Contacts of the helix formed by residues 161 - 169 (chain B) in PDB entry 1PJS
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 LEU 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B TYR* 3.9 37.0 - - + +
158B ALA 3.0 7.2 + - - +
160B GLN* 1.3 96.0 - - - +
162B ARG* 1.3 68.8 + - - +
163B ALA 3.2 2.7 - - - -
164B ARG* 3.1 13.0 + - + +
165B VAL* 2.9 25.1 + - + +
178B PHE* 4.8 2.7 - - + -
179B TRP* 4.4 6.7 - - + -
182B PHE* 3.5 34.3 - - + -
204B THR* 4.1 14.6 - - + -
207B LEU* 5.4 2.5 - - + -
208B PHE* 4.0 27.8 - - + -
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Residues in contact with ARG 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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130A GLY 5.2 3.8 + - - -
131A THR 3.0 28.9 + - - -
132A SER* 4.5 5.1 - - - +
133A PRO* 4.6 9.1 - - - +
158B ALA* 3.1 14.0 + - - +
159B GLY* 3.6 29.6 + - - +
161B LEU* 1.3 75.8 - - - +
163B ALA* 1.3 64.2 + - - +
165B VAL* 3.3 3.3 + - - +
166B LYS* 3.1 53.5 + - - +
179B TRP* 4.1 19.7 - - + -
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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 GLY 4.9 1.4 + - - -
160B GLN 6.4 0.2 - - - -
161B LEU* 3.2 1.0 - - - -
162B ARG* 1.3 78.3 - - - +
164B ARG* 1.3 63.1 + - - +
166B LYS* 3.1 19.8 + - - +
167B LYS* 3.1 13.5 + - - +
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Residues in contact with ARG 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 GLN 5.7 0.4 - - - +
161B LEU* 3.1 16.0 + - + +
163B ALA* 1.3 79.0 - - - +
165B VAL* 1.3 60.8 + - - +
167B LYS* 3.5 9.8 + - + +
168B GLN* 3.2 48.7 + - + +
204B THR* 4.4 7.7 - - - +
205B GLU* 2.5 39.3 + - - +
208B PHE* 3.2 66.1 - - + +
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Residues in contact with VAL 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 LEU* 2.9 19.7 + - + +
162B ARG 3.5 7.4 - - - +
163B ALA 3.1 0.2 - - - -
164B ARG* 1.3 75.2 - - - +
166B LYS* 1.3 60.7 + - + +
167B LYS 3.1 0.4 - - - -
169B PHE* 3.0 41.2 + - + +
175B ARG* 3.8 27.6 - - + -
178B PHE* 3.5 38.4 - - + -
179B TRP* 3.9 21.1 - - + +
208B PHE* 3.8 11.7 - - + -
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Residues in contact with LYS 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 ARG* 3.1 40.4 + - + +
163B ALA* 3.1 9.3 + - - +
165B VAL* 1.3 76.4 - - + +
167B LYS* 1.3 61.7 + - - +
169B PHE 3.2 12.0 - - - +
170B ALA* 4.3 4.7 + - - +
175B ARG* 3.7 35.2 + - - +
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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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163B ALA 3.1 14.3 + - - +
164B ARG* 3.7 12.8 - - + +
165B VAL 3.1 0.4 - - - -
166B LYS* 1.3 82.1 - - - +
168B GLN* 1.3 63.3 + - + +
169B PHE 4.9 0.3 - - - -
170B ALA* 5.1 2.9 + - - +
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Residues in contact with GLN 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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164B ARG* 3.2 43.3 + - + +
167B LYS* 1.3 78.9 - - + +
169B PHE* 1.3 82.8 + - + +
170B ALA* 4.0 2.1 + - - -
174B GLU* 5.0 1.9 - - - +
208B PHE* 3.4 43.4 + - + +
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Residues in contact with PHE 169 (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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165B VAL* 3.0 32.9 + - + +
166B LYS 3.2 9.5 - - - +
168B GLN* 1.3 97.4 - - + +
170B ALA* 1.3 60.2 + - - +
171B THR 3.5 1.6 - - - -
174B GLU* 3.8 30.3 - - + -
175B ARG* 2.9 35.5 + - + -
178B PHE* 3.3 36.1 - + + -
207B LEU 5.2 2.9 - - - -
208B PHE* 4.4 16.2 - + - -
210B GLU 5.8 2.5 - - - -
212B LEU* 3.5 32.8 - - + -
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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