Contacts of the helix formed by residues 191 - 205 (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 GLN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.3 10.1 - - - +
126A PHE* 3.9 25.3 - - + -
159A LYS* 2.6 40.2 + - - +
160A LYS* 3.9 19.2 + - - +
161A LYS 5.4 5.1 + - - -
162A MET 5.6 3.8 + - - -
189A ASP* 3.4 3.4 + - - -
190A PRO* 1.3 87.3 - - + +
192A ALA* 1.3 58.2 + - - +
193A ASP* 3.1 2.9 - - - +
194A THR* 3.6 16.6 - - - +
195A LYS* 2.8 35.1 + - + +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASP* 3.3 41.4 + - + +
190A PRO 3.3 3.8 - - - -
191A GLN* 1.3 77.0 - - - +
193A ASP* 1.3 63.0 + - - +
195A LYS* 3.3 7.1 + - - +
196A SER* 3.0 24.9 + - - -
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Residues in contact with ASP 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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155A ASP* 2.8 39.4 - - - +
160A LYS* 5.7 7.4 - - - +
190A PRO 4.7 4.2 + - - +
191A GLN* 3.1 0.6 - - - -
192A ALA* 1.3 80.7 - - - +
194A THR* 1.3 64.0 + - - +
196A SER* 3.2 8.7 + - - -
197A LYS* 3.0 36.4 + - - +
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Residues in contact with THR 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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124A LEU* 4.3 3.6 - - + -
126A PHE* 3.9 10.5 - - + -
155A ASP* 5.6 0.9 + - - -
156A LEU* 3.7 26.4 - - + +
159A LYS* 3.6 30.7 - - + +
160A LYS* 4.1 9.9 + - - -
191A GLN* 3.1 18.7 + - - +
193A ASP* 1.3 77.6 + - - +
195A LYS* 1.3 68.6 + - - +
196A SER 3.0 0.3 + - - -
197A LYS* 3.1 2.0 + - - +
198A LEU* 2.8 41.2 + - + +
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Residues in contact with LYS 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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126A PHE* 3.7 46.1 - - + +
132A ASP 3.7 17.5 + - - +
133A LEU* 3.7 37.3 - - + +
134A ILE* 6.0 0.2 - - - -
189A ASP* 3.2 26.7 + - - +
191A GLN* 2.8 25.2 + - - +
192A ALA* 3.6 6.5 - - - +
194A THR* 1.3 73.5 - - - +
196A SER* 1.3 56.7 + - - +
198A LEU* 3.9 1.7 - - - +
199A VAL* 3.1 31.4 + - - +
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Residues in contact with SER 196 (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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134A ILE* 6.0 1.1 - - - -
192A ALA 3.0 14.4 + - - -
193A ASP* 3.3 12.8 - - - -
195A LYS* 1.3 75.3 - - - +
197A LYS* 1.3 71.4 + - - +
199A VAL* 3.3 15.6 - - - +
200A LYS* 3.2 34.7 - - - +
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Residues in contact with LYS 197 (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 5.2 0.4 - - - +
151A ARG* 4.1 22.0 - - - +
152A ALA* 3.4 27.3 - - + +
155A ASP* 3.6 31.4 - - + +
156A LEU* 3.9 19.3 - - + -
193A ASP* 3.0 28.7 + - - +
194A THR* 3.8 3.1 - - - +
196A SER* 1.3 88.2 + - - +
198A LEU* 1.3 62.9 + - - +
200A LYS* 3.3 26.5 + - + +
201A LEU* 3.5 18.9 + - - +
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Residues in contact with LEU 198 (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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86A LEU* 5.6 0.9 - - + -
95A LEU* 4.2 18.8 - - + -
98A PHE* 4.0 19.3 - - + -
108A PHE* 4.1 19.7 - - + -
124A LEU* 3.7 30.7 - - + -
126A PHE* 4.1 5.2 - - + -
133A LEU* 4.8 2.7 - - + -
156A LEU* 3.5 23.8 - - + -
194A THR* 2.8 34.4 + - + +
195A LYS* 3.9 4.5 - - - +
197A LYS* 1.3 78.2 - - - +
199A VAL* 1.3 57.2 + - - +
200A LYS 3.1 0.6 + - - -
201A LEU* 3.2 9.1 + - + +
202A VAL* 3.0 32.8 + - - +
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Residues in contact with VAL 199 (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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130A TYR* 3.8 27.4 - - + -
133A LEU* 3.7 26.9 - - + +
134A ILE* 3.7 29.6 - - + -
142A VAL* 3.5 21.4 - - + +
195A LYS 3.1 16.2 + - - +
196A SER* 3.3 18.2 - - - +
198A LEU* 1.3 73.2 - - - +
200A LYS* 1.3 61.9 + - + +
201A LEU 3.4 0.2 - - - -
202A VAL* 3.9 3.8 - - + -
203A VAL* 3.3 19.9 + - - +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.8 15.7 - - + +
143A THR* 2.8 44.0 + - - +
144A MET* 4.4 0.9 - - + +
148A GLU* 3.4 32.6 + - + +
152A ALA* 4.9 2.2 - - + -
196A SER* 3.2 31.6 + - - +
197A LYS* 3.6 26.2 - - + +
198A LEU 3.1 0.6 - - - -
199A VAL* 1.3 78.4 - - + +
201A LEU* 1.3 59.7 + - - +
203A VAL* 3.7 1.9 + - - +
204A MET* 3.1 49.2 + - + +
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Residues in contact with LEU 201 (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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77A LEU* 3.9 15.9 - - + -
84A ILE* 3.9 19.3 - - + -
86A LEU* 4.3 19.7 - - + -
95A LEU* 5.5 3.1 - - + -
149A MET* 3.7 33.9 - - + +
152A ALA* 4.2 13.2 - - + -
153A VAL* 4.7 1.6 - - + -
156A LEU* 3.9 28.0 - - + -
197A LYS 3.6 8.7 - - - +
198A LEU* 3.2 8.2 + - + +
200A LYS* 1.3 75.8 - - - +
202A VAL* 1.3 60.1 + - + +
203A VAL 3.2 0.2 - - - -
204A MET* 4.2 11.0 - - + +
205A VAL* 2.8 37.2 + - + +
206A CYS* 5.0 0.3 - - - -
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Residues in contact with VAL 202 (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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94A TYR* 3.5 39.9 - - + +
95A LEU* 3.9 26.7 - - + -
108A PHE* 4.7 5.8 - - + -
130A TYR* 3.9 14.8 - - + +
133A LEU* 4.5 10.3 - - + -
198A LEU 3.0 25.2 + - - +
199A VAL* 4.1 11.4 - - + +
200A LYS 3.4 0.2 - - - -
201A LEU* 1.3 76.9 - - - +
203A VAL* 1.3 57.3 + - - +
206A CYS* 3.2 20.4 + - + +
207A GLU* 3.0 23.8 + - + +
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Residues in contact with VAL 203 (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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130A TYR* 3.4 28.9 - - + +
139A LEU* 4.5 9.2 - - + -
142A VAL* 4.5 11.4 - - + -
144A MET* 3.4 17.9 - - + -
199A VAL* 3.3 20.6 + - + +
200A LYS 4.2 0.9 - - - +
201A LEU 3.2 0.2 - - - -
202A VAL* 1.3 76.2 - - - +
204A MET* 1.3 60.0 + - - +
207A GLU* 3.2 12.9 - - + +
208A GLY 3.0 23.4 + - - -
214A VAL* 3.6 8.2 - - + +
230A LEU* 3.3 33.7 - - + -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 2.4 38.4 + - + +
40A ILE* 4.4 1.0 - - - +
144A MET* 3.6 28.0 - - + -
145A GLY 3.6 29.8 - - - +
148A GLU 4.5 1.8 - - - -
149A MET* 3.6 52.5 - - + +
200A LYS* 3.1 45.9 + - + +
201A LEU* 4.2 6.3 - - + +
203A VAL* 1.3 77.5 - - - +
205A VAL* 1.3 59.4 + - - +
208A GLY* 3.5 5.2 - - - -
218A VAL* 4.1 9.4 - - + -
222A PHE* 4.3 5.2 - - - -
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Residues in contact with VAL 205 (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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36A TYR* 5.5 1.6 - - + -
39A PHE* 5.1 13.0 - - + -
40A ILE* 5.0 3.3 - - + +
75A THR* 4.3 14.6 - - + +
77A LEU* 4.6 13.0 - - + -
86A LEU* 4.2 16.6 - - + -
88A ILE* 4.0 24.5 - - + -
149A MET* 4.3 19.1 - - + -
201A LEU* 2.8 23.6 + - - +
204A MET* 1.3 75.3 - - - +
206A CYS* 1.3 68.7 + - - +
208A GLY* 3.6 0.2 - - - -
209A LEU* 2.8 38.3 + - + +
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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