Contacts of the helix formed by residues 153 - 169 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ARG* 6.0 3.1 - - - -
475B LYS* 5.9 0.9 - - - -
476B GLU* 3.9 12.6 - - + +
100C TRP* 3.5 16.4 - - - -
151C ASP* 3.0 19.3 + - + -
152C LEU* 1.3 75.6 - - - +
154C GLU* 1.3 66.3 + - - +
155C GLY* 3.0 14.8 - - - -
156C THR* 2.9 30.4 + - - -
157C LEU 3.0 8.7 + - - -
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Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LYS* 2.4 38.2 + - - +
476B GLU* 4.6 0.6 + - - -
512B CYS 5.6 0.7 - - - +
513B GLY* 5.7 4.6 - - - -
515B ASP* 4.7 10.0 - - - +
100C TRP* 3.4 38.0 - - + +
153C CYS* 1.3 70.4 - - - +
155C GLY* 1.3 70.3 - - - +
157C LEU* 3.5 14.6 - - + +
158C LEU* 3.0 31.2 + - + +
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Residues in contact with GLY 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 5.9 5.6 - - - -
153C CYS* 3.0 13.1 + - - +
154C GLU* 1.3 82.2 - - - +
156C THR* 1.3 59.8 + - - +
158C LEU* 3.3 22.1 + - - +
159C LEU* 3.3 17.1 + - - +
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 5.7 2.5 + - - +
141C PHE* 3.7 5.6 - - + -
144C PHE* 3.5 7.0 - - + -
145C ARG* 3.8 20.9 - - + -
150C LEU* 3.4 41.4 - - + +
151C ASP* 2.8 28.2 + - - +
153C CYS* 2.9 12.1 + - - -
155C GLY* 1.3 71.9 - - - +
157C LEU* 1.3 64.3 + - - +
159C LEU* 3.5 6.2 + - - -
160C TRP* 3.1 22.7 + - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 4.4 23.8 - - + -
97C CYS* 4.1 24.2 - - + -
100C TRP* 3.5 45.5 - - + -
115C LEU* 4.3 4.3 - - + -
141C PHE* 3.7 11.6 - - + -
153C CYS 3.0 7.0 + - - +
154C GLU* 3.5 20.0 - - + +
156C THR* 1.3 73.7 - - - +
158C LEU* 1.3 65.9 + - + +
160C TRP* 3.5 21.2 + - + +
161C CYS* 3.0 27.1 + - - -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLY* 5.4 8.5 - - - -
92C VAL* 4.2 23.6 - - + -
154C GLU* 3.0 27.1 + - + +
155C GLY* 3.4 14.4 - - - +
157C LEU* 1.3 74.7 - - + +
159C LEU* 1.3 67.9 + - + +
161C CYS* 2.9 9.6 + - - +
162C ASP* 2.9 29.4 + - - +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 5.8 7.9 - - - +
144C PHE* 3.8 12.1 - - + -
150C LEU* 3.7 28.3 - - + -
155C GLY 3.3 13.1 + - - +
156C THR* 3.7 7.6 - - - +
158C LEU* 1.3 80.3 - - + +
160C TRP* 1.3 64.7 + - - +
162C ASP* 2.9 26.1 + - + +
163C ILE* 3.1 15.8 + - + +
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Residues in contact with TRP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.7 20.4 - + + -
114C LEU* 4.1 5.2 - - + -
115C LEU* 3.3 38.1 - - + -
118C LEU* 3.4 26.7 - - + -
135C TRP* 4.3 2.9 - + - -
139C TYR 2.9 19.5 + - - -
140C CYS 3.8 0.4 - - - -
141C PHE* 3.6 27.9 - + + +
144C PHE* 3.3 48.8 - + + -
156C THR 3.1 11.6 + - - +
157C LEU* 3.6 13.5 - - + +
159C LEU* 1.3 78.6 - - - +
161C CYS* 1.3 82.6 + - - +
163C ILE* 3.3 3.7 + - - +
164C ILE* 2.9 48.4 + - + +
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Residues in contact with CYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLY 5.2 9.2 - - - +
92C VAL* 5.5 7.6 - - + -
96C TYR* 3.3 55.2 + - + -
157C LEU* 3.0 24.5 + - - +
158C LEU* 2.9 12.3 + - - +
160C TRP* 1.3 83.7 - - - +
162C ASP* 1.3 70.7 + - - +
163C ILE 2.9 0.5 + - - -
164C ILE* 2.9 1.4 + - - -
165C GLY* 2.7 23.2 + - - -
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Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C LEU* 2.9 23.4 + - - +
159C LEU* 3.5 17.8 - - + +
161C CYS* 1.3 77.6 - - - +
163C ILE* 1.3 57.9 + - + +
165C GLY* 3.3 1.1 + - - -
166C GLN* 2.9 46.4 + - + +
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Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 3.5 31.9 - - + +
139C TYR* 5.3 1.3 - - + -
144C PHE* 4.4 14.1 - - + -
148C PHE* 6.1 3.4 - - + -
159C LEU* 3.1 15.0 + - + +
160C TRP* 3.6 7.0 - - - +
161C CYS 3.0 0.8 - - - -
162C ASP* 1.3 74.2 - - + +
164C ILE* 1.3 64.8 + - - +
165C GLY 3.0 1.6 - - - -
166C GLN* 3.5 24.5 + - + +
167C THR* 2.8 37.2 + - - +
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 4.2 13.0 - - + -
114C LEU* 3.4 33.2 - - + -
118C LEU* 4.4 3.6 - - + -
135C TRP* 4.2 5.6 - - + -
139C TYR* 3.6 49.4 - - + +
160C TRP* 2.9 45.6 + - + +
161C CYS 3.8 2.9 - - - +
163C ILE* 1.3 75.1 - - - +
165C GLY* 1.3 56.7 + - - +
167C THR* 3.8 4.1 - - - -
168C THR* 3.0 34.6 + - + +
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 3.8 16.5 - - - -
161C CYS 2.7 15.0 + - - -
162C ASP* 3.6 2.0 - - - -
164C ILE* 1.3 74.4 - - - +
166C GLN* 1.3 65.6 + - - +
167C THR 3.0 1.3 - - - -
168C THR* 3.1 9.5 + - - -
169C TYR* 3.0 33.2 + - - +
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Residues in contact with GLN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASP* 2.9 33.4 + - - +
163C ILE* 3.8 26.6 - - + +
165C GLY* 1.3 72.7 - - - +
167C THR* 1.3 62.4 + - - +
169C TYR* 3.4 20.8 - - - +
170C ARG 3.9 6.1 - - - -
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Residues in contact with THR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR* 3.6 41.2 + - + +
163C ILE* 2.8 26.2 + - - +
164C ILE* 3.8 4.9 - - - -
165C GLY 3.0 0.6 - - - -
166C GLN* 1.3 76.6 - - - +
168C THR* 1.3 66.5 + - + +
169C TYR 3.1 2.3 + - - -
170C ARG* 3.9 15.1 + - - +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 5.1 1.6 + - - -
114C LEU* 5.0 7.2 - - + -
164C ILE* 3.0 31.0 + - + +
165C GLY* 3.1 15.4 + - - -
167C THR* 1.3 78.8 - - + +
169C TYR* 1.3 81.4 - - - +
170C ARG 3.6 3.4 + - - -
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Residues in contact with TYR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 5.2 9.5 + - - -
165C GLY* 3.0 18.5 + - - +
166C GLN* 3.4 8.7 - - - +
167C THR 3.1 0.2 - - - -
168C THR* 1.3 98.9 - - - +
170C ARG* 1.3 69.8 + - - +
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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