Contacts of the helix formed by residues 151 - 166 (chain D) in PDB entry 2PK9
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 ARG 151 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 3.8 24.7 - - + +
169A VAL 5.7 5.0 + - - -
172A LEU* 3.8 16.2 - - - +
212A THR 4.2 5.9 + - - -
213A ASN* 3.6 23.7 - - - +
214A ASP* 3.3 28.2 + - - +
150D VAL* 1.3 82.5 - - - +
152D CYS* 1.3 61.5 + - - +
153D HIS* 3.4 4.7 - - + +
154D GLU* 3.0 50.2 + - + +
155D LEU 3.4 0.5 + - - -
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Residues in contact with CYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU* 2.6 26.3 + - - +
141D ASN* 4.2 3.6 - - - -
142D ALA* 3.6 37.0 - - + +
145D ALA* 3.8 13.2 - - + -
150D VAL 3.7 0.4 + - - -
151D ARG* 1.3 73.3 - - - +
153D HIS* 1.3 61.0 + - - +
155D LEU* 3.5 2.9 + - - +
156D ASN* 3.2 38.4 + - - -
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Residues in contact with HIS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU* 4.8 2.2 + - - +
151D ARG* 3.4 4.2 - - + +
152D CYS* 1.3 77.8 - - - +
154D GLU* 1.3 61.6 + - + +
156D ASN* 3.4 13.9 + - + -
157D ILE* 3.3 43.5 + - + +
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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
----------------------------------------------------------
214A ASP* 4.6 10.8 - - - +
121D ARG* 3.7 25.7 + - - +
150D VAL* 3.7 12.1 - - + +
151D ARG* 3.0 53.6 + - + +
153D HIS* 1.3 74.7 - - + +
155D LEU* 1.3 64.5 + - - +
157D ILE* 3.1 28.5 - - + +
158D LEU* 3.2 15.2 + - + +
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Residues in contact with LEU 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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124D LEU* 3.8 38.6 - - + +
125D THR* 4.5 9.6 - - - +
128D THR* 3.8 15.0 - - - +
141D ASN* 3.8 30.7 - - + +
144D TYR* 3.8 29.2 - - + -
145D ALA* 3.9 8.5 - - + +
150D VAL* 4.1 16.0 - - + +
151D ARG 3.4 3.4 + - - -
152D CYS 3.5 5.6 + - - +
154D GLU* 1.3 75.8 - - - +
156D ASN* 1.3 55.1 + - - +
158D LEU* 3.2 8.6 - - + +
159D GLU* 2.6 38.2 + - + +
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Residues in contact with ASN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY* 3.4 27.0 + - - +
46C THR* 5.3 0.5 + - - -
141D ASN* 2.9 36.9 + - - +
152D CYS* 3.2 26.1 + - - +
153D HIS* 3.6 20.2 - - + +
154D GLU 3.3 0.4 - - - -
155D LEU* 1.3 75.9 - - - +
157D ILE* 1.3 59.1 + - + +
159D GLU* 3.3 5.3 + - - +
160D ASN* 3.0 27.9 + - - +
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Residues in contact with ILE 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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66D ARG* 4.1 33.2 - - - +
153D HIS* 3.3 37.9 + - + +
154D GLU* 3.1 21.8 - - + +
156D ASN* 1.3 75.0 - - + +
158D LEU* 1.3 63.9 + - + +
160D ASN* 2.9 12.7 + - - +
161D ASP* 2.6 37.7 + - - +
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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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66D ARG* 3.4 41.7 - - + +
67D TYR* 3.8 19.5 + - + -
121D ARG* 4.1 32.8 - - + +
124D LEU* 5.0 9.4 - - + -
125D THR* 3.1 28.8 - - - +
150D VAL* 5.6 1.8 - - + -
154D GLU* 3.2 18.8 - - + +
155D LEU* 3.2 14.6 - - + +
157D ILE* 1.3 81.8 - - + +
159D GLU* 1.3 62.5 + - - +
161D ASP* 3.3 5.6 + - - +
162D PHE* 3.0 18.2 + - - +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY* 4.1 1.9 - - - -
46C THR* 3.1 33.7 + - - +
51C ILE* 3.3 13.2 - - - +
125D THR* 4.2 10.7 - - - +
128D THR* 4.2 6.6 - - - +
129D VAL* 3.8 17.5 - - + +
132D LYS* 2.7 30.7 + - - +
141D ASN* 3.3 15.8 - - - +
155D LEU* 2.6 28.2 + - + +
156D ASN* 3.6 4.1 - - - +
157D ILE 3.2 0.2 - - - -
158D LEU* 1.3 71.4 - - - +
160D ASN* 1.3 58.3 + - - +
162D PHE* 3.3 3.6 + - - +
163D LEU* 2.9 36.0 + - + +
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Residues in contact with ASN 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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46C THR* 4.7 8.7 + - - +
73C HIS* 3.1 32.1 + - - -
156D ASN 3.0 13.4 + - - +
157D ILE* 2.9 13.1 + - - +
159D GLU* 1.3 75.7 - - - +
161D ASP* 1.3 60.4 + - - +
163D LEU* 3.3 8.4 + - - +
164D LYS* 2.9 50.9 + - - +
168D TYR* 4.8 0.3 + - - -
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ARG* 3.6 30.8 + - + +
67D TYR* 2.7 32.6 + - - +
157D ILE 2.6 19.5 + - - +
158D LEU* 3.4 7.6 - - - +
160D ASN* 1.3 73.9 - - - +
162D PHE* 1.3 56.8 + - - +
164D LYS* 3.1 10.1 + - - +
165D ARG* 2.9 68.6 + - - +
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Residues in contact with PHE 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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67D TYR* 3.2 14.7 + + - +
101D TYR* 3.8 41.7 - + + -
104D LEU* 4.4 2.0 - - + -
105D LEU* 4.0 29.2 - - + -
122D PHE* 4.3 14.4 - + - -
125D THR* 3.6 27.1 - - + -
126D ALA* 5.1 3.8 - - - -
129D VAL* 4.2 29.8 - - + -
158D LEU 3.0 3.0 + - - -
159D GLU 3.7 3.6 - - - +
161D ASP* 1.3 78.3 - - - +
163D LEU* 1.3 68.2 + - + +
165D ARG* 3.2 12.2 + - - +
166D VAL* 3.2 36.7 + - + +
170D ILE* 4.4 10.5 - - + -
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Residues in contact with LEU 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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46C THR* 3.8 23.3 - - + +
51C ILE* 3.8 22.4 - - + -
129D VAL* 3.6 28.7 - - + -
159D GLU* 2.9 31.0 + - + +
160D ASN* 3.7 7.0 - - - +
162D PHE* 1.3 76.5 - - + +
164D LYS* 1.3 61.0 + - - +
166D VAL* 5.2 0.9 - - - -
167D ASN* 3.2 4.5 + - - -
168D TYR* 3.1 71.0 + - + +
170D ILE* 4.2 12.1 - - + -
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Residues in contact with LYS 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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73C HIS* 3.6 42.3 - - + +
160D ASN* 2.9 52.3 + - - +
161D ASP* 3.1 7.2 + - - +
163D LEU* 1.3 77.8 - - - +
165D ARG* 1.3 74.1 + - - +
166D VAL 3.3 0.5 + - - -
167D ASN* 3.3 19.9 + - - +
168D TYR* 5.4 1.6 - - - -
184D GLN* 5.1 0.7 + - - -
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Residues in contact with ARG 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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65D THR* 5.8 0.2 - - - +
66D ARG* 5.2 4.2 - - - +
67D TYR* 4.5 1.1 - - - +
105D LEU* 3.9 19.7 - - + -
108D VAL* 3.6 8.5 - - - +
109D TYR* 2.9 60.0 + - + -
161D ASP* 2.9 61.8 + - - +
162D PHE 3.2 5.6 + - - +
164D LYS* 1.3 85.3 - - - +
166D VAL* 1.3 58.3 + - - +
167D ASN 3.5 0.2 - - - -
184D GLN* 2.9 32.1 + - - +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.3 31.4 - - + -
105D LEU* 4.3 11.9 - - + -
108D VAL* 4.6 2.2 - - + -
162D PHE* 3.2 46.0 + - + +
163D LEU* 4.6 0.7 - - - +
164D LYS 3.2 0.4 - - - -
165D ARG* 1.3 79.7 - - - +
167D ASN* 1.3 70.4 + - - +
168D TYR* 3.2 4.3 - - - +
169D ARG* 3.1 25.9 + - - +
170D ILE* 5.3 1.1 - - + -
180D CYS* 3.3 27.4 - - - -
184D GLN* 4.8 0.2 - - - -
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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
------------------------------------------------------------
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