Contacts of the helix formed by residues 159 - 167 (chain B) in PDB entry 3EU9
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 4.7 0.7 - - - -
150B PRO 3.8 7.4 - - - -
151B SER* 3.1 20.6 + - - -
152B LEU 3.2 13.1 + - - -
153B ILE* 3.7 10.9 - - - +
157B GLY 4.0 0.4 + - - -
158B CYS* 1.3 72.6 - - - +
160B CYS* 1.3 67.5 + - - +
161B ILE* 3.4 2.9 - - - -
162B HIS* 3.1 29.4 + - - -
163B LEU* 3.0 27.3 + - - +
185B MET* 4.5 9.0 - - - -
187B ASP* 5.5 0.9 - - - -
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Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 3.6 24.2 - - - -
129B HIS* 3.6 20.4 - - - -
132B THR* 3.3 32.8 - - - +
140B VAL* 6.1 0.2 - - - -
150B PRO* 3.1 35.9 + - + +
152B LEU 4.3 0.6 + - - -
159B SER* 1.3 75.6 - - - +
161B ILE* 1.3 58.0 + - - +
163B LEU* 3.1 4.1 + - - -
164B ALA* 2.8 28.4 + - - +
176B LEU* 3.7 12.3 - - + -
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Residues in contact with ILE 161 (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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150B PRO 4.7 0.8 + - - -
159B SER* 4.4 1.3 - - - -
160B CYS* 1.3 79.3 - - - +
162B HIS* 1.3 84.0 + - + +
164B ALA* 3.5 1.9 + - - +
165B ALA* 3.0 27.2 + - - +
173B VAL* 4.7 11.8 - - + +
176B LEU* 3.5 18.7 - - + +
177B ILE* 3.7 33.4 - - + -
181B GLN* 4.2 14.4 - - + -
182B ASP 4.0 13.7 - - - +
183B VAL* 4.6 0.9 - - - -
185B MET* 4.1 16.2 - - + -
193B PRO* 3.8 29.2 - - + -
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Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B CYS* 4.1 7.0 - - + -
159B SER* 3.1 45.1 + - - +
160B CYS 3.2 0.8 - - - -
161B ILE* 1.3 83.8 - - + +
163B LEU* 1.3 59.7 + - - +
165B ALA* 3.6 3.5 - - - +
166B GLN* 2.9 34.2 + - - +
185B MET* 2.9 34.3 + - + -
186B MET 4.0 1.8 - - - -
187B ASP* 3.3 30.0 + - + +
191B MET 3.6 16.2 - - - -
193B PRO* 4.2 10.8 - - + -
196B TRP* 3.8 25.0 - + + +
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Residues in contact with LEU 163 (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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129B HIS* 3.8 44.4 - - + +
132B THR* 3.9 9.9 - - + -
133B ARG* 3.9 33.7 - - + +
154B ASP* 3.6 26.5 - - - +
158B CYS* 4.0 10.8 - - + -
159B SER 3.0 19.3 + - - +
160B CYS* 3.4 7.9 - - - +
162B HIS* 1.3 75.2 - - - +
164B ALA* 1.3 65.3 + - - +
166B GLN* 3.4 14.1 + - - +
167B PHE* 3.1 33.3 + - + +
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Residues in contact with ALA 164 (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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132B THR* 3.6 15.3 - - + +
160B CYS 2.8 19.7 + - - +
161B ILE* 3.8 5.8 - - - +
163B LEU* 1.3 73.1 - - - +
165B ALA* 1.3 59.3 + - - +
167B PHE 3.9 0.2 - - - -
168B GLY 3.4 1.6 + - - -
169B HIS* 2.8 42.9 + - + +
172B ILE* 3.8 20.2 - - + -
173B VAL* 3.7 19.4 - - + +
176B LEU* 4.4 0.4 - - + -
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Residues in contact with ALA 165 (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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161B ILE 3.0 18.5 + - - +
162B HIS 3.6 4.3 - - - +
163B LEU 3.1 0.2 - - - -
164B ALA* 1.3 76.1 - - - +
166B GLN* 1.3 63.9 + - - +
168B GLY* 3.2 10.6 + - - -
173B VAL* 4.0 11.2 - - + +
193B PRO* 3.5 36.1 - - + +
196B TRP* 4.3 2.2 - - + -
197B ALA* 3.8 13.8 - - + +
201B THR* 3.3 12.1 - - - +
206B PRO* 4.2 4.9 - - + +
210B LEU* 5.1 2.9 - - + -
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Residues in contact with GLN 166 (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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133B ARG* 4.9 3.8 - - - +
156B GLU* 5.4 2.8 + - - -
158B CYS* 3.9 13.6 - - - -
162B HIS 2.9 22.4 + - - +
163B LEU* 3.4 18.6 - - - +
165B ALA* 1.3 76.7 - - - +
167B PHE* 1.3 84.2 + - + +
168B GLY 3.4 0.9 - - - -
196B TRP* 3.7 42.3 - - + -
200B ARG* 3.3 63.6 + - + +
201B THR* 4.0 3.7 - - - +
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Residues in contact with PHE 167 (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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75A GLU* 4.9 17.0 - - + -
133B ARG* 3.1 58.6 - - + -
163B LEU* 3.1 29.3 + - + +
166B GLN* 1.3 100.4 - - + +
168B GLY* 1.3 63.6 + - - +
169B HIS* 3.3 31.0 + - + +
200B ARG* 3.7 20.2 - - - -
201B THR* 4.3 1.3 - - - -
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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