Contacts of the helix formed by residues 213 - 232 (chain A) in PDB entry 4TTB
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 ASN 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY 5.4 1.6 - - - +
132A THR* 4.3 11.3 + - - +
134A PRO* 3.3 24.7 - - + +
196A LYS* 4.0 11.0 - - + -
197A GLN 2.9 28.6 + - - +
198A VAL* 4.5 10.3 + - + +
212A TYR* 1.3 81.2 + - - +
214A GLU* 1.3 61.9 + - - +
216A SER* 3.5 7.3 - - - -
217A VAL* 2.8 35.3 + - - +
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Residues in contact with GLU 214 (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* 3.7 31.4 + - + +
212A TYR 3.4 0.6 - - - -
213A ASN* 1.3 76.3 - - - +
215A ILE* 1.3 64.3 + - + +
217A VAL* 3.9 1.6 - - - +
218A SER* 2.9 33.2 + - - +
260A LEU* 4.2 15.7 - - + +
214B GLU* 3.9 30.2 - - + +
215B ILE* 3.7 22.2 - - + +
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Residues in contact with ILE 215 (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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212A TYR* 3.5 19.7 + - + +
213A ASN 3.3 0.2 - - - -
214A GLU* 1.3 77.2 - - + +
216A SER* 1.3 52.7 + - - +
218A SER* 3.2 2.4 + - - -
219A ILE* 2.8 51.2 + - + +
214B GLU* 3.6 22.0 - - + +
218B SER* 3.7 22.4 - - - +
239B THR* 4.2 16.8 - - + -
241B LEU* 4.5 20.0 - - + -
260B LEU* 4.6 13.7 - - + -
261B MET* 3.9 15.0 - - + -
301B FMN 4.3 7.6 - - + -
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Residues in contact with SER 216 (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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127A PRO 4.3 1.1 - - - +
128A SER* 3.9 20.9 - - - -
129A GLY 3.2 23.0 + - - -
134A PRO* 4.2 8.0 - - - +
135A TRP* 3.7 12.0 - - - -
212A TYR 3.0 15.5 + - - -
213A ASN* 3.5 11.2 - - - -
215A ILE* 1.3 79.1 - - - +
217A VAL* 1.3 64.4 + - - +
219A ILE* 3.4 6.7 + - - +
220A ALA 3.1 16.5 + - - -
301B FMN 3.4 15.8 - - - +
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Residues in contact with VAL 217 (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 PRO* 3.2 36.8 - - + +
135A TRP* 4.1 14.6 - - + -
194A ILE* 3.5 29.8 - - + -
195A PHE 4.4 4.0 - - - +
196A LYS* 4.0 11.9 - - + -
213A ASN 2.8 25.0 + - - +
214A GLU 3.9 2.7 - - - +
216A SER* 1.3 73.0 - - - +
218A SER* 1.3 57.6 + - - +
220A ALA* 3.2 4.2 + - + +
221A CYS* 2.9 27.3 + - - -
260A LEU* 4.2 19.7 - - + -
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Residues in contact with SER 218 (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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214A GLU* 2.9 19.2 + - - +
215A ILE 3.7 0.2 - - - -
217A VAL* 1.3 72.7 - - - +
219A ILE* 1.3 61.6 + - - +
221A CYS* 3.1 11.5 + - - +
222A GLY* 2.8 27.2 + - - -
260A LEU* 4.0 7.8 - - - +
215B ILE* 3.7 36.6 - - - +
218B SER* 3.4 27.0 + - - -
219B ILE* 3.8 5.8 - - - -
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Residues in contact with ILE 219 (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 ALA* 4.3 3.8 - - + -
127A PRO* 4.1 16.2 - - + +
215A ILE* 2.8 30.5 + - + +
216A SER* 3.5 5.2 - - - +
218A SER* 1.3 76.1 - - - +
220A ALA* 1.3 60.1 + - - +
222A GLY 3.2 2.3 + - - -
223A ILE* 3.1 20.9 + - + +
218B SER 3.7 19.3 + - - +
222B GLY* 3.6 22.1 - - - +
225B LEU* 3.8 17.7 - - + -
237B THR* 4.3 8.5 - - + -
261B MET* 3.7 27.8 - - + -
301B FMN 4.2 20.9 - - + -
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Residues in contact with ALA 220 (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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123A ALA* 3.6 23.3 - - - +
126A ALA* 3.7 17.3 - - + -
135A TRP* 3.8 15.5 - - + -
137A PHE* 4.2 14.1 - - + -
216A SER 3.1 11.9 + - - +
217A VAL* 3.4 9.0 - - - +
219A ILE* 1.3 77.6 - - - +
221A CYS* 1.3 50.7 + - - +
223A ILE* 3.1 5.2 + - - +
224A LEU* 2.8 34.2 + - - +
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Residues in contact with CYS 221 (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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137A PHE* 5.1 0.9 - - - -
194A ILE* 3.8 35.2 - - - -
217A VAL 2.9 18.1 + - - -
218A SER 3.4 8.1 - - - +
220A ALA* 1.3 74.7 - - - +
222A GLY* 1.3 57.2 + - - +
224A LEU* 3.1 13.0 - - + +
225A LEU* 2.8 35.1 + - - +
260A LEU* 4.1 8.7 - - - -
261A MET* 3.5 43.3 - - + -
219B ILE* 4.6 0.7 - - + -
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Residues in contact with GLY 222 (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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218A SER 2.8 15.3 + - - -
219A ILE 3.2 3.3 + - - -
221A CYS* 1.3 73.3 - - - +
223A ILE* 1.3 55.6 + - - +
225A LEU* 3.3 4.3 + - - +
226A ALA* 3.1 22.2 + - - +
219B ILE* 3.5 37.8 - - - +
223B ILE* 3.6 18.2 - - - +
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Residues in contact with ILE 223 (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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122A THR* 3.4 26.9 - - + +
123A ALA* 3.9 3.6 - - - -
125A THR* 4.7 2.5 - - - +
126A ALA* 3.8 34.3 - - + +
127A PRO* 4.7 3.6 - - + -
219A ILE* 3.1 18.4 + - + +
220A ALA 3.1 7.4 + - - +
222A GLY* 1.3 72.6 - - - +
224A LEU* 1.3 60.9 + - - +
226A ALA* 3.3 8.1 + - - +
227A ALA* 2.9 27.0 + - - +
93B PHE* 4.6 0.5 - - - -
97B LEU* 3.5 28.3 - - + -
100B ARG* 5.4 4.9 - - - +
222B GLY 3.6 22.0 - - - +
225B LEU* 5.3 4.7 - - + -
226B ALA* 4.7 4.3 - - + +
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Residues in contact with LEU 224 (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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119A VAL* 3.3 37.7 - - + +
120A ILE* 4.5 9.6 - - + -
123A ALA* 3.9 12.3 - - + +
137A PHE* 4.0 15.0 - - + -
192A ILE* 4.5 11.4 - - + -
194A ILE* 3.8 20.0 - - + -
220A ALA 2.8 15.9 + - - +
221A CYS* 3.1 11.2 - - - +
223A ILE* 1.3 74.4 - - - +
225A LEU* 1.3 57.0 + - - +
227A ALA* 3.0 7.4 + - - +
228A LEU* 2.8 34.7 + - + +
263A LEU* 3.5 31.2 - - + -
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Residues in contact with LEU 225 (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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100A ARG* 4.7 20.0 - - - +
221A CYS 2.8 22.8 + - - +
222A GLY 3.3 5.3 + - - +
224A LEU* 1.3 71.4 - - - +
226A ALA* 1.3 62.7 + - - +
228A LEU* 3.3 6.5 + - + +
229A GLN* 3.0 24.3 + - - +
235A THR* 3.7 27.8 - - + -
237A THR* 3.6 27.4 - - + +
261A MET* 5.1 2.0 - - - -
263A LEU* 4.1 17.7 - - + -
127B PRO* 3.8 21.3 - - + -
219B ILE* 3.9 22.4 - - + -
223B ILE* 5.3 3.6 - - + -
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Residues in contact with ALA 226 (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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93A PHE* 4.9 0.4 - - + -
97A LEU* 4.1 32.1 - - + +
100A ARG* 6.1 0.2 - - - +
222A GLY 3.1 13.1 + - - +
223A ILE* 3.5 11.9 - - - +
225A LEU* 1.3 77.1 - - - +
227A ALA* 1.3 57.9 + - - +
229A GLN* 3.5 1.7 + - - +
230A ASN* 3.0 31.0 + - - +
93B PHE* 4.1 17.5 - - + -
223B ILE* 4.7 7.0 - - + +
226B ALA* 4.8 9.4 - - + -
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Residues in contact with ALA 227 (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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119A VAL* 3.7 28.1 - - + +
122A THR* 4.1 14.6 - - + +
223A ILE 2.9 13.9 + - - +
224A LEU 3.0 9.2 + - - +
226A ALA* 1.3 76.4 - - - +
228A LEU* 1.3 59.9 + - - +
230A ASN* 3.5 2.6 + - - +
231A ALA* 3.0 30.3 + - - +
90B SER* 5.8 0.5 - - - -
93B PHE* 3.8 21.2 - - + -
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Residues in contact with LEU 228 (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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116A ILE* 5.7 1.3 - - + -
119A VAL* 3.8 23.1 - - + -
192A ILE* 5.2 2.0 - - + -
224A LEU* 2.8 20.7 + - + +
225A LEU* 3.6 9.9 - - - +
227A ALA* 1.3 72.4 - - - +
229A GLN* 1.3 67.7 + - - +
231A ALA* 3.1 3.8 + - - +
232A GLY 3.0 5.0 + - - -
233A LEU* 2.9 49.3 + - + +
234A VAL 5.3 0.7 - - - +
235A THR* 3.8 28.9 - - + -
263A LEU* 4.2 15.0 - - + -
265A VAL* 4.1 37.5 - - + -
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Residues in contact with GLN 229 (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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96A LEU* 3.1 39.1 + - + +
97A LEU* 3.9 17.0 - - + -
99A LYS* 3.5 24.6 + - - +
100A ARG* 3.6 32.8 - - + +
101A ARG 4.9 0.2 + - - -
225A LEU 3.0 16.5 + - - +
226A ALA 3.8 3.8 - - - +
228A LEU* 1.3 75.0 - - - +
230A ASN* 1.3 54.5 - - - +
232A GLY* 2.8 26.0 + - - -
233A LEU 4.0 10.4 + - - +
234A VAL* 5.4 4.2 - - - +
76B PHE* 5.7 2.4 - - - -
79B ASN* 4.3 14.6 + - - +
81B TYR* 4.7 0.3 - - - -
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Residues in contact with ASN 230 (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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93A PHE* 5.6 0.6 - - + -
96A LEU* 3.6 22.1 - - + +
97A LEU* 5.7 0.2 - - + -
226A ALA 3.0 17.1 + - - +
227A ALA 3.8 4.1 + - - +
229A GLN* 1.3 75.5 - - - +
231A ALA* 1.3 60.7 + - - +
232A GLY 3.2 0.7 + - - -
81B TYR* 3.5 1.9 - - - -
89B ARG* 2.9 80.9 + - - +
90B SER* 4.4 2.0 - - - +
93B PHE* 3.5 32.4 - - + +
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Residues in contact with ALA 231 (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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115A VAL* 4.1 24.2 - - + -
119A VAL* 4.3 8.7 - - + -
227A ALA 3.0 18.2 + - - +
228A LEU 3.7 3.8 - - - +
230A ASN* 1.3 78.2 - - - +
232A GLY* 1.3 62.6 + - - +
233A LEU* 4.4 4.3 - - + -
81B TYR* 3.9 4.4 - - - -
86B MET* 3.3 35.2 - - + +
89B ARG* 5.0 2.7 - - - +
90B SER* 4.4 11.9 - - - -
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Residues in contact with GLY 232 (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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229A GLN* 2.8 12.3 + - - -
230A ASN 3.2 1.6 + - - -
231A ALA* 1.3 80.0 - - - +
233A LEU* 1.3 65.2 + - - +
234A VAL* 5.4 1.3 - - - +
267A TYR* 4.4 13.3 - - - -
268A PRO* 5.2 2.3 - - - +
78B HIS* 4.6 9.0 - - - -
79B ASN* 3.3 30.9 + - - +
81B TYR* 3.8 7.2 - - - -
86B MET* 4.8 1.0 - - - +
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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
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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