Contacts of the helix formed by residues 145 - 157 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B MET* 1.3 79.9 - - - +
146B ARG* 1.3 61.1 + - - -
147B ALA 3.4 2.0 - - - -
148B GLU* 3.4 3.1 + - - -
149B MET* 2.9 29.3 + - - +
204B MET* 3.5 5.3 - - - +
218B VAL* 5.4 0.2 - - - +
221B GLY 4.5 1.6 - - - -
222B PHE* 3.5 30.1 - - - -
227B GLY* 5.0 2.0 - - - -
228B VAL* 4.1 2.9 - - - +
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Residues in contact with ARG 146 (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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27B PHE* 3.9 6.1 - - - -
28B PRO 4.2 0.2 + - - -
29B VAL* 2.8 45.6 + - + +
30B GLU* 4.7 7.2 - - - +
31B ASP 3.1 20.4 + - - -
32B ALA* 3.9 19.1 + - - +
34B TYR 3.2 23.4 + - - -
35B PRO* 4.2 4.9 - - - +
145B GLY* 1.3 68.6 - - - -
147B ALA* 1.3 60.5 + - - +
149B MET* 3.3 2.2 + - - +
150B THR* 2.8 36.4 + - - +
222B PHE* 2.7 58.4 + - + +
223B ASN* 2.7 36.0 + - - +
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Residues in contact with ALA 147 (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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145B GLY 3.4 0.2 - - - -
146B ARG* 1.3 78.6 - - - +
148B GLU* 1.3 64.4 + - + +
150B THR* 3.3 8.3 + - - -
151B ARG* 3.1 46.6 + - - +
222B PHE 4.6 0.4 + - - -
224B SER 5.9 3.1 - - - +
225B GLN 6.0 1.8 - - - +
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Residues in contact with GLU 148 (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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143B THR* 3.3 41.0 - - + +
144B MET* 3.5 23.6 - - - +
145B GLY* 3.4 8.5 + - - +
146B ARG 3.1 0.2 - - - -
147B ALA* 1.3 78.6 - - + +
149B MET* 1.3 65.0 + - - +
151B ARG* 3.1 33.5 + - - +
152B ALA* 3.0 22.8 + - - +
197B LYS* 5.2 2.1 - - - +
200B LYS* 3.3 30.1 + - + +
204B MET* 4.6 1.8 - - + -
226B HIS 5.8 0.5 - - - -
227B GLY* 5.0 3.8 - - - -
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Residues in contact with MET 149 (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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27B PHE* 3.9 25.1 - - + -
29B VAL* 3.8 22.7 - - + -
36B TYR* 4.6 7.6 - - + -
39B PHE* 6.4 1.3 - - + -
77B LEU* 4.5 8.5 - - + -
145B GLY 2.9 18.2 + - - +
146B ARG* 3.8 5.4 - - - +
148B GLU* 1.3 75.0 - - - +
150B THR* 1.3 62.1 + - - +
152B ALA* 3.8 1.0 - - - +
153B VAL* 3.1 34.7 + - + +
201B LEU* 3.6 20.4 - - + -
204B MET* 3.8 38.7 - - + +
205B VAL* 4.3 17.7 - - + -
222B PHE* 4.3 12.8 - - + -
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Residues in contact with THR 150 (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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29B VAL* 3.3 20.6 + - - +
30B GLU* 3.8 26.0 + - - +
79B THR* 3.9 17.7 - - + +
146B ARG* 2.8 24.9 + - - +
147B ALA* 3.5 9.0 - - - +
149B MET* 1.3 78.0 - - - +
151B ARG* 1.3 65.0 + - + +
154B ASN* 3.2 32.0 + - - +
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Residues in contact with ARG 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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147B ALA* 3.1 38.2 + - - +
148B GLU* 3.1 43.4 + - - +
150B THR* 1.3 76.9 - - + +
152B ALA* 1.3 61.2 + - - +
154B ASN* 4.1 4.6 - - - +
155B ASP* 2.8 33.5 + - - +
197B LYS* 4.2 14.0 - - - +
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Residues in contact with ALA 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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148B GLU 3.0 16.2 + - - +
149B MET* 3.8 4.7 - - - +
150B THR 3.3 0.2 - - - -
151B ARG* 1.3 78.7 - - - +
153B VAL* 1.3 56.6 + - - +
155B ASP* 3.7 0.5 - - - +
156B LEU* 2.9 38.8 + - - +
197B LYS* 3.4 44.1 - - + +
200B LYS* 4.8 4.3 - - + -
201B LEU* 4.1 15.7 - - + -
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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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29B VAL* 4.4 5.8 - - + -
77B LEU* 3.3 57.0 - - + +
79B THR* 4.1 15.3 - - + -
83B SER* 3.8 19.1 - - - -
84B ILE* 3.6 14.8 - - + +
149B MET* 3.1 20.3 + - + +
150B THR 3.9 3.4 - - - +
152B ALA* 1.3 74.3 - - - +
154B ASN* 1.3 66.7 + - - +
156B LEU 3.5 0.2 + - - -
157B ALA* 3.0 23.6 + - - +
201B LEU* 4.6 2.5 - - + -
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Residues in contact with ASN 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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30B GLU* 5.0 1.7 - - - +
79B THR* 2.8 37.5 + - - +
81B THR* 4.4 14.7 + - + -
82B SER* 3.6 16.4 - - - +
150B THR* 3.2 24.3 + - - +
151B ARG* 4.1 4.4 - - - +
153B VAL* 1.3 75.8 - - - +
155B ASP* 1.3 67.0 - - - +
157B ALA* 3.6 11.2 + - - +
158B LYS* 3.5 26.0 + - - +
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Residues in contact with ASP 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 ARG 2.8 20.9 + - - +
152B ALA 3.7 2.9 - - - +
154B ASN* 1.3 77.8 - - - +
156B LEU* 1.3 65.2 + - - +
158B LYS* 3.3 23.7 + - - +
159B LYS* 3.8 3.8 + - - +
193B ASP* 2.5 32.6 - - - +
194B THR* 5.4 0.9 + - - -
197B LYS* 4.1 21.9 + - + +
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Residues in contact with LEU 156 (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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84B ILE* 4.3 13.5 - - + -
98B PHE* 3.7 27.6 - - + -
100B THR* 3.8 2.3 - - - +
152B ALA 2.9 20.8 + - - +
153B VAL 4.1 2.0 - - - +
155B ASP* 1.3 72.6 - - - +
157B ALA* 1.3 57.2 + - - +
158B LYS 3.0 5.8 - - - -
159B LYS* 3.0 30.4 + - + +
194B THR* 3.8 36.3 - - + +
197B LYS* 3.9 23.6 - - + -
198B LEU* 3.9 18.6 - - + -
201B LEU* 3.8 26.5 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.2 27.1 - - - +
83B SER 3.7 7.6 - - - +
84B ILE* 3.8 6.2 - - - +
100B THR* 4.1 7.3 - - - +
101B PRO* 3.5 29.2 - - + +
153B VAL 3.0 19.5 + - - +
154B ASN 3.8 5.6 - - - +
155B ASP 3.3 0.4 - - - -
156B LEU* 1.3 75.0 - - - +
158B LYS* 1.3 59.7 + - + +
159B LYS 3.4 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