +
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Residues in contact with LEU 164 (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 TYR* 3.1 62.2 - - + +
205A LEU* 5.2 9.6 - - + -
135C PHE* 3.8 31.4 - - + +
136C VAL* 4.2 10.1 - - + -
139C GLN 5.5 0.4 - - - +
160C LEU* 2.8 34.0 + - + +
161C THR* 3.7 2.0 - - - +
162C GLN 3.1 1.0 - - - -
163C ALA* 1.3 79.2 - - + +
165C ASN* 1.3 61.1 + - - +
166C HIS 3.1 0.7 - - - -
167C MSE 3.2 36.1 + - + +
168C TYR* 3.4 2.4 + - - +
171C ARG* 5.4 2.0 - - - +
146D PHE* 5.7 0.7 - - + -
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Residues in contact with ASN 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 6.2 0.7 - - - -
168A ASP 4.1 1.2 - - - +
169A SER* 3.0 24.8 - - - -
170A TYR* 2.9 27.7 + - - +
161C THR* 3.1 35.4 + - - +
162C GLN* 2.5 20.7 + - - +
164C LEU* 1.3 71.4 - - - +
166C HIS* 1.3 64.1 + - + -
168C TYR* 5.4 2.7 - - - +
169C LYS* 3.2 32.0 + - - +
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Residues in contact with HIS 166 (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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162C GLN* 3.0 31.5 + - + +
163C ALA 3.0 7.6 + - - +
165C ASN* 1.3 88.3 - - + +
167C MSE 1.3 69.3 + - - +
169C LYS* 3.8 5.8 - - + -
170C LEU* 2.9 26.9 + - - +
13D LEU* 4.2 17.4 - - + +
142D PHE* 3.7 17.1 - - + -
171D MSE 3.0 45.6 - - + +
175D LEU* 4.8 5.8 - - + +
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Residues in contact with MSE 167 (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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136C VAL* 3.2 54.1 - - + +
139C GLN* 4.1 8.3 - - - +
163C ALA* 3.0 39.8 + - + +
164C LEU* 3.2 22.2 + - + +
166C HIS* 1.3 73.3 - - - +
168C TYR* 1.3 54.3 + - - +
169C LYS 2.7 3.3 + - - -
170C LEU* 2.6 9.2 + - - +
171C ARG* 2.5 66.0 + - - +
139D LEU* 4.1 4.4 - - - +
142D PHE* 3.9 17.5 - - + -
143D ILE* 4.0 11.7 - - + -
146D PHE* 4.9 0.4 - - + -
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Residues in contact with TYR 168 (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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168A ASP* 2.9 54.4 + - + -
170A TYR* 3.6 26.2 - + + +
207A ARG* 3.4 33.6 + - - -
164C LEU 3.4 1.9 + - - +
165C ASN* 5.4 2.7 - - - +
167C MSE 1.3 78.2 - - - +
169C LYS* 1.3 66.6 + - - +
171C ARG* 3.3 17.9 - - - +
172C THR* 2.7 42.0 + - + +
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Residues in contact with LYS 169 (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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166A ASP* 2.8 29.7 + - - -
168A ASP* 5.5 2.2 + - - +
165C ASN* 3.2 24.7 + - - +
166C HIS* 3.8 8.7 - - + +
167C MSE 2.7 5.7 + - - -
168C TYR* 1.3 94.0 - - - +
170C LEU* 1.3 52.6 + - - +
172C THR* 3.1 4.3 + - - -
173C ASN* 2.8 24.6 + - - -
11D GLY* 5.2 5.2 - - - +
13D LEU* 3.0 26.5 - - + +
14D GLY* 3.4 34.3 - - - +
15D PRO* 5.8 1.3 - - - -
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Residues in contact with LEU 170 (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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166C HIS 2.9 18.7 + - - +
167C MSE 2.6 7.7 + - - -
169C LYS* 1.3 70.7 - - - +
171C ARG* 1.3 53.7 + - - +
172C THR 2.9 5.8 - - - -
173C ASN* 2.7 31.9 + - + +
13D LEU* 4.0 38.8 - - + +
117D TYR* 3.7 21.3 - - + +
121D SER* 4.7 5.2 - - - -
138D LEU* 3.5 47.6 - - + +
139D LEU* 3.0 24.0 - - + +
142D PHE* 4.1 15.7 - - + -
171D MSE 5.3 0.2 - - - -
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Residues in contact with ARG 171 (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 TYR* 3.1 27.3 + - - -
139C GLN* 2.9 68.4 + - - +
164C LEU* 5.4 2.6 - - - +
167C MSE 2.5 38.7 + - - +
168C TYR* 3.3 23.5 - - - +
170C LEU* 1.3 70.5 - - - +
172C THR* 1.3 63.3 + - + +
173C ASN* 4.5 2.2 - - - -
139D LEU* 3.5 15.2 - - + +
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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