Contacts of the helix formed by residues 145 - 157 (chain A) in PDB entry 2PQG
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 GLY 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MET* 1.3 79.3 - - - +
146A ARG* 1.3 60.7 + - - -
147A ALA 3.4 2.5 - - - -
148A GLU* 3.5 5.1 - - - +
149A MET* 2.9 27.2 + - - +
204A MET* 3.6 6.6 - - - +
221A GLY 4.6 1.8 - - - -
222A PHE* 3.6 28.2 - - - -
224A SER 6.0 0.9 - - - -
227A GLY* 5.0 2.2 - - - -
228A VAL* 4.3 3.1 - - - +
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Residues in contact with ARG 146 (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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27A PHE* 3.9 4.6 - - - -
29A VAL* 2.4 46.2 + - + +
30A GLU* 4.4 11.9 - - - +
31A ASP 3.2 16.1 + - - -
32A ALA* 3.7 22.6 + - - +
34A TYR 3.2 23.8 + - - -
35A PRO* 4.2 4.9 - - - +
145A GLY* 1.3 69.1 - - - -
147A ALA* 1.3 61.2 + - - +
149A MET* 3.0 4.5 + - - +
150A THR* 2.8 34.2 + - - +
222A PHE* 2.8 57.4 + - + +
223A ASN* 2.8 31.0 + - - +
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Residues in contact with ALA 147 (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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145A GLY* 3.4 0.6 - - - -
146A ARG* 1.3 79.2 - - - +
148A GLU* 1.3 63.3 + - + +
150A THR* 3.3 8.9 + - - -
151A ARG* 3.1 48.5 + - - +
222A PHE 4.7 0.2 + - - -
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Residues in contact with GLU 148 (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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143A THR* 3.4 32.5 - - + +
144A MET* 3.5 25.8 - - - +
145A GLY* 3.4 13.9 + - - +
146A ARG 3.1 0.4 - - - -
147A ALA* 1.3 79.3 - - + +
149A MET* 1.3 59.1 + - - +
151A ARG* 3.4 27.6 + - - +
152A ALA* 3.2 23.0 + - - +
197A LYS* 5.2 0.7 - - - +
200A LYS* 3.4 32.0 + - + +
204A MET* 4.5 3.4 - - + -
226A HIS 5.3 1.0 - - - +
227A GLY* 4.9 4.5 - - - -
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Residues in contact with MET 149 (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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27A PHE* 3.9 33.4 - - + -
29A VAL* 3.9 17.5 - - + -
36A TYR* 4.7 6.7 - - + -
39A PHE* 6.5 0.7 - - + -
77A LEU* 4.5 8.1 - - + -
145A GLY 2.9 16.7 + - - +
146A ARG* 3.0 6.0 + - - +
148A GLU* 1.3 73.9 - - - +
150A THR* 1.3 65.1 + - - +
152A ALA* 3.8 3.4 - - - +
153A VAL* 3.1 27.5 + - + +
201A LEU* 3.7 15.0 - - + -
204A MET* 3.6 42.4 - - + -
205A VAL* 4.3 16.2 - - + -
222A PHE* 4.3 11.4 - - + -
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Residues in contact with THR 150 (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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29A VAL* 3.2 18.6 - - - +
30A GLU* 3.6 35.5 - - + +
79A THR* 3.9 7.9 - - + +
146A ARG* 2.8 20.1 + - - +
147A ALA* 3.3 11.9 + - - -
149A MET* 1.3 78.4 - - - +
151A ARG* 1.3 60.9 + - + +
154A ASN* 3.1 42.3 + - - +
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Residues in contact with ARG 151 (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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147A ALA* 3.1 34.8 + - - +
148A GLU* 3.4 40.0 + - - +
150A THR* 1.3 76.4 - - + +
152A ALA* 1.3 59.8 + - - +
154A ASN* 4.0 5.6 - - - +
155A ASP* 2.9 32.4 + - - +
197A LYS* 4.1 13.8 - - - +
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Residues in contact with ALA 152 (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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148A GLU 3.2 18.1 + - - +
149A MET 3.8 4.5 - - - +
150A THR 3.3 0.2 - - - -
151A ARG* 1.3 78.5 - - - +
153A VAL* 1.3 57.5 + - - +
155A ASP* 3.6 0.7 - - - +
156A LEU* 2.9 37.3 + - - +
197A LYS* 3.4 41.2 - - + +
200A LYS* 4.9 4.3 - - + -
201A LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 153 (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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29A VAL* 4.4 5.8 - - + -
77A LEU* 3.4 55.6 - - + +
79A THR* 4.1 14.6 - - + -
83A SER* 3.8 17.9 - - - +
84A ILE* 3.8 19.9 - - + +
149A MET* 3.1 18.6 + - + +
150A THR 3.9 3.1 - - - +
152A ALA* 1.3 73.9 - - - +
154A ASN* 1.3 61.3 + - - +
157A ALA* 2.8 33.3 + - - +
201A LEU* 4.7 2.7 - - + -
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Residues in contact with ASN 154 (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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30A GLU* 4.9 0.9 - - - +
79A THR* 3.0 35.9 + - - +
81A THR* 4.2 11.1 + - + -
82A SER* 3.6 17.8 - - - +
150A THR* 3.1 34.5 + - - +
151A ARG* 4.0 6.0 - - - +
153A VAL* 1.3 77.1 - - - +
155A ASP* 1.3 61.5 + - - +
157A ALA* 3.7 7.0 + - - +
158A LYS* 3.2 29.5 - - - +
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Residues in contact with ASP 155 (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 ARG 2.9 19.8 + - - +
152A ALA 3.6 4.0 - - - +
154A ASN* 1.3 76.9 - - - +
156A LEU* 1.3 60.6 + - - +
158A LYS* 3.0 26.8 + - - +
159A LYS* 3.6 3.6 + - - -
160A LYS* 6.0 1.9 - - - -
193A ASP* 2.8 36.8 - - - +
194A THR* 5.6 1.6 + - - -
197A LYS* 3.6 21.1 - - + -
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Residues in contact with LEU 156 (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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84A ILE* 4.1 14.4 - - + -
98A PHE* 3.6 28.3 - - + -
100A THR* 3.7 2.9 - - - +
152A ALA 2.9 22.9 + - - +
153A VAL 4.1 1.3 - - - +
155A ASP* 1.3 70.5 - - - +
157A ALA* 1.3 62.3 + - - +
158A LYS 2.9 5.4 - - - -
159A LYS* 2.9 23.2 + - + +
194A THR* 3.7 35.4 - - + +
197A LYS* 3.9 21.1 - - + -
198A LEU* 3.5 29.6 - - + +
201A LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 2.8 31.6 - - - +
83A SER 3.8 11.2 - - - +
84A ILE* 3.6 10.7 - - - +
100A THR* 4.0 5.9 - - - -
101A PRO* 3.2 21.6 - - + +
153A VAL 2.8 19.6 + - - +
154A ASN 3.7 8.1 - - - +
155A ASP 3.2 0.4 - - - -
156A LEU* 1.3 76.2 - - - +
158A LYS* 1.3 60.1 + - + +
159A LYS 3.5 0.2 - - - -
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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