Contacts of the helix formed by residues 157 - 170 (chain B) in PDB entry 1PT6
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 PRO 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 5.1 0.4 - - - -
156B TYR* 1.3 110.2 - - + +
158B TRP* 1.3 64.1 + - - +
159B ASP* 4.3 12.8 - - + +
160B SER* 3.0 40.8 + - - +
161B VAL* 4.0 2.1 + - - +
317B GLU* 4.3 5.9 - - + +
318B LEU* 4.6 18.2 - - + -
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Residues in contact with TRP 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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149B LEU* 4.3 16.8 - - + -
150B ASP 3.7 23.3 - - - -
151B GLY* 4.0 8.1 - - - -
155B ILE* 3.9 15.1 + - + -
156B TYR* 4.0 5.1 - - - +
157B PRO* 1.3 70.8 - - - +
159B ASP* 1.3 60.5 + - - +
161B VAL* 2.9 50.1 + - + +
162B THR* 3.1 22.2 + - + +
185B GLN* 3.8 26.9 - - - -
212B ILE* 3.0 32.3 + - + -
213B VAL* 4.5 1.1 - - - -
214B GLN* 3.5 50.7 - - + +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PRO* 3.2 12.2 + - + +
158B TRP* 1.3 78.7 + - - +
160B SER* 1.3 57.7 + - - +
162B THR* 3.2 13.3 + - - +
163B ALA* 2.9 30.1 + - - +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PRO* 3.0 20.6 + - - +
159B ASP* 1.3 78.4 - - - +
161B VAL* 1.3 58.5 + - - +
163B ALA* 3.7 5.8 + - - +
164B PHE* 3.1 25.8 + - - +
317B GLU* 3.5 27.4 - - - -
318B LEU* 3.2 35.6 + - - +
320B LEU* 4.3 4.4 - - - +
321B VAL* 4.5 5.2 - - - +
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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
----------------------------------------------------------
149B LEU* 4.2 22.9 - - + -
155B ILE* 3.7 30.7 - - + -
157B PRO 4.7 1.3 - - - +
158B TRP* 2.9 44.3 + - + +
160B SER* 1.3 77.8 - - - +
162B THR* 1.3 58.9 + - - +
164B PHE* 3.3 6.8 + - + +
165B LEU* 3.0 29.2 + - + +
251B VAL* 5.9 2.9 - - + -
281B ILE* 5.3 3.6 - - + -
317B GLU* 5.4 1.8 - - + -
320B LEU* 4.2 20.6 - - + -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TRP* 3.1 29.1 + - + +
159B ASP* 3.2 25.5 + - - -
161B VAL* 1.3 76.4 - - - +
163B ALA* 1.3 56.7 + - - +
165B LEU* 3.3 13.0 + - + +
166B ASN* 2.9 28.2 + - - +
209B ALA 3.6 24.2 - - - +
210B LYS* 4.3 17.3 + - - +
212B ILE* 3.8 9.6 - - + +
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Residues in contact with ALA 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 ASP 2.9 19.2 + - - +
160B SER* 3.8 7.6 - - - +
162B THR* 1.3 76.7 + - - +
164B PHE* 1.3 60.5 + - - +
166B ASN* 3.3 6.9 + - - +
167B ASP* 3.0 32.7 + - - +
321B VAL* 3.9 15.3 - - + -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 5.2 1.6 - - + -
149B LEU* 5.1 0.9 - - + -
160B SER 3.1 15.6 + - - +
161B VAL* 3.3 14.8 - - + +
163B ALA* 1.3 72.3 - - - +
165B LEU* 1.3 82.7 + - + +
167B ASP* 3.3 1.7 + - - +
168B LEU* 3.0 35.9 + - + +
249B VAL* 4.7 2.7 - - + -
251B VAL* 4.0 20.0 - - + -
279B ILE* 3.7 21.8 - - + -
320B LEU* 3.6 52.3 - - + -
321B VAL* 3.8 9.8 - - + +
323B ILE* 4.2 4.9 - - + -
324B VAL* 3.6 16.8 - - + +
327B LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 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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147B ILE* 3.9 36.8 - - + -
149B LEU* 4.0 24.7 - - + -
158B TRP* 5.9 0.2 - - + -
161B VAL* 3.0 21.9 + - + +
162B THR* 3.3 17.5 + - + +
164B PHE* 1.3 92.1 - - + +
166B ASN* 1.3 63.6 + - - +
168B LEU* 4.7 2.0 - - + -
169B LEU* 3.0 35.0 + - + +
183B ILE* 4.3 7.4 - - + -
209B ALA* 4.1 29.8 - - + +
212B ILE* 4.5 8.1 - - + -
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Residues in contact with ASN 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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162B THR 2.9 13.8 + - - +
163B ALA* 3.3 11.6 + - - +
165B LEU* 1.3 76.1 - - - +
167B ASP* 1.3 78.1 + - - +
170B LYS* 2.9 48.9 + - - +
206B LEU* 3.5 22.0 - - - +
209B ALA* 5.3 2.4 - - - +
210B LYS* 3.5 32.1 + - + +
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Residues in contact with ASP 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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163B ALA* 3.0 18.9 + - - +
164B PHE* 4.0 2.5 - - - +
166B ASN* 1.3 98.7 + - - +
168B LEU* 1.3 64.5 + - - +
170B LYS* 3.6 32.3 + - - +
171B ARG* 3.9 12.8 + - - +
321B VAL* 3.7 21.3 - - - +
324B VAL* 3.8 23.2 - - + +
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Residues in contact with LEU 168 (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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145B ILE* 6.2 0.7 - - + -
147B ILE* 4.3 24.5 - - + -
164B PHE* 3.0 30.9 + - + +
165B LEU* 3.9 3.4 - - - +
167B ASP* 1.3 76.7 - - - +
169B LEU* 1.3 58.3 + - + +
171B ARG* 2.8 30.2 - - - +
172B MET* 3.8 16.5 - - + +
249B VAL* 5.1 4.0 - - + -
324B VAL* 4.0 17.0 - - + +
327B LEU* 3.8 32.8 - - + -
328B GLY* 4.0 26.9 - - - +
331B ILE* 4.2 12.8 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.0 15.0 - - + -
165B LEU* 3.0 30.3 + - + +
168B LEU* 1.3 74.6 - - + +
170B LYS* 1.3 59.9 + - - +
171B ARG 3.2 2.9 - - - -
172B MET* 3.0 37.7 + - + +
174B ILE* 4.1 2.0 - - + +
181B VAL* 3.8 35.9 - - + -
183B ILE* 4.6 8.5 - - + -
202B THR* 3.5 10.6 - - - +
205B VAL* 3.7 25.4 - - + -
206B LEU* 3.9 11.9 - - + -
209B ALA* 4.0 21.1 - - + -
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Residues in contact with LYS 170 (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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166B ASN* 2.9 40.3 + - - +
167B ASP* 3.6 26.8 + - - +
168B LEU 3.4 0.2 - - - -
169B LEU* 1.3 76.2 - - - +
171B ARG* 1.3 60.9 + - - +
172B MET 3.3 3.9 + - - +
202B THR* 4.1 9.5 - - - +
206B LEU* 3.7 24.2 - - + +
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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