Contacts of the helix formed by residues 187 - 209 (chain A) in PDB entry 2XTM
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 GLU 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG 3.7 9.8 + - - +
186A ALA* 1.3 79.9 - - - +
188A GLY* 1.3 70.2 + - - +
189A SER 3.5 0.2 + - - -
190A ASN* 3.3 15.8 + - - +
191A GLN* 3.2 16.9 + - - +
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 1.3 74.4 - - - +
189A SER* 1.3 63.9 + - - -
191A GLN* 3.1 11.4 + - - +
192A ASP* 3.0 28.5 + - - +
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU 3.5 0.4 + - - -
188A GLY* 1.3 67.9 - - - -
190A ASN* 1.3 63.5 + - - +
192A ASP* 3.6 12.7 + - - +
193A ASP* 2.7 49.5 + - - +
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Residues in contact with ASN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 4.1 15.0 - - + +
187A GLU 3.3 11.5 + - - +
188A GLY 3.2 0.6 - - - -
189A SER* 1.3 84.2 + - - +
191A GLN* 1.3 60.4 + - - +
193A ASP* 3.8 9.4 - - - +
194A GLN* 3.2 25.6 + - - +
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 4.3 1.2 + - - -
41A SER* 3.4 37.2 + - - +
44A ARG* 3.6 30.8 - - + +
184A ASN 5.9 0.4 + - - -
186A ALA* 3.8 20.8 + - - +
187A GLU* 3.2 15.9 + - - +
188A GLY 3.1 18.3 + - - +
190A ASN* 1.3 72.5 - - - +
192A ASP* 1.3 69.0 - - - +
193A ASP 3.2 0.2 + - - -
194A GLN* 3.3 13.5 + - - +
195A VAL* 3.1 29.8 + - + +
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.4 20.7 + - - +
68A TRP* 3.5 18.3 - - + -
188A GLY 3.0 19.3 + - - +
189A SER* 3.6 14.1 - - - +
191A GLN* 1.3 77.4 - - - +
193A ASP* 1.3 60.9 + - - +
195A VAL* 3.3 0.8 + - - -
196A LYS* 2.9 30.2 + - - +
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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
----------------------------------------------------------
189A SER* 2.7 35.9 + - - +
190A ASN* 3.8 10.6 - - - +
191A GLN 3.2 0.2 - - - -
192A ASP* 1.3 75.8 - - - +
194A GLN* 1.3 61.5 + - - +
196A LYS* 3.4 8.0 + - - +
197A GLU* 3.1 27.6 + - + +
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Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 4.2 15.2 + - - -
148A LYS* 4.2 12.0 - - + +
180A CYS* 4.4 1.4 - - - -
181A ALA 4.2 6.7 - - - +
182A PHE* 3.4 33.4 - - + -
183A ASN* 2.8 52.5 + - - +
186A ALA* 3.8 11.2 + - - +
190A ASN 3.2 12.2 + - - +
191A GLN* 3.3 15.5 + - - +
193A ASP* 1.3 76.4 - - - +
195A VAL* 1.3 69.2 + - + +
197A GLU* 3.2 10.9 + - - +
198A LEU 3.1 16.8 + - - -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.4 30.1 - - - +
42A ILE* 4.1 18.6 - - + +
44A ARG* 4.7 2.2 - - - -
68A TRP* 3.5 32.1 - - + -
182A PHE* 4.2 14.1 - - + -
191A GLN* 3.1 21.8 + - + +
192A ASP 3.8 3.4 - - - +
194A GLN* 1.3 78.4 - - + +
196A LYS* 1.3 59.4 + - - +
198A LEU* 3.2 3.6 + - + +
199A MET* 2.8 38.3 + - + +
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Residues in contact with LYS 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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68A TRP* 3.7 28.6 - - + +
192A ASP 2.9 18.4 + - - +
193A ASP* 3.6 8.7 - - - +
194A GLN 3.3 0.2 - - - -
195A VAL* 1.3 77.6 - - - +
197A GLU* 1.3 55.9 + - + +
199A MET* 3.2 3.8 + - + -
200A ASP* 2.8 64.8 + - - +
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Residues in contact with GLU 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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180A CYS* 4.0 12.1 - - - -
181A ALA 5.9 0.4 - - - +
193A ASP* 3.1 18.2 + - + +
194A GLN* 3.6 10.1 - - - +
195A VAL 3.2 0.2 - - - -
196A LYS* 1.3 76.5 - - + +
198A LEU* 1.3 63.8 + - - +
200A ASP* 3.2 11.8 + - - +
201A CYS* 3.0 25.9 + - - -
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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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25A ILE* 5.5 0.2 - - + -
42A ILE* 3.6 34.5 - - + -
110A LEU* 3.8 31.4 - - + -
142A ILE* 4.3 9.4 - - + -
144A LEU* 4.5 6.1 - - + -
180A CYS* 3.6 29.5 - - + -
182A PHE* 3.7 22.2 - - + -
194A GLN 3.1 6.1 + - - -
195A VAL* 3.2 8.0 + - - +
197A GLU* 1.3 76.8 - - - +
199A MET* 1.3 64.8 + - + +
201A CYS* 3.0 5.6 + - + +
202A ILE* 2.9 35.8 + - + +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.2 19.7 - - + -
25A ILE* 5.1 0.9 - - + -
42A ILE* 3.9 28.9 - - + -
68A TRP* 3.5 41.3 - - + +
73A ILE* 4.0 24.5 - - + -
195A VAL* 2.8 26.1 + - + +
196A LYS* 3.7 8.1 - - + +
198A LEU* 1.3 79.4 - - + +
200A ASP* 1.3 54.2 + - - +
202A ILE* 3.3 13.5 + - + +
203A GLU* 2.8 35.3 + - - +
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Residues in contact with ASP 200 (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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196A LYS* 2.8 54.3 + - - +
197A GLU* 3.5 11.6 - - - +
198A LEU 3.2 0.2 - - - -
199A MET* 1.3 78.5 - - - +
201A CYS* 1.3 61.6 + - - +
203A GLU* 3.4 16.9 + - - +
204A ASP* 3.1 29.0 + - - +
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Residues in contact with CYS 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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142A ILE* 4.1 19.4 - - + -
178A ARG* 5.2 6.2 - - + -
179A ILE 3.7 25.1 - - - +
180A CYS* 4.1 10.8 - - - -
197A GLU* 3.0 20.0 + - - -
198A LEU* 3.0 11.5 + - + +
200A ASP* 1.3 75.1 - - - +
202A ILE* 1.3 62.5 - - - +
204A ASP* 3.3 6.9 - - - +
205A LEU* 3.0 22.9 - - - -
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Residues in contact with ILE 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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23A LEU* 3.9 37.9 - - + -
25A ILE* 4.2 14.6 - - + -
108A VAL* 3.7 29.8 - - + -
110A LEU* 5.1 0.9 - - + -
142A ILE* 3.7 22.4 - - + -
198A LEU* 2.9 32.5 + - + +
199A MET* 3.6 16.4 - - - +
201A CYS* 1.3 73.2 + - - +
203A GLU* 1.3 66.0 + - - +
205A LEU* 3.2 3.2 + - - +
206A LEU* 2.9 30.7 + - + +
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Residues in contact with GLU 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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199A MET 2.8 20.2 + - - +
200A ASP* 3.5 20.4 - - - +
201A CYS 3.3 0.2 - - - +
202A ILE* 1.3 73.5 - - - +
204A ASP* 1.3 65.0 + - - +
206A LEU* 3.4 5.3 + - - +
207A MET* 3.0 41.7 + - + +
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Residues in contact with ASP 204 (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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200A ASP* 3.1 13.6 + - - +
201A CYS* 3.8 8.7 - - - +
202A ILE 3.3 0.2 - - - -
203A GLU* 1.3 83.2 - - - +
205A LEU* 1.3 66.2 + - - +
207A MET* 3.4 9.0 + - - +
208A GLU* 3.1 21.8 + - - +
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Residues in contact with LEU 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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107A HIS 4.2 13.2 - - - +
108A VAL* 4.2 8.3 - - + -
139A GLY 3.7 20.9 - - - +
140A HIS* 3.9 27.1 - - - +
142A ILE* 4.2 21.8 - - + -
178A ARG* 3.8 31.8 - - - +
201A CYS 3.0 13.5 - - - -
202A ILE* 3.6 7.2 - - - +
204A ASP* 1.3 77.1 - - - +
206A LEU* 1.3 67.1 + - + +
208A GLU* 3.1 13.2 + - - +
209A LYS* 3.1 34.7 + - + +
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Residues in contact with LEU 206 (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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23A LEU* 3.8 29.2 - - + -
71A ARG* 5.8 3.1 - - - +
107A HIS* 4.0 34.3 - - + +
108A VAL* 5.2 0.2 - - + -
140A HIS* 4.9 2.2 - - + -
202A ILE* 2.9 26.1 + - + +
203A GLU* 4.0 5.4 - - - +
205A LEU* 1.3 84.9 - - + +
207A MET* 1.3 61.0 + - - +
209A LYS* 3.1 3.4 + - + +
210A ASN 3.0 4.0 + - - -
211A GLY* 2.7 39.6 + - - +
212A ASP 3.7 22.7 - - - +
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Residues in contact with MET 207 (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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203A GLU* 3.0 31.8 + - + +
204A ASP* 3.4 9.9 - - - +
205A LEU 3.2 0.2 - - - -
206A LEU* 1.3 75.8 - - - +
208A GLU* 1.3 63.2 - - - +
210A ASN* 3.1 17.1 - - - +
211A GLY 5.0 0.2 + - - -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 4.1 20.1 + - - -
204A ASP 3.1 9.3 + - - +
205A LEU* 3.1 13.4 + - - +
207A MET* 1.3 79.7 + - - +
209A LYS* 1.3 84.9 + - - +
210A ASN* 3.3 11.0 + - - -
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY* 3.3 31.6 + - - -
140A HIS* 3.7 26.9 - - + +
205A LEU* 3.1 23.1 + - + +
206A LEU* 3.1 6.4 + - - +
208A GLU* 1.3 103.1 + - - +
210A ASN* 1.3 73.4 + - - +
211A GLY 3.1 0.4 - - - -
212A ASP* 3.0 37.0 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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