Contacts of the helix formed by residues 159 - 175 (chain B) 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 SER 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.3 19.0 + - - -
158B VAL* 1.3 78.7 - - - +
160B SER* 1.3 58.4 + - - +
161B ALA* 2.8 13.0 + - - +
162B VAL* 3.0 29.5 + - - +
163B LYS* 2.8 32.5 + - - +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL 3.9 0.4 + - - -
159B SER* 1.3 73.6 - - - +
161B ALA* 1.3 58.6 + - - +
163B LYS* 4.1 23.1 + - - +
164B ALA* 3.7 17.4 + - - +
167B ARG* 5.2 1.6 + - - -
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Residues in contact with ALA 161 (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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159B SER* 2.8 10.9 - - - +
160B SER* 1.3 81.7 - - - +
162B VAL* 1.3 65.5 + - + +
164B ALA* 3.3 7.6 - - - +
165B GLU* 3.3 22.5 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.7 22.9 - - + +
129B VAL* 3.8 35.7 - - + -
158B VAL* 3.6 23.1 - - + -
159B SER* 3.0 18.6 + - - +
161B ALA* 1.3 76.7 - - + +
163B LYS* 1.3 67.0 + - - +
165B GLU* 3.0 20.8 + - + +
166B LEU* 2.8 22.4 + - + +
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Residues in contact with LYS 163 (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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155B TYR* 3.1 65.2 - - + +
156B PRO 4.5 9.2 + - - -
158B VAL* 3.4 22.2 - - + +
159B SER 2.8 23.8 + - - +
160B SER* 4.3 17.5 + - - +
162B VAL* 1.3 75.2 - - - +
164B ALA* 1.3 56.9 + - - +
166B LEU* 2.7 26.3 + - - +
167B ARG* 2.9 19.0 + - - +
197B GLU* 3.8 22.0 + - - +
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Residues in contact with ALA 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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160B SER 3.7 12.7 + - - +
161B ALA* 3.3 12.5 + - - +
163B LYS* 1.3 80.0 - - - +
165B GLU* 1.3 62.5 + - + +
167B ARG* 3.3 28.5 + - - +
168B GLN* 3.1 22.2 + - - +
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Residues in contact with GLU 165 (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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133B LYS* 2.9 37.6 + - - +
161B ALA 3.3 9.9 + - - +
162B VAL* 3.0 26.1 + - - +
164B ALA* 1.3 80.1 - - + +
166B LEU* 1.3 64.2 + - - +
168B GLN* 3.3 6.1 + - - +
169B TYR* 3.0 32.5 + - + -
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Residues in contact with LEU 166 (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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129B VAL* 4.1 22.0 - - + +
132B VAL* 4.5 8.3 - - + -
133B LYS* 5.3 5.8 - - + -
151B PHE* 3.7 27.4 - - + +
154B CYS* 3.9 15.5 - - - -
155B TYR* 3.6 48.7 - - + +
158B VAL* 4.3 8.5 - - + -
162B VAL* 2.8 21.1 + - + +
163B LYS* 2.7 14.9 + - - +
165B GLU* 1.3 71.6 - - - +
167B ARG* 1.3 52.6 + - - +
169B TYR* 3.0 7.7 + - - +
170B PHE* 2.7 35.6 + - - +
192B PHE* 4.8 1.8 - - + -
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Residues in contact with ARG 167 (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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155B TYR* 3.2 34.7 + - + -
160B SER 5.2 1.4 + - - -
163B LYS* 2.9 15.2 + - - +
164B ALA* 3.5 40.2 + - - +
166B LEU* 1.3 73.7 - - - +
168B GLN* 1.3 64.5 + - - +
170B PHE* 3.2 2.6 + - - +
171B ARG* 3.1 25.9 + - - +
192B PHE* 4.1 18.1 - - + -
196B LEU* 3.9 17.7 - - - -
197B GLU* 4.7 1.2 + - - -
200B ASN* 3.3 22.5 + - - +
204B GLU* 2.6 39.2 + - - +
208B MET* 4.8 7.2 - - + +
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Residues in contact with GLN 168 (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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164B ALA 3.1 10.8 + - - +
165B GLU* 3.4 11.9 - - - +
167B ARG* 1.3 81.4 - - - +
169B TYR* 1.3 64.0 + - + +
171B ARG* 2.8 54.5 + - - +
172B ASN* 3.3 26.0 + - - +
204B GLU* 5.1 0.2 + - - -
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Residues in contact with TYR 169 (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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133B LYS* 3.3 61.9 + - + +
136B ALA* 4.2 17.9 - - + -
137B GLY* 5.2 6.3 - - - -
151B PHE* 3.8 13.9 - + + -
165B GLU* 3.0 27.4 + - + -
166B LEU* 3.0 10.0 + - + +
168B GLN* 1.3 79.2 - - + +
170B PHE* 1.3 63.6 + - - +
171B ARG 3.1 0.9 + - - -
172B ASN* 3.2 27.9 + - + +
173B LEU* 3.3 16.7 + - - +
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Residues in contact with PHE 170 (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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148B CYS* 4.4 10.3 - - - -
151B PHE* 3.8 32.2 - + + -
166B LEU 2.7 17.9 + - - +
167B ARG 3.2 4.0 + - - +
169B TYR* 1.3 72.8 - - - +
171B ARG* 1.3 60.4 + - - +
173B LEU* 3.5 13.8 + - + +
174B CYS* 3.2 26.0 + - - -
185B ALA* 3.4 32.1 - - + -
188B LYS* 4.2 15.0 - - + -
189B LEU* 3.4 36.3 - - + -
192B PHE* 3.9 31.0 - + + -
208B MET* 3.7 13.7 - - + -
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Residues in contact with ARG 171 (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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167B ARG 3.1 11.9 + - - +
168B GLN* 2.8 53.4 + - - +
169B TYR 3.0 0.2 - - - -
170B PHE* 1.3 75.8 - - - +
172B ASN* 1.3 55.8 + - - +
173B LEU 2.8 5.3 + - - -
174B CYS* 2.7 25.8 + - + +
175B SER* 3.1 17.6 + - - +
204B GLU* 2.7 44.1 + - - +
208B MET* 3.9 29.4 - - + +
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Residues in contact with ASN 172 (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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168B GLN* 3.4 30.0 + - - +
169B TYR* 3.2 23.1 + - + +
171B ARG* 1.3 77.5 - - - +
173B LEU* 1.3 60.8 + - + +
175B SER* 3.6 12.0 + - - -
176B ASP* 3.5 19.4 + - - +
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Residues in contact with LEU 173 (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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136B ALA* 4.1 17.7 - - + +
144B ARG* 3.7 45.5 - - + +
147B ALA* 4.7 0.7 - - + -
148B CYS* 4.1 9.2 - - - -
151B PHE* 3.4 39.9 - - + -
169B TYR 3.3 12.9 + - - +
170B PHE* 3.5 12.1 - - + +
171B ARG 2.8 0.8 + - - -
172B ASN* 1.3 79.0 - - + +
174B CYS* 1.3 61.3 + - - +
175B SER 2.9 5.9 + - - -
176B ASP* 3.1 18.9 + - - +
181B VAL* 3.5 18.3 - - + +
182B ARG* 4.1 1.6 - - - -
185B ALA* 3.9 14.4 - - + +
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Residues in contact with CYS 174 (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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170B PHE* 3.2 38.6 - - - -
171B ARG* 2.7 8.5 + - + +
173B LEU* 1.3 75.4 - - - +
175B SER* 1.3 58.2 + - - +
176B ASP 3.4 0.4 - - - -
182B ARG* 3.5 20.4 - - - +
185B ALA* 3.7 16.2 - - - -
189B LEU* 4.5 0.2 - - - -
208B MET* 3.8 22.0 - - + +
212B LEU* 3.9 33.7 - - + +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.1 19.9 + - - +
172B ASN* 3.8 11.2 - - - -
173B LEU 2.9 0.8 - - - -
174B CYS* 1.3 82.4 - - - +
176B ASP* 1.3 65.9 + - - +
177B ASP* 3.3 5.0 + - - +
182B ARG* 4.5 3.4 - - - +
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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