Contacts of the helix formed by residues 151 - 166 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 1.3 79.3 - - - +
152B CYS* 1.3 68.2 + - - +
153B HIS* 3.3 5.2 - - + +
154B GLU* 3.1 44.8 + - + +
155B LEU 3.2 3.8 + - - -
168C GLU* 3.2 31.2 - - + +
172C LEU* 3.9 13.1 - - - +
212C THR 4.9 3.0 + - - -
213C ASN* 3.8 16.8 - - - +
214C ASP* 3.1 44.8 + - - +
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER 4.6 0.4 - - - -
43A GLU* 4.2 15.0 - - - -
141B ASN 4.3 0.4 - - - -
142B ALA* 3.6 41.1 - - + -
145B ALA* 3.6 10.7 - - + +
150B VAL 3.8 1.0 + - - -
151B ARG* 1.3 70.9 - - - +
153B HIS* 1.3 57.7 + - - +
155B LEU* 3.0 9.7 + - - +
156B ASN* 2.9 44.6 + - - +
168C GLU* 2.6 21.3 + - - +
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Residues in contact with HIS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.3 5.1 - - + +
152B CYS* 1.3 74.9 - - - +
154B GLU* 1.3 65.8 + - - +
156B ASN* 3.0 25.3 + - + +
157B ILE* 3.1 46.5 + - + +
168C GLU* 5.3 0.8 + - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 2.7 36.7 + - - +
150B VAL* 3.8 19.2 - - + +
151B ARG* 3.1 48.3 + - + +
153B HIS* 1.3 78.3 - - - +
155B LEU* 1.3 57.8 + - - +
157B ILE* 3.5 12.4 - - - +
158B LEU* 3.1 31.2 + - + +
214C ASP* 5.6 2.9 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.9 25.4 - - + -
125B THR* 4.5 16.6 - - - +
128B THR* 4.2 17.5 - - + +
141B ASN* 3.3 40.4 - - + +
144B TYR* 3.6 14.8 - - + -
145B ALA* 3.6 15.3 - - + +
150B VAL* 3.9 15.0 - - + +
151B ARG 3.2 1.0 + - - -
152B CYS 3.0 9.6 + - - +
154B GLU* 1.3 78.2 - - - +
156B ASN* 1.3 53.4 + - - +
158B LEU* 3.3 5.1 + - + +
159B GLU* 2.8 39.4 + - + +
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Residues in contact with ASN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER 3.7 14.6 + - - +
45A GLY* 3.2 30.0 - - - -
46A THR* 4.9 1.2 + - - -
141B ASN* 3.3 19.8 + - - +
152B CYS* 2.9 28.4 + - - +
153B HIS* 3.0 22.0 + - + +
155B LEU* 1.3 75.9 - - - +
157B ILE* 1.3 59.8 + - + +
159B GLU* 3.3 9.8 + - - +
160B ASN* 3.0 28.1 + - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 4.4 32.8 + - - +
153B HIS* 3.1 39.7 + - + +
154B GLU* 3.5 16.4 - - + +
156B ASN* 1.3 76.5 - - + +
158B LEU* 1.3 63.5 + - + +
159B GLU 3.2 0.2 - - - -
160B ASN* 3.8 10.8 - - - +
161B ASP* 2.9 29.8 + - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 3.2 45.3 - - + +
67B TYR* 4.0 14.6 + - + -
121B ARG* 3.7 37.5 - - + +
124B LEU* 4.9 7.4 - - + -
125B THR* 2.9 42.5 - - - +
150B VAL* 5.6 2.5 - - + -
154B GLU* 3.1 21.2 + - + +
155B LEU* 3.5 15.3 - - + +
156B ASN 3.3 0.2 - - - -
157B ILE* 1.3 80.4 - - + +
159B GLU* 1.3 58.5 + - - +
161B ASP* 3.8 4.3 - - - +
162B PHE* 3.6 12.1 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.9 1.2 - - - -
46A THR* 3.1 31.9 + - - -
51A ILE* 3.7 8.2 - - - +
125B THR* 4.2 8.3 - - + -
128B THR* 4.6 7.0 + - - +
129B VAL* 3.8 19.3 - - + +
132B LYS* 2.6 35.9 + - - +
141B ASN* 3.0 20.7 + - - +
155B LEU* 2.8 21.7 + - + +
156B ASN 3.5 4.4 - - - +
158B LEU* 1.3 76.3 - - - +
160B ASN* 1.3 62.3 + - - +
162B PHE* 3.7 3.6 + - - +
163B LEU* 3.2 27.8 + - + +
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 5.6 10.5 - - - +
46A THR* 4.6 13.2 - - - +
73A HIS* 3.6 14.3 + - - -
156B ASN 3.0 16.7 + - - +
157B ILE* 3.9 11.4 - - - +
159B GLU* 1.3 75.7 + - - +
161B ASP* 1.3 68.4 + - - +
163B LEU* 3.4 5.7 + - - +
164B LYS* 3.0 51.8 + - - +
168B TYR* 5.0 0.2 + - - -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 3.3 33.3 + - + +
67B TYR* 2.8 31.9 + - + +
109B TYR* 4.4 0.9 + - - -
157B ILE 2.9 19.2 + - - +
158B LEU* 3.8 5.8 - - - +
160B ASN* 1.3 73.1 - - - +
162B PHE* 1.3 62.9 + - - +
164B LYS* 2.9 20.0 + - - +
165B ARG* 3.0 50.0 + - - +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 2.9 16.3 + + - +
101B TYR* 3.6 46.2 - + + -
104B LEU* 4.6 1.1 - - + -
105B LEU* 3.7 37.2 - - + -
122B PHE* 3.9 16.4 - + - -
125B THR* 3.8 25.1 - - + -
126B ALA* 5.3 2.0 - - + -
129B VAL* 4.3 21.3 - - + -
158B LEU 3.6 1.6 + - - -
159B GLU 3.9 4.5 - - - +
160B ASN 3.5 0.2 - - - -
161B ASP* 1.3 76.7 - - - +
163B LEU* 1.3 65.9 + - + +
165B ARG* 3.2 5.0 + - - -
166B VAL* 3.1 58.3 + - + +
170B ILE* 4.7 1.6 - - + -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 4.1 16.6 - - + +
51A ILE* 3.9 30.3 - - + -
129B VAL* 3.8 26.5 - - + -
159B GLU* 3.2 22.4 + - + +
160B ASN* 3.8 5.6 - - - +
161B ASP 3.3 0.4 - - - -
162B PHE* 1.3 79.8 - - + +
164B LYS* 1.3 58.8 + - - +
166B VAL* 4.8 0.4 - - - -
167B ASN* 3.1 5.9 + - - -
168B TYR* 3.0 74.2 + - + +
170B ILE* 4.0 17.9 - - + -
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Residues in contact with LYS 164 (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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73A HIS* 3.3 47.9 + - + +
160B ASN* 3.0 44.2 + - - +
161B ASP* 2.9 11.4 + - - +
163B LEU* 1.3 76.8 - - - +
165B ARG* 1.3 62.8 + - + +
166B VAL 3.2 2.7 + - - -
167B ASN* 3.3 18.9 + - - +
168B TYR* 5.1 2.7 - - - -
184B GLN* 5.7 0.3 - - - +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.6 1.8 - - - -
105B LEU* 4.1 13.2 - - + -
108B VAL* 3.5 22.7 - - - +
109B TYR* 3.1 63.2 + - + -
161B ASP* 3.0 49.7 + - - +
162B PHE 3.8 4.7 - - - +
164B LYS* 1.3 78.6 - - + +
166B VAL* 1.3 59.8 + - - +
167B ASN 3.4 0.2 - - - -
184B GLN* 4.0 13.3 + - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.5 28.0 - - + -
105B LEU* 4.0 16.2 - - + +
108B VAL* 4.3 3.8 - - + -
162B PHE* 3.1 42.8 + - + +
163B LEU* 5.2 0.2 - - - -
165B ARG* 1.3 80.3 - - - +
167B ASN* 1.3 65.5 + - - +
168B TYR* 4.0 2.9 - - - +
169B ARG* 3.1 35.2 + - - +
170B ILE* 4.1 5.6 - - + -
180B CYS* 3.1 22.7 - - - -
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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
------------------------------------------------------------
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