Contacts of the helix formed by residues 150 - 155 (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 LEU 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B VAL* 3.4 32.3 - - + +
112B LEU* 4.1 22.9 - - + -
113B ARG* 4.0 13.7 - - + +
128B PHE* 4.3 10.5 - - + -
131B LEU* 4.4 6.1 - - + -
132B VAL* 4.0 23.9 - - + +
135B LEU* 4.1 25.6 - - + -
146B SER 3.9 6.3 - - - +
147B ALA* 2.7 20.0 + - - +
149B GLY* 1.3 74.9 - - - +
151B PHE* 1.3 65.8 + - - +
152B SER 3.4 1.1 - - - -
153B VAL* 3.4 18.8 - - - +
154B CYS* 3.5 11.8 - - - -
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Residues in contact with PHE 151 (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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132B VAL* 3.4 23.8 - - + -
136B ALA* 4.2 8.5 - - + -
147B ALA* 3.5 24.9 - - + -
148B CYS* 4.0 8.0 + - - +
149B GLY 3.7 0.8 - - - -
150B LEU* 1.3 77.9 - - - +
152B SER* 1.3 70.0 + - - +
153B VAL 2.9 1.6 + - - -
154B CYS* 4.5 4.5 - - - -
155B TYR* 3.3 26.2 + - - +
166B LEU* 3.7 42.8 - - + -
169B TYR* 3.8 12.1 - + + -
170B PHE* 3.8 24.0 - + + -
173B LEU* 3.4 32.5 - - + -
192B PHE* 3.9 20.9 - + + -
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Residues in contact with SER 152 (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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113B ARG* 4.2 8.3 + - - -
148B CYS 5.4 1.7 + - - -
149B GLY 4.8 4.0 - - - -
151B PHE* 1.3 79.6 - - - +
153B VAL* 1.3 60.1 + - - +
156B PRO* 3.2 25.1 - - - +
188B LYS* 6.1 0.2 - - - -
191B GLU* 3.7 44.5 + - - +
192B PHE* 4.0 19.5 - - - +
195B VAL* 3.8 10.8 - - - +
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Residues in contact with VAL 153 (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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113B ARG* 4.2 31.0 - - + +
116B SER* 3.6 31.6 + - - +
117B HIS* 4.4 22.4 - - + +
124B LEU* 5.3 0.2 - - - +
128B PHE* 4.0 11.0 - - + -
149B GLY 5.2 0.2 - - - +
150B LEU* 3.4 21.1 - - + +
151B PHE 2.9 1.4 + - - -
152B SER* 1.3 82.7 - - - +
154B CYS* 1.3 66.5 + - - +
156B PRO* 3.2 10.6 - - - +
157B ARG* 5.0 7.6 + - - +
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Residues in contact with CYS 154 (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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116B SER* 5.3 0.7 - - - -
124B LEU* 3.8 20.8 - - + +
128B PHE* 3.8 25.4 - - + -
129B VAL* 4.1 17.5 - - + -
132B VAL* 4.3 8.3 - - - -
150B LEU 3.5 17.7 - - - -
151B PHE* 3.9 3.1 - - - -
153B VAL* 1.3 74.9 - - - +
155B TYR* 1.3 74.4 + - - +
156B PRO* 3.1 3.3 - - - +
157B ARG* 2.8 19.1 + - - +
158B VAL* 3.6 11.6 + - + +
166B LEU* 3.9 18.2 - - - -
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Residues in contact with TYR 155 (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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151B PHE 3.3 15.2 + - - +
154B CYS* 1.3 81.2 - - - +
156B PRO* 1.3 69.1 - - + +
157B ARG 3.2 1.0 + - - -
158B VAL* 3.8 4.7 + - - -
163B LYS* 3.1 69.3 - - + +
166B LEU* 3.6 19.3 - - + -
167B ARG* 3.2 24.6 + - + -
192B PHE* 3.7 18.8 - + + -
195B VAL* 3.6 29.4 - - + -
196B LEU* 3.2 28.4 - - + +
197B GLU* 2.9 23.2 + - - -
200B ASN* 4.4 0.3 + - - -
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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