Contacts of the helix formed by residues 173 - 186 (chain B) in PDB entry 2PJ7
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 GLU 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR* 2.5 36.4 + - + +
131B SER* 2.6 25.8 + - - -
141B THR* 3.5 31.6 + - + -
143B PRO* 5.6 0.7 - - + -
146B ASN* 3.1 18.6 + - + +
171B GLU 4.2 0.4 - - - -
172B SER* 1.3 84.9 + - - +
174B LYS* 1.3 66.0 + - - +
175B GLU* 3.8 12.5 - - - +
176B THR* 3.1 12.0 + - + +
177B LYS* 3.1 25.2 + - - +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 5.9 0.4 + - - -
122A LYS* 6.3 1.2 - - - +
40B THR* 2.9 45.3 + - - +
41B THR 3.2 19.9 + - - +
42B PHE* 4.1 16.6 + - + +
44B GLY* 5.5 1.0 - - - -
172B SER 3.8 2.3 + - - +
173B GLU* 1.3 71.4 - - - +
175B GLU* 1.3 65.1 + - - +
177B LYS* 3.6 5.8 + - - +
178B ALA* 3.0 29.6 + - - +
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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
----------------------------------------------------------
41B THR* 3.2 25.0 - - + +
42B PHE* 3.1 27.9 + - - +
47B ILE* 3.9 11.6 - - + +
111B LEU* 3.6 51.8 - - + +
112B ASN* 4.9 4.9 - - - +
114B ASP* 3.5 8.5 + - - +
129B THR* 4.4 16.5 - - + +
173B GLU* 3.8 15.1 - - + +
174B LYS* 1.3 83.4 + - - +
176B THR* 1.3 63.2 + - + +
178B ALA* 3.3 3.6 + - - +
179B LEU* 3.1 16.6 + - - +
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Residues in contact with THR 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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111B LEU* 5.0 3.6 - - + -
143B PRO* 3.8 26.9 - - + +
146B ASN* 2.6 34.5 + - + +
147B PHE* 3.6 38.4 - - + -
171B GLU* 3.6 7.5 - - - -
173B GLU* 3.1 13.1 + - + +
175B GLU* 1.3 76.1 - - + +
177B LYS* 1.3 62.4 + - - +
179B LEU* 3.3 2.6 + - - +
180B ALA* 2.9 31.2 + - - +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA 5.1 0.8 + - - -
171B GLU* 2.8 51.9 + - - +
173B GLU 3.1 14.5 + - - +
174B LYS* 3.8 6.5 - - - +
176B THR* 1.3 82.7 + - - +
178B ALA* 1.3 57.1 + - - +
180B ALA 3.8 0.2 - - - -
181B ASP* 2.8 56.9 + - - +
184B ARG* 4.2 3.6 - - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.6 32.6 - - + +
39B GLY* 4.3 4.3 - - - -
40B THR 5.4 0.4 - - - +
47B ILE* 4.1 16.8 - - + -
174B LYS 3.0 18.7 + - - +
175B GLU 3.6 6.3 - - - +
176B THR 3.2 0.2 - - - -
177B LYS* 1.3 78.9 - - - +
179B LEU* 1.3 61.3 + - - +
181B ASP* 3.7 7.3 - - - +
182B PHE* 3.1 23.9 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.2 9.1 - - + +
63B PHE* 4.3 14.1 - - + -
65B ASP* 3.7 22.0 - - - +
68B PHE* 3.7 25.4 - - + -
108B LEU* 4.3 9.4 - - + -
111B LEU* 4.2 14.8 - - + -
147B PHE* 4.2 16.6 - - + -
175B GLU 3.1 13.6 + - - +
176B THR 3.7 6.7 - - - +
177B LYS 3.3 0.2 - - - -
178B ALA* 1.3 75.2 - - - +
180B ALA* 1.3 67.4 + - - +
182B PHE* 3.2 4.3 + - - +
183B ILE* 3.1 47.3 + - + +
192B TYR* 4.4 4.7 - - + +
254B SER* 5.6 0.4 - - - -
257B TRP* 4.7 1.3 - - + -
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Residues in contact with ALA 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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147B PHE* 4.4 6.5 - - + -
171B GLU* 3.6 33.0 - - + +
176B THR 2.9 18.5 + - - +
177B LYS 3.9 0.7 - - - +
179B LEU* 1.3 77.7 - - - +
181B ASP* 1.3 57.9 + - - +
184B ARG* 3.0 39.4 + - - +
257B TRP* 3.4 27.0 - - + -
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Residues in contact with ASP 181 (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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38B ILE 6.1 0.4 - - - +
177B LYS* 2.8 39.4 + - - +
178B ALA* 3.7 7.8 - - - +
180B ALA* 1.3 78.4 - - - +
182B PHE* 1.3 61.3 + - - +
184B ARG* 2.7 33.1 + - - +
185B ASN* 3.0 37.0 + - - +
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Residues in contact with PHE 182 (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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36B THR* 5.4 2.2 - - - -
38B ILE* 3.8 28.0 - - + -
49B LEU* 3.2 28.0 - - + -
63B PHE* 3.6 31.6 - + + -
106B TYR* 3.4 30.5 - + - -
178B ALA 3.1 17.6 + - - +
179B LEU* 3.2 4.2 + - - +
181B ASP* 1.3 77.7 - - - +
183B ILE* 1.3 65.1 + - - +
185B ASN* 3.1 6.2 + - + +
186B ASN* 2.9 55.6 + - + +
189B ILE* 4.7 1.6 - - + -
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Residues in contact with ILE 183 (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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63B PHE* 4.4 16.2 - - + -
179B LEU* 3.1 37.9 + - + +
182B PHE* 1.3 76.7 - - - +
184B ARG* 1.3 58.2 + - - +
186B ASN 3.1 1.9 + - - -
187B LEU* 2.9 36.4 + - + -
189B ILE* 4.1 20.4 - - + -
192B TYR* 4.0 26.9 - - + -
257B TRP* 3.9 26.7 - - + -
258B ALA* 5.0 2.9 - - + -
261B GLN* 5.5 0.7 - - + -
263B ILE* 3.9 24.7 - - + -
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU* 2.8 42.4 + - - -
177B LYS* 4.1 4.2 - - - +
180B ALA* 3.0 25.2 + - - +
181B ASP* 2.7 33.1 + - - +
183B ILE* 1.3 77.0 - - - +
185B ASN* 1.3 64.3 + - - +
186B ASN 3.3 0.5 + - - -
187B LEU* 3.6 20.3 + - + +
257B TRP* 3.6 27.8 - - + +
261B GLN* 4.2 12.1 - - - +
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Residues in contact with ASN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 3.0 30.7 + - - +
182B PHE* 3.1 8.3 + - + +
184B ARG* 1.3 78.9 - - - +
186B ASN* 1.3 69.0 + - - +
187B LEU 3.6 0.2 - - - -
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Residues in contact with ASN 186 (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 TYR* 4.0 14.0 + - + +
182B PHE* 2.9 56.1 + - + +
183B ILE 3.1 5.3 + - - -
185B ASN* 1.3 86.8 - - - +
187B LEU* 1.3 69.7 + - - +
188B SER* 3.0 23.5 + - - -
189B ILE* 3.3 25.6 + - + +
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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