Contacts of the helix formed by residues 188 - 195 (chain A) 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 LYS 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ARG* 4.9 9.4 - - - +
148A CYS* 3.8 26.0 - - + +
149A GLY* 4.1 18.3 - - - +
170A PHE* 3.9 7.9 - - + -
184A ALA 3.0 11.0 + - - +
185A ALA* 2.8 11.4 + - - +
186A ALA 2.7 1.0 - - - -
187A SER* 1.3 99.9 + - - +
189A LEU* 1.3 58.6 + - - +
190A GLY* 2.9 6.2 + - - +
191A GLU* 3.3 29.8 + - + +
192A PHE* 3.3 26.7 + - + +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.7 24.9 - - + -
185A ALA 2.7 11.2 + - - +
186A ALA* 3.0 14.5 + - - +
188A LYS* 1.3 74.5 - - - +
190A GLY* 1.3 68.1 + - - +
192A PHE* 4.3 1.1 - - - -
193A ALA* 3.3 21.5 + - - +
205A ILE* 4.3 19.3 - - + +
208A MET* 3.8 22.7 - - + -
209A PHE* 3.4 44.2 - - + +
212A LEU* 4.2 16.6 - - + -
224A ALA* 5.5 3.4 - - - -
227A ALA* 4.4 10.9 - - + +
231A ILE* 4.4 3.6 - - + +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ALA 3.9 4.2 + - - -
187A SER 4.6 3.1 + - - -
188A LYS* 2.9 4.0 - - - +
189A LEU* 1.3 86.0 - - - +
191A GLU* 1.3 60.3 + - - +
193A ALA* 3.4 11.4 + - - +
194A LYS* 3.8 11.0 + - - +
227A ALA* 4.4 16.9 - - - +
230A ASN* 4.7 17.6 - - - +
231A ILE* 5.6 1.8 - - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.3 27.8 + - - -
149A GLY* 5.2 1.6 - - - +
152A SER* 2.9 31.8 + - - +
187A SER 5.6 0.6 + - - +
188A LYS* 3.3 37.6 - - + +
190A GLY* 1.3 68.4 - - - +
192A PHE* 1.3 65.9 + - - +
193A ALA 3.0 2.5 - - - -
194A LYS* 2.8 39.4 + - + +
195A VAL* 3.5 4.9 + - - +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.5 41.5 - + + -
152A SER* 3.6 17.7 - - - +
155A TYR* 3.9 27.4 - + + -
166A LEU* 4.8 0.4 - - + -
167A ARG* 4.4 13.2 - - - -
170A PHE* 3.7 45.3 - + + -
188A LYS* 3.3 17.0 + - + +
189A LEU 4.7 0.4 - - - +
191A GLU* 1.3 82.0 - - - +
193A ALA* 1.3 58.9 + - - +
195A VAL* 3.1 22.1 - - + +
196A LEU* 3.2 38.3 - - + +
205A ILE* 4.6 4.0 - - + -
208A MET* 5.4 2.5 - - + -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU 3.3 18.9 + - - +
190A GLY 3.4 5.7 + - - +
191A GLU 3.0 0.8 - - - -
192A PHE* 1.3 76.1 - - - +
194A LYS* 1.3 64.3 + - - +
196A LEU* 3.3 5.0 + - - +
201A VAL* 3.3 24.7 - - + +
205A ILE* 3.3 40.8 - - + +
231A ILE* 4.8 7.2 - - + -
234A LEU* 4.2 12.7 - - + +
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY 3.9 7.6 - - - +
191A GLU* 2.8 23.7 + - + +
193A ALA* 1.3 78.6 - - - +
195A VAL* 1.3 59.6 + - + +
196A LEU 3.5 7.1 + - - +
230A ASN* 3.2 40.4 - - - +
233A GLN* 5.7 1.5 + - - -
234A LEU* 3.7 33.1 - - + +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 3.7 19.1 - - - +
155A TYR* 3.8 15.6 - - + -
156A PRO* 3.3 35.8 - - + +
163A LYS* 5.3 0.5 + - - -
191A GLU 3.5 2.2 + - - +
192A PHE* 3.1 44.0 - - + +
194A LYS* 1.3 76.3 - - + +
196A LEU* 1.3 65.0 + - - +
197A GLU* 3.9 5.5 - - - +
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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