Contacts of the helix formed by residues 169 - 180 (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 GLY 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B GLU* 3.5 20.1 + - - -
166B ALA 4.8 1.8 + - - -
167B LYS 3.7 1.4 - - - -
168B SER* 1.3 77.8 - - - +
170B THR* 1.4 63.5 + - - +
171B SER* 3.2 3.6 - - - -
172B ASN* 3.1 35.7 + - - +
173B PHE* 3.5 10.2 - - - -
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Residues in contact with THR 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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80B GLU* 3.0 8.4 + - - -
84B LEU* 4.2 3.1 - - + -
165B ILE* 5.1 1.9 + - - -
168B SER* 3.4 17.6 + - - -
169B GLY* 1.4 71.6 - - - +
171B SER* 1.3 64.9 + - - +
173B PHE* 3.0 24.7 + - + +
174B LEU* 3.0 13.0 + - + +
190B PHE* 3.7 44.3 + - + -
192B VAL* 3.9 29.1 - - + +
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Residues in contact with SER 171 (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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80B GLU* 2.6 34.6 + - - -
83B ARG* 3.0 44.6 + - - -
84B LEU* 3.7 14.2 - - - +
87B ILE* 3.4 8.6 - - - +
169B GLY 4.3 0.9 - - - -
170B THR* 1.3 76.5 - - - +
172B ASN* 1.4 55.2 + - - -
174B LEU* 3.3 2.4 + - - -
175B GLU* 2.7 36.6 + - - +
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Residues in contact with ASN 172 (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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83B ARG* 2.6 32.4 + - - +
169B GLY* 3.1 23.1 + - - +
171B SER* 1.4 81.2 + - - +
173B PHE* 1.4 66.1 + - + +
175B GLU* 3.4 4.4 + - - +
176B ALA* 3.0 24.5 + - - +
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Residues in contact with PHE 173 (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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168B SER 4.6 9.2 - - - -
169B GLY 3.5 17.5 - - - -
170B THR* 3.0 16.4 + - + +
172B ASN* 1.4 78.8 - - + +
174B LEU* 1.4 51.8 + - - +
176B ALA* 3.4 6.3 + - - +
177B ILE* 2.9 41.4 + - + +
190B PHE* 3.9 31.0 - + + -
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Residues in contact with LEU 174 (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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84B LEU* 3.8 26.9 - - + +
87B ILE* 3.8 17.7 - - + -
88B ILE* 4.2 15.5 - - + -
170B THR* 3.0 16.6 + - + +
171B SER* 3.7 5.8 - - - +
173B PHE* 1.4 73.5 - - - +
175B GLU* 1.4 54.5 + - - +
177B ILE* 3.1 12.8 + - + +
178B SER* 2.8 35.3 + - - -
184B MET* 3.8 11.9 - - + +
186B LEU* 5.5 0.9 - - + -
187B ILE* 4.0 30.1 - - + +
190B PHE* 3.8 31.0 - - + -
192B VAL* 4.2 5.4 - - + -
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Residues in contact with GLU 175 (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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83B ARG* 2.8 41.6 + - - +
87B ILE* 3.7 17.6 - - + +
171B SER 2.7 21.1 + - - +
172B ASN* 3.6 5.6 - - - +
174B LEU* 1.4 70.7 - - - +
176B ALA* 1.3 57.4 + - - +
178B SER* 3.3 4.6 + - - -
179B LYS* 2.9 69.8 + - + +
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Residues in contact with ALA 176 (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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172B ASN 3.0 13.2 + - - +
173B PHE* 3.5 11.0 - - - +
175B GLU* 1.3 74.6 - - - +
177B ILE* 1.4 59.2 + - - +
179B LYS* 3.5 8.2 + - - +
180B SER* 2.8 33.6 + - - +
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Residues in contact with ILE 177 (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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173B PHE* 2.9 28.6 + - + +
174B LEU* 3.1 14.1 + - + +
176B ALA* 1.4 74.9 - - + +
178B SER* 1.3 57.5 + - - +
180B SER* 3.2 10.7 + - - -
182B GLY* 2.8 43.4 + - - -
183B ASP 3.3 28.3 - - - +
184B MET* 3.8 7.9 - - + -
186B LEU* 4.4 18.4 - - + -
190B PHE* 3.9 24.5 - - + -
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.2 11.3 - - - +
90B ASN* 4.2 12.4 + - - -
91B SER* 3.0 24.8 + - - -
174B LEU 2.8 19.9 + - - -
175B GLU* 3.6 4.7 - - - -
177B ILE* 1.3 73.3 - - - +
179B LYS* 1.3 61.8 + - - +
181B GLY* 3.1 14.4 + - - -
182B GLY 4.5 8.2 - - - +
184B MET* 4.5 1.8 - - - -
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Residues in contact with LYS 179 (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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175B GLU* 2.9 51.8 + - + +
176B ALA* 3.9 7.0 - - - +
177B ILE 3.4 0.2 - - - -
178B SER* 1.3 75.9 - - - +
180B SER* 1.4 59.5 + - - +
181B GLY 3.4 0.6 + - - -
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Residues in contact with SER 180 (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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176B ALA* 2.8 22.9 + - - +
177B ILE* 3.6 6.5 - - - -
178B SER 3.1 0.6 - - - -
179B LYS* 1.4 75.4 - - - +
181B GLY* 1.3 60.4 + - - +
182B GLY* 3.3 1.7 + - - -
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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