Contacts of the helix formed by residues 140 - 149 (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 TRP 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 3.6 39.0 - - + -
99B VAL* 5.5 0.7 - - - -
100B GLU* 5.4 8.3 - - + -
138B GLY 3.2 0.6 - - - -
139B ASP* 1.3 88.5 + - + +
141B PHE* 1.3 67.9 + - - +
142B THR* 3.0 17.7 + - - +
143B SER* 3.1 24.7 + - - +
144B ARG* 3.2 8.3 + - - -
130D LYS* 4.3 19.1 - - + -
131D ASP* 2.6 40.4 + - - -
132D PRO* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU* 5.9 2.2 - - + -
105B ARG* 4.5 7.9 - - - -
139B ASP 3.4 1.0 + - - -
140B TRP* 1.3 71.6 - - - +
142B THR* 1.3 85.2 + - + +
144B ARG* 3.0 43.8 + - - +
145B THR* 3.1 22.9 + - - -
178B THR* 4.1 11.4 - - + +
180B MET* 3.7 36.3 - - + -
181B VAL* 3.9 5.9 - - + +
132D PRO* 4.4 21.1 - - + +
133D LEU 4.6 0.2 - - - -
134D VAL* 3.8 31.2 - - + -
146D MET* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 5.0 0.2 - - - -
98B THR 4.3 2.8 + - - -
99B VAL 4.5 4.3 - - - -
100B GLU* 4.3 17.7 - - + +
105B ARG* 3.1 43.5 + - - +
140B TRP* 3.4 25.8 - - - +
141B PHE* 1.3 102.0 - - + +
143B SER* 1.3 64.1 + - - +
145B THR* 3.1 8.2 + - - -
146B SER* 3.0 22.2 + - - -
132D PRO* 4.4 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 4.7 4.7 - - - -
98B THR* 3.3 24.9 + - - +
134B ARG 5.4 0.2 - - - -
135B LEU* 3.4 34.8 - - - +
138B GLY* 4.5 7.7 - - - -
140B TRP* 3.1 17.8 + - - +
142B THR* 1.3 77.8 - - - +
144B ARG* 1.3 63.9 + - - +
146B SER* 3.0 11.6 + - - -
147B ALA* 2.8 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 3.6 4.9 - - - +
136B ALA 3.4 24.2 - - - +
138B GLY 3.0 21.6 + - - +
139B ASP 2.8 28.7 + - - -
140B TRP 3.6 5.6 + - - -
141B PHE* 3.0 28.5 + - - +
143B SER* 1.3 77.8 - - - +
145B THR* 1.3 66.4 + - - +
147B ALA* 2.8 17.7 + - - +
148B CYS* 3.0 16.9 + - - -
173B LEU* 3.7 15.9 - - + +
176B ASP* 2.4 39.5 + - - +
177B ASP* 5.0 5.5 + - - +
178B THR* 3.4 14.5 + - - -
181B VAL* 3.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 4.7 15.9 - - - +
141B PHE* 3.1 27.1 + - + -
142B THR* 3.1 9.3 + - - -
144B ARG* 1.3 77.3 - - - +
146B SER* 1.3 65.3 + - - +
148B CYS* 3.1 17.8 + - - +
149B GLY 3.9 1.9 + - - -
180B MET* 4.6 5.2 - - + +
181B VAL* 4.1 11.7 + - - +
184B ALA* 3.7 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 2.9 35.7 + - - -
105B ARG* 3.5 15.6 + - - +
109B VAL* 3.6 29.5 - - - +
135B LEU* 4.8 3.6 - - - -
142B THR 3.0 6.2 + - - -
143B SER* 3.0 10.0 + - - -
145B THR* 1.3 77.0 - - - +
147B ALA* 1.3 66.3 + - - +
149B GLY* 3.2 10.4 + - - -
150B LEU* 3.9 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 4.2 4.5 - - + +
135B LEU* 3.8 8.0 - - + +
136B ALA* 3.6 40.8 - - + +
143B SER 2.8 8.5 + - - +
144B ARG 2.8 17.4 + - - +
146B SER* 1.3 72.6 - - - +
148B CYS* 1.3 51.7 + - - +
149B GLY 2.6 14.7 + - - -
150B LEU* 2.7 25.1 + - - +
151B PHE* 3.5 14.2 - - + -
173B LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG 3.0 19.0 + - - -
145B THR 3.1 8.0 + - - +
147B ALA* 1.3 75.4 - - - +
149B GLY* 1.3 59.8 + - - +
150B LEU 3.3 0.7 + - - -
151B PHE* 4.0 18.6 + - - +
152B SER* 5.4 1.2 + - - -
170B PHE* 4.4 4.9 - - + -
173B LEU* 4.1 20.2 - - - -
181B VAL* 4.1 4.7 - - - -
184B ALA* 3.7 27.1 - - + +
185B ALA* 3.7 29.6 - - - -
188B LYS* 3.3 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.4 9.2 - - - -
113B ARG* 3.5 27.3 + - - +
145B THR 3.9 1.8 + - - -
146B SER 3.2 8.2 + - - -
147B ALA 2.6 8.3 + - - -
148B CYS* 1.3 76.4 - - - +
150B LEU* 1.3 63.7 + - - +
151B PHE 3.7 0.7 - - - -
152B SER* 4.8 4.5 - - - -
153B VAL* 5.0 1.0 - - - +
188B LYS* 4.1 20.6 - - - +
191B GLU* 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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