Contacts of the helix formed by residues 153 - 169 (chain D) in PDB entry 2PKG
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 CYS 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A GLU* 3.7 16.4 - - - +
258B ARG* 6.3 1.3 - - - -
100D TRP* 3.5 16.6 - - - -
151D ASP* 3.2 17.5 + - + -
152D LEU* 1.3 76.8 - - - +
154D GLU* 1.3 56.0 + - - +
155D GLY* 3.3 17.3 - - - -
156D THR* 2.8 40.4 + - - -
157D LEU* 3.0 9.0 + - - +
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A LYS* 3.1 32.9 + - - +
476A GLU* 4.3 0.4 + - - -
515A ASP* 4.8 14.0 - - - +
100D TRP* 3.3 41.2 - - + +
153D CYS* 1.3 73.2 - - - +
155D GLY* 1.3 56.5 + - - +
157D LEU* 3.6 10.9 - - + +
158D LEU* 2.7 44.6 + - + +
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D CYS* 2.9 12.5 + - - -
154D GLU* 1.3 79.7 - - - +
156D THR* 1.3 59.5 - - - +
158D LEU* 3.5 13.6 - - - +
159D LEU* 3.3 27.0 + - - +
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PHE* 4.1 4.7 - - + -
144D PHE* 3.7 12.3 - - + -
145D ARG* 3.7 21.8 - - + -
150D LEU* 3.3 28.1 - - + +
151D ASP* 2.6 31.9 + - - +
153D CYS* 2.8 19.2 + - - -
155D GLY* 1.3 70.4 - - - -
157D LEU* 1.3 64.8 + - - +
159D LEU* 3.2 11.4 + - - +
160D TRP* 3.0 20.8 + - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D VAL* 4.4 23.3 - - + -
97D CYS* 4.2 15.5 - - + -
100D TRP* 3.3 40.6 - - + -
115D LEU* 4.1 17.7 - - + -
141D PHE* 3.5 9.3 - - + -
153D CYS 3.0 6.9 + - - +
154D GLU* 3.1 17.2 + - + +
156D THR* 1.3 76.8 - - - +
158D LEU* 1.3 56.6 + - - +
160D TRP* 3.3 16.4 + - + +
161D CYS* 2.9 51.3 + - - -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLY* 6.0 4.7 - - - -
92D VAL* 4.5 22.4 - - + +
154D GLU* 2.7 39.4 + - + +
155D GLY* 3.5 13.9 - - - +
157D LEU* 1.3 75.8 - - + +
159D LEU* 1.3 65.4 + - + +
161D CYS* 3.1 10.3 + - - +
162D ASP* 2.9 31.9 + - - +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 4.1 10.8 - - + -
150D LEU* 3.7 27.4 - - + -
155D GLY 3.3 18.1 + - - +
156D THR* 3.2 9.8 + - - +
158D LEU* 1.3 80.9 - - + +
160D TRP* 1.3 61.9 + - - +
162D ASP* 3.2 14.3 + - + +
163D ILE* 3.2 24.1 + - - +
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Residues in contact with TRP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 3.6 27.6 - - + -
114D LEU* 3.9 8.1 - - + -
115D LEU* 3.4 35.9 - - + -
118D LEU* 3.9 9.9 - - + -
135D TRP* 4.2 4.7 - + - -
139D TYR 3.0 26.9 + - - -
140D CYS 3.8 0.4 - - - -
141D PHE* 3.5 31.2 - + + +
144D PHE* 3.6 46.1 - + + -
156D THR 3.0 12.9 + - - +
157D LEU* 3.5 17.5 - - + +
159D LEU* 1.3 71.4 - - - +
161D CYS* 1.3 86.9 + - - +
163D ILE* 2.9 5.2 + - - +
164D ILE* 2.8 39.3 + - + +
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Residues in contact with CYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLY 5.3 5.4 - - - +
92D VAL* 5.2 11.4 - - + -
96D TYR* 3.6 51.3 - - + -
157D LEU* 2.9 43.3 + - - -
158D LEU* 3.3 11.0 - - - +
160D TRP* 1.3 79.8 - - - +
162D ASP* 1.3 56.2 + - - +
164D ILE* 2.8 3.9 + - - +
165D GLY* 2.7 33.6 + - - -
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Residues in contact with ASP 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LEU* 2.9 23.4 + - - +
159D LEU* 3.2 16.3 + - + +
161D CYS* 1.3 76.1 - - - +
163D ILE* 1.3 60.7 + - + +
165D GLY* 3.5 1.8 + - - -
166D GLN* 3.2 35.9 + - - +
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D TRP* 3.6 31.4 - - + +
139D TYR* 5.2 2.2 - - + -
144D PHE* 4.2 15.7 - - + -
148D PHE* 6.2 2.5 - - + -
159D LEU 3.3 15.0 - - - +
160D TRP* 2.9 8.7 + - - +
162D ASP* 1.3 73.7 - - + +
164D ILE* 1.3 68.1 + - - +
165D GLY 3.0 1.7 + - - -
166D GLN* 3.3 27.0 + - + +
167D THR* 2.9 31.6 + - - +
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 4.1 10.1 - - + -
114D LEU* 3.5 31.0 - - + -
118D LEU* 4.6 5.6 - - + -
135D TRP* 4.6 1.8 - - + -
139D TYR* 3.8 35.9 - - + +
160D TRP* 2.8 60.8 + - + +
161D CYS 3.6 5.2 - - - +
163D ILE* 1.3 72.9 - - - +
165D GLY* 1.3 52.7 + - - +
167D THR* 3.3 5.0 + - + -
168D THR* 2.7 44.6 + - + -
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Residues in contact with GLY 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 4.0 15.4 - - - -
161D CYS 2.7 15.0 + - - -
162D ASP* 3.8 3.4 - - - -
163D ILE 3.0 0.8 - - - -
164D ILE* 1.3 75.4 - - - +
166D GLN* 1.3 63.1 + - - -
168D THR* 2.9 20.8 + - - -
169D TYR* 3.1 23.4 + - - -
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Residues in contact with GLN 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ASP* 3.2 25.7 + - - +
163D ILE* 3.3 29.4 + - + +
165D GLY* 1.3 73.4 - - - +
167D THR* 1.3 62.9 + - - +
169D TYR* 3.4 19.7 + - - +
170D ARG 3.8 6.2 - - - -
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D TYR* 3.6 43.8 + - + +
163D ILE* 2.9 15.4 + - - +
164D ILE* 3.4 10.8 - - + -
165D GLY 3.0 0.4 - - - -
166D GLN* 1.3 76.9 - - - +
168D THR* 1.3 64.4 + - + +
169D TYR 3.0 5.8 + - - -
170D ARG 3.7 16.2 + - - +
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Residues in contact with THR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 5.0 1.9 + - - -
114D LEU* 5.2 6.3 - - + -
164D ILE* 2.7 33.7 + - + +
165D GLY* 2.9 14.6 + - - -
167D THR* 1.3 74.8 - - + +
169D TYR* 1.3 82.1 + - - +
170D ARG 3.6 2.2 + - - -
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Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 4.7 11.0 + - - -
165D GLY* 3.1 27.9 + - - +
166D GLN* 3.6 6.3 - - - +
167D THR 3.0 2.4 - - - -
168D THR* 1.3 99.2 - - - +
170D ARG* 1.3 70.3 + - - +
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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