Contacts of the helix formed by residues 154 - 167 (chain B) in PDB entry 3PEJ
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 THR 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B MET* 1.3 74.8 - - - +
155B LYS* 1.3 59.0 + - - +
156B VAL* 3.7 7.7 + - - +
157B ASP* 3.2 34.5 + - - +
158B LEU* 2.9 30.6 + - - +
210B ASN* 3.4 27.8 - - - +
212B ASP* 4.2 12.1 - - + +
213B ASP* 3.6 28.7 - - + -
216B TYR* 5.3 1.6 - - - -
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Residues in contact with LYS 155 (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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71B SER* 5.9 7.0 - - - +
154B THR* 1.3 70.5 - - - +
156B VAL* 1.4 58.0 + - + +
158B LEU* 3.5 7.4 + - - +
159B ILE* 2.9 57.0 + - + +
213B ASP* 3.1 17.8 + - - +
216B TYR* 3.6 50.9 + - + +
228B ILE* 4.4 15.9 - - + -
229B TYR* 5.8 0.8 - - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 3.1 7.5 - - - +
155B LYS* 1.4 76.5 - - + +
157B ASP* 1.4 62.9 + - - +
159B ILE* 4.1 4.3 - - - +
160B ASN* 2.8 43.6 + - + +
213B ASP* 4.7 1.5 + - - +
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Residues in contact with ASP 157 (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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152B GLY 4.9 2.1 - - - +
153B MET* 4.6 4.3 - - + -
154B THR* 3.2 39.6 + - - +
156B VAL* 1.4 80.2 - - - +
158B LEU* 1.3 57.7 + - - +
160B ASN* 4.2 3.3 - - - +
161B ASN* 3.0 33.4 + - - +
210B ASN* 5.0 3.8 + - - -
1001B BC2 3.4 35.7 - - - +
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Residues in contact with LEU 158 (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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153B MET* 3.8 24.0 - - + +
154B THR 2.9 16.4 + - - +
155B LYS* 3.7 6.7 - - - +
157B ASP* 1.3 74.1 - - - +
159B ILE* 1.3 59.4 + - - +
161B ASN* 4.0 2.3 - - + +
162B LEU* 3.0 40.6 + - + +
208B THR* 4.4 19.3 - - + -
216B TYR* 5.1 7.4 - - + -
218B TRP* 3.7 52.7 - - + -
228B ILE* 4.0 26.2 - - + -
1001B BC2 4.7 3.6 - - + -
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Residues in contact with ILE 159 (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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71B SER 5.6 7.4 - - - +
155B LYS* 2.9 49.3 + - + +
156B VAL* 4.1 4.5 - - - +
158B LEU* 1.3 71.7 - - - +
160B ASN* 1.4 62.7 + - - +
162B LEU* 3.5 4.4 + - - +
163B GLY* 3.0 24.9 + - - -
228B ILE* 4.0 23.6 - - + -
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Residues in contact with ASN 160 (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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156B VAL* 2.8 28.7 + - + +
157B ASP* 4.2 3.6 - - - +
159B ILE* 1.4 75.7 - - + +
161B ASN* 1.4 55.7 + - - +
163B GLY* 3.1 4.1 + - - -
164B THR* 3.0 33.7 + - + +
167B LYS* 5.0 0.7 + - - -
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Residues in contact with ASN 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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157B ASP 3.0 21.7 + - - +
158B LEU* 4.1 4.0 - - + +
160B ASN* 1.4 71.5 - - - +
162B LEU* 1.4 64.9 + - + +
164B THR* 2.7 25.7 + - - -
165B ILE* 3.3 15.9 + - + +
1001B BC2 3.6 39.5 - - + +
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Residues in contact with LEU 162 (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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77B TYR* 3.4 37.7 - - + +
158B LEU* 3.0 22.0 + - + +
159B ILE* 3.9 4.5 - - - +
161B ASN* 1.4 76.3 - - + +
163B GLY* 1.3 59.7 + - - +
165B ILE* 3.7 8.8 + - + -
166B ALA* 3.4 17.2 + - - +
195B TYR* 3.7 6.5 - - - +
218B TRP* 3.4 54.3 - - + +
226B PHE* 3.9 17.3 - - + -
228B ILE* 3.8 24.5 - - + -
1001B BC2 5.6 0.9 - - + -
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Residues in contact with GLY 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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76B GLN* 5.7 0.2 + - - -
159B ILE 3.0 13.9 + - - -
160B ASN* 3.1 6.9 + - - -
162B LEU* 1.3 77.1 - - - +
164B THR* 1.4 61.7 + - - +
166B ALA* 3.6 7.7 + - - +
167B LYS* 3.3 33.8 + - - +
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Residues in contact with THR 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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160B ASN* 3.0 17.6 + - + +
161B ASN* 2.7 25.7 + - - +
163B GLY* 1.4 73.8 - - - +
165B ILE* 1.4 60.7 + - - +
167B LYS* 3.5 22.3 + - - +
168B SER* 2.6 36.5 + - - -
1001B BC2 6.1 0.9 - - - -
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Residues in contact with ILE 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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77B TYR* 4.2 9.0 - - + -
80B GLU* 3.4 16.8 - - + +
81B VAL* 4.2 4.3 - - + -
84B LEU* 4.2 23.1 - - + -
161B ASN* 3.3 15.8 + - + +
162B LEU* 3.7 15.9 - - + +
163B GLY 3.4 0.2 - - - -
164B THR* 1.4 77.7 + - - +
166B ALA* 1.3 61.6 + - - +
168B SER* 3.4 16.0 + - - -
170B THR* 5.1 1.8 + - - -
191B GLY 4.3 10.3 - - - +
192B VAL* 4.8 6.7 - - + -
195B TYR* 3.5 32.5 - - + +
1001B BC2 3.7 31.4 - - + +
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Residues in contact with ALA 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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74B SER* 5.7 2.2 - - - -
76B GLN* 3.3 31.0 - - + +
77B TYR* 3.7 37.2 - - + +
80B GLU* 4.1 11.3 - - - +
162B LEU 3.4 15.2 + - - +
163B GLY* 3.7 9.0 - - - +
164B THR 3.4 0.2 - - - -
165B ILE* 1.3 79.7 - - - +
167B LYS* 1.3 57.9 + - - +
169B GLY 4.8 2.1 + - - -
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Residues in contact with LYS 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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76B GLN* 3.3 24.0 - - - +
160B ASN 5.0 0.6 + - - -
163B GLY 3.3 21.9 + - - +
164B THR* 3.5 28.2 - - - +
165B ILE 3.4 0.2 - - - -
166B ALA* 1.3 75.1 - - - +
168B SER* 1.4 59.5 + - - +
169B GLY 3.7 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