Contacts of the helix formed by residues 152 - 163 (chain B) in PDB entry 2PI8
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 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B TYR* 3.5 8.2 - - - -
150B SER* 3.1 17.3 + - - -
151B ASN* 1.3 83.6 + - - +
153B LEU* 1.3 64.7 + - - +
154B MSE 3.4 9.5 + - - +
155B ASP* 3.3 41.5 + - - +
156B ASN* 3.5 12.0 + - - +
212B ARG* 5.3 0.5 + - - -
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Residues in contact with LEU 153 (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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118B TYR* 3.8 36.1 - - + -
119B PRO* 6.4 0.2 - - + -
137B TYR* 3.9 32.3 + - + +
152B SER* 1.3 71.3 + - - +
154B MSE 1.3 61.1 + - - +
156B ASN* 3.5 9.8 + - + +
157B PHE* 3.1 25.8 + - - +
220B GLU* 3.3 27.3 + - - +
223B VAL* 4.7 5.2 - - + -
224B ARG* 3.8 33.9 - - + +
227B LEU* 3.6 15.9 - - + +
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Residues in contact with MSE 154 (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 SER* 3.2 9.6 + - - +
153B LEU* 1.3 78.1 - - - +
155B ASP* 1.3 61.6 + - - +
157B PHE* 3.2 8.2 + - - +
158B ILE* 2.8 53.3 + - + +
211B ILE* 3.4 44.0 - - + +
212B ARG* 4.3 17.5 - - + +
214B TRP* 4.9 5.8 - - + -
215B GLY* 4.0 18.8 - - - +
223B VAL* 4.1 20.0 - - + +
226B LEU* 5.3 1.6 - - + -
227B LEU* 4.1 21.9 - - + +
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Residues in contact with ASP 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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104B PRO* 5.4 1.0 - - - +
106B ILE* 3.2 37.1 - - + +
107B GLN 5.6 0.3 + - - -
151B ASN* 4.1 8.7 - - - +
152B SER* 3.3 28.8 + - - +
153B LEU 3.4 0.2 - - - -
154B MSE 1.3 77.5 - - - +
156B ASN* 1.3 58.1 + - - +
158B ILE* 3.3 2.3 + - - +
159B MSE 2.9 25.3 + - - -
212B ARG* 2.9 40.9 + - - +
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Residues in contact with ASN 156 (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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106B ILE* 4.0 8.5 - - - +
118B TYR* 3.2 27.3 + - - +
119B PRO 3.7 13.1 + - - +
120B ILE* 3.9 12.9 - - - +
133B ARG* 5.5 1.8 - - - +
137B TYR* 6.1 0.7 - - - +
150B SER* 2.6 35.7 + - - -
152B SER 3.5 3.2 + - - +
153B LEU* 3.7 14.4 - - + +
154B MSE 3.3 0.4 - - - -
155B ASP* 1.3 77.0 - - - +
157B PHE* 1.3 57.5 + - - +
159B MSE 3.8 14.3 - - + +
160B ASP* 2.9 27.6 + - - +
236B PHE* 5.2 0.5 - - - -
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Residues in contact with PHE 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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133B ARG* 3.5 26.2 - - - +
153B LEU 3.1 14.4 + - - +
154B MSE 3.2 14.8 + - - +
156B ASN* 1.3 76.5 - - - +
158B ILE* 1.3 63.0 + - + +
160B ASP* 3.1 8.0 - - - +
161B VAL* 3.0 47.0 + - + +
188B TYR* 5.2 2.9 - + - -
191B ILE* 3.3 36.1 - - + -
208B MSE 6.6 0.2 - - - -
211B ILE* 5.9 4.3 - - + -
227B LEU* 3.5 51.6 - - + -
230B ASN* 3.5 26.7 - - + -
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Residues in contact with ILE 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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102B TYR* 3.7 23.1 - - + +
104B PRO* 5.1 2.7 - - + -
154B MSE 2.8 37.5 + - + +
155B ASP* 3.8 4.5 - - - +
157B PHE* 1.3 75.4 - - + +
159B MSE 1.3 61.0 + - - +
161B VAL* 3.1 7.9 + - - +
162B GLN* 2.9 52.2 + - + +
208B MSE 5.1 26.0 - - + +
211B ILE* 5.9 1.8 - - + -
212B ARG* 3.2 42.6 - - + +
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Residues in contact with MSE 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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104B PRO* 4.0 15.0 - - + +
106B ILE* 3.5 25.8 - - + -
120B ILE* 3.9 26.2 - - + -
155B ASP 2.9 17.3 + - - +
156B ASN* 3.8 15.0 - - + +
158B ILE* 1.3 76.6 - - - +
160B ASP* 1.3 61.4 + - - +
162B GLN* 3.3 1.2 + - - -
163B GLY 3.0 19.9 + - - -
164B SER 3.5 25.7 + - - +
165B GLY* 4.2 13.7 - - - +
167B ILE* 4.0 17.5 - - - -
178B PHE* 5.0 2.9 - - - -
236B PHE* 3.6 33.3 - - + -
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Residues in contact with ASP 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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133B ARG* 2.9 31.0 + - - +
156B ASN 2.9 16.2 + - - +
157B PHE* 3.1 14.8 - - - +
159B MSE 1.3 79.8 - - - +
161B VAL* 1.3 59.7 + - + +
163B GLY* 3.5 7.6 + - - -
188B TYR* 5.9 1.6 - - - -
230B ASN* 4.9 3.3 + - - -
232B SER* 4.4 2.1 + - - +
233B PHE* 3.9 8.5 + - - -
234B VAL* 2.9 55.9 + - - +
236B PHE* 4.0 11.9 - - + -
3F NAG 5.2 2.8 + - - +
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Residues in contact with VAL 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 PHE* 3.0 37.6 + - + +
158B ILE* 3.1 8.3 + - - +
160B ASP* 1.3 79.0 - - + +
162B GLN* 1.3 72.5 + - - +
163B GLY 3.4 0.3 + - - -
188B TYR* 4.2 23.6 - - + +
208B MSE 5.4 10.3 - - + -
230B ASN* 5.4 0.4 - - - +
2F NAG 3.3 22.7 + - - +
3F NAG 2.6 48.2 + - + -
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Residues in contact with GLN 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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101B TYR* 3.2 24.1 - - + +
102B TYR* 3.2 52.6 + - + +
104B PRO* 4.0 10.5 - - + -
158B ILE* 2.9 40.1 + - + +
159B MSE 3.3 4.9 + - - +
161B VAL* 1.3 82.4 - - - +
163B GLY* 1.3 58.4 + - - +
164B SER 3.4 11.2 + - - +
208B MSE 5.3 1.2 - - - +
2F NAG 3.0 34.7 + - - +
3F NAG 3.4 21.2 + - - +
4F NAG 4.2 4.5 - - - +
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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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159B MSE 3.0 8.3 + - - -
160B ASP 3.5 7.1 + - - -
161B VAL 3.2 3.2 - - - -
162B GLN* 1.3 78.0 - - - +
164B SER* 1.3 61.3 + - - +
180B TYR* 3.3 38.4 - - - +
234B VAL* 5.2 0.2 - - - -
236B PHE* 3.5 10.1 - - - -
3F NAG 3.8 16.4 - - - -
4F NAG 3.4 3.8 - - - -
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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