Contacts of the helix formed by residues 191 - 211 (chain A) in PDB entry 1XT9
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 THR 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 4.4 2.2 - - - -
187A LEU 5.5 2.0 - - - +
188A GLN 3.9 19.5 - - - +
189A LEU 2.9 6.1 + - - +
190A LEU* 1.3 77.0 - - - +
192A PRO* 1.3 77.0 - - - +
193A ALA* 3.6 8.0 + - - +
194A TYR* 3.0 22.6 + - - +
195A ILE* 3.1 20.3 + - - +
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Residues in contact with PRO 192 (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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156A ALA 5.3 1.3 - - - +
158A GLN* 3.4 48.7 - - + +
159A ASN* 5.9 5.6 - - - +
162A ASP* 5.2 0.8 - - - +
166A TYR* 3.9 15.9 - - - +
190A LEU 4.8 0.4 - - - +
191A THR* 1.3 89.1 - - + +
193A ALA* 1.3 60.2 + - - +
195A ILE* 3.1 6.5 + - + +
196A THR* 2.9 32.6 + - + +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 3.2 7.8 + - - +
192A PRO* 1.3 77.6 - - - +
194A TYR* 1.3 66.7 + - - +
196A THR* 3.4 9.2 + - - +
197A LYS* 2.9 25.3 + - - +
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Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A CYS* 4.7 5.8 - - + -
172A GLU* 4.9 2.8 + - - -
173A ALA* 5.8 0.7 - - - +
189A LEU* 3.4 42.5 - - + +
190A LEU* 3.3 33.2 - - + -
191A THR* 3.0 27.6 + - - +
193A ALA* 1.3 77.5 - - - +
195A ILE* 1.3 60.3 + - + +
197A LYS* 3.2 19.3 - - + +
198A LYS* 3.1 67.5 + - + +
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.7 26.9 - - + +
165A MET* 3.5 28.6 - - + +
166A TYR* 3.6 38.4 - - + +
169A CYS* 3.4 34.8 - - + -
190A LEU* 4.7 7.6 - - + -
191A THR 3.1 13.1 + - - +
192A PRO* 3.1 8.3 + - + +
194A TYR* 1.3 73.2 - - + +
196A THR* 1.3 65.6 + - - +
197A LYS 3.1 1.3 - - - -
198A LYS* 3.2 7.9 + - - +
199A ARG* 3.0 19.2 + - - +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 5.7 6.7 - - - -
159A ASN* 5.8 2.5 - - - +
161A TYR* 6.1 0.9 - - - +
162A ASP* 4.6 10.5 - - - +
192A PRO* 2.9 22.4 - - + +
193A ALA* 3.4 8.2 + - - +
195A ILE* 1.3 76.8 - - - +
197A LYS* 1.3 61.9 + - - +
199A ARG* 3.2 30.2 - - - +
200A GLY* 3.4 4.7 + - - -
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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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193A ALA 2.9 14.0 + - - +
194A TYR* 3.2 27.4 - - + +
196A THR* 1.3 79.9 + - - +
198A LYS* 1.3 59.5 + - + +
200A GLY* 3.1 4.9 + - - -
201A GLU* 2.8 53.9 + - + +
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Residues in contact with LYS 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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165A MET* 3.6 17.0 - - + -
169A CYS* 3.7 17.5 - - - -
172A GLU* 3.2 32.5 + - - +
194A TYR* 3.1 45.8 + - + +
195A ILE 3.2 8.3 + - - +
197A LYS* 1.3 80.0 - - + +
199A ARG* 1.3 60.7 + - - +
200A GLY 3.1 0.4 - - - -
201A GLU* 3.0 35.8 + - + +
202A TRP* 2.8 43.5 + - + +
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Residues in contact with ARG 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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20A LEU 3.0 19.6 + - - -
21A LEU* 2.8 53.5 + - + +
22A ASP 3.8 4.2 - - - -
23A PRO* 3.9 27.9 - - + +
25A SER 2.8 22.6 + - - -
27A LEU* 4.1 10.6 - - - +
161A TYR* 3.5 17.6 + - - -
162A ASP* 2.5 31.1 + - - +
165A MET* 3.7 28.3 - - + +
195A ILE 3.0 7.5 + - - +
196A THR* 3.2 21.5 - - - +
197A LYS 3.2 0.2 - - - -
198A LYS* 1.3 76.1 - - - +
200A GLY* 1.3 57.9 + - - +
203A LYS* 3.2 26.4 + - - +
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Residues in contact with GLY 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 THR 3.4 4.5 + - - -
197A LYS 3.1 7.8 + - - -
198A LYS 3.1 0.2 - - - -
199A ARG* 1.3 79.8 - - - +
201A GLU* 1.3 58.1 + - - +
203A LYS* 3.1 8.6 + - - +
204A ASP* 2.8 40.4 + - - +
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Residues in contact with GLU 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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197A LYS* 2.8 49.5 + - + +
198A LYS* 3.0 45.6 + - + +
200A GLY* 1.3 74.8 - - - +
202A TRP* 1.3 58.7 + - + +
204A ASP* 3.3 8.4 + - - +
205A LEU* 2.9 27.9 + - - +
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Residues in contact with TRP 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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21A LEU* 3.9 15.9 - - + -
34A PHE* 3.6 35.7 - + - -
35A ALA* 3.6 25.1 - - + -
38A TYR* 3.9 15.9 - + - -
39A PHE* 3.6 34.8 - + - -
43A GLN* 5.0 3.1 - - - -
165A MET* 3.9 18.2 - - + +
168A ILE* 3.7 19.1 - - + +
169A CYS* 5.4 1.6 - - - -
172A GLU* 4.8 8.2 + - - -
198A LYS* 2.8 40.5 + - + +
199A ARG 4.0 3.4 - - - +
201A GLU* 1.3 78.4 - - + +
203A LYS* 1.3 62.2 + - - +
205A LEU* 3.4 20.0 + - + +
206A ILE* 3.2 29.8 + - + +
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Residues in contact with LYS 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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18A VAL* 4.3 21.1 - - + +
19A SER* 5.8 0.8 - - - +
21A LEU* 3.5 25.5 - - + +
22A ASP* 2.8 37.7 + - - +
199A ARG 3.2 18.9 + - - +
200A GLY* 3.1 10.2 + - - +
202A TRP* 1.3 76.6 - - - +
204A ASP* 1.3 63.9 + - - +
206A ILE* 3.6 3.8 + - - +
207A THR* 3.0 38.1 + - + +
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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 GLY* 2.8 24.7 + - - +
201A GLU* 3.7 7.5 - - - +
203A LYS* 1.3 79.3 - - - +
205A LEU* 1.3 55.6 + - - +
207A THR* 2.6 23.6 + - - +
208A THR* 2.7 29.0 + - - +
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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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34A PHE* 3.9 13.0 - - + -
38A TYR* 3.9 34.5 - - + +
201A GLU 2.9 16.3 + - - +
202A TRP* 3.6 37.7 - - + +
203A LYS 3.3 0.2 - - - -
204A ASP* 1.3 75.4 - - - +
206A ILE* 1.3 57.2 + - - +
208A THR* 3.0 12.0 + - + -
209A LEU* 2.8 52.8 + - + +
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Residues in contact with ILE 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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5A VAL* 4.1 23.1 - - + -
6A LEU* 4.1 14.4 - - + +
13A LEU* 3.4 30.7 - - + -
18A VAL* 4.2 17.0 - - + -
21A LEU* 3.7 23.3 - - + -
31A ILE* 4.7 6.7 - - + -
34A PHE* 3.7 26.5 - - + -
202A TRP* 3.2 16.7 + - + +
203A LYS 3.7 4.0 - - - +
205A LEU* 1.3 80.3 - - - +
207A THR* 1.3 59.7 + - + +
209A LEU* 3.2 2.5 + - - +
210A ALA* 2.8 30.5 + - - +
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Residues in contact with THR 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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5A VAL* 5.7 2.2 - - + -
18A VAL* 5.1 5.6 - - + -
203A LYS* 3.0 27.3 + - + +
204A ASP* 2.6 30.2 + - - +
206A ILE* 1.3 80.6 - - + +
208A THR* 1.3 62.3 + - - +
210A ALA* 3.0 21.3 + - - +
211A LYS* 3.3 10.6 + - - -
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Residues in contact with THR 208 (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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204A ASP* 2.7 26.3 + - - +
205A LEU* 3.3 14.9 - - + -
207A THR* 1.3 73.6 + - - +
209A LEU* 1.3 63.8 + - + +
211A LYS* 3.0 23.9 + - - +
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Residues in contact with LEU 209 (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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6A LEU* 3.5 16.0 - - + +
8A TYR* 4.1 29.2 - - + -
34A PHE* 3.9 29.6 - - + -
38A TYR* 4.4 9.2 - - + -
205A LEU* 2.8 39.0 + - + +
206A ILE 3.7 3.4 - - - +
208A THR* 1.3 76.0 - - + +
210A ALA* 1.3 57.8 + - - +
211A LYS* 2.8 33.6 + - - +
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Residues in contact with ALA 210 (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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5A VAL* 3.6 33.3 - - + +
6A LEU* 4.2 7.9 - - + -
206A ILE 2.8 13.9 + - - +
207A THR* 3.0 16.1 + - - +
209A LEU* 1.3 75.3 - - - +
211A LYS* 1.3 75.1 + - - +
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Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.9 5.7 - - - +
207A THR 3.3 7.8 + - - -
208A THR* 3.0 14.9 + - - +
209A LEU* 2.8 32.1 + - - +
210A ALA* 1.3 87.8 - - - +
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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
------------------------------------------------------------
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