Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 1TF4
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 4.7 4.2 + - - -
210A SER 5.0 3.7 + - - +
211A GLY 3.7 1.0 - - - -
212A TYR* 1.3 88.5 - - + +
214A ASP* 1.3 63.4 + - - +
216A LEU* 3.2 23.6 + - - +
217A VAL* 3.4 13.2 + - - +
239A GLU* 3.0 53.5 + - - +
242A PHE* 3.5 38.8 - - + +
243A LEU* 4.1 9.4 - - + -
244A SER* 5.8 2.0 - - - +
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 3.1 14.3 + - - +
211A GLY 3.3 4.3 - - - +
213A GLN* 1.3 75.3 - - - +
215A GLU* 1.3 70.8 + - - +
217A VAL* 3.3 4.6 + - - +
218A TRP* 3.0 29.5 + - - +
243A LEU* 3.7 11.8 - - + +
261A ASP 3.1 1.0 - - - +
262A ASP* 3.6 21.3 - - - +
263A LYS* 3.0 18.5 + - - +
264A SER* 3.7 20.4 - - - +
267A THR* 4.6 1.8 - - - +
3001A CA 2.3 31.2 - - - -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.5 3.0 - - - -
150A SER 4.4 0.2 - - - +
151A ASP* 3.4 36.8 - - - +
154A ALA* 3.4 20.5 - - + +
155A GLU* 4.2 7.6 - - + +
211A GLY 2.8 13.2 - - - +
212A TYR* 3.0 9.7 + - - +
214A ASP* 1.3 89.0 - - - +
216A LEU* 1.3 57.3 + - - +
218A TRP* 3.9 7.1 - - - +
219A GLY* 2.8 23.8 + - - -
261A ASP 2.9 2.3 - - - +
263A LYS* 2.8 32.9 + - + +
3001A CA 2.4 30.4 - - - -
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Residues in contact with LEU 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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150A SER* 5.0 2.0 - - - -
154A ALA* 4.7 4.0 - - + -
186A TYR* 2.8 41.7 + - + +
189A ALA* 4.3 12.3 - - + +
190A ASP* 4.3 21.3 - - - +
193A ARG* 3.7 36.1 - - - +
212A TYR* 3.1 31.4 + - + +
213A GLN* 3.2 17.9 + - - +
215A GLU* 1.3 75.0 - - - +
217A VAL* 1.3 64.7 + - - +
220A ALA* 3.3 13.3 + - - +
239A GLU* 4.3 18.5 - - + +
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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
----------------------------------------------------------
213A GLN 3.6 13.5 - - - +
214A ASP 3.3 5.5 + - - +
216A LEU* 1.3 74.7 - - - +
218A TRP* 1.3 65.4 + - - +
220A ALA* 3.4 2.3 + - - +
221A TYR* 3.1 24.0 + - + +
236A ALA* 3.7 24.3 - - + +
239A GLU* 3.7 13.7 - - + +
240A TYR* 3.7 37.0 - - + +
243A LEU* 4.0 12.6 - - + -
267A THR* 3.8 26.0 - - + +
271A LEU* 4.3 7.4 - - + -
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Residues in contact with TRP 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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68A PHE* 4.2 13.7 - + - -
71A THR* 3.4 27.0 - - + +
72A MET* 4.6 2.7 - - - -
75A TRP* 3.7 30.3 - + - -
155A GLU* 3.0 37.0 + - - -
158A ALA* 3.8 10.7 - - + +
214A ASP 3.0 18.6 + - - +
215A GLU* 3.9 6.5 - - - +
217A VAL* 1.3 78.6 - - - +
219A GLY* 1.3 61.9 + - - +
221A TYR* 3.4 3.1 + - - +
222A TRP* 3.2 44.5 + - - -
258A ILE* 3.9 16.4 - - + -
263A LYS* 3.8 25.1 - - + -
266A GLY* 4.3 4.3 - - - -
267A THR* 3.9 16.5 - - + +
270A LEU* 3.6 27.1 - - + -
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA 4.0 8.7 - - - -
157A ALA* 5.6 0.2 - - - -
158A ALA* 4.0 19.8 - - - -
186A TYR* 3.9 12.6 - - - -
215A GLU 2.8 21.8 + - - -
218A TRP* 1.3 75.1 - - - +
220A ALA* 1.3 61.9 + - - +
222A TRP* 3.4 2.8 + - - +
223A LEU* 3.0 27.5 + - - +
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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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186A TYR* 3.6 17.9 - - + +
216A LEU 3.3 20.9 + - - +
217A VAL 3.7 3.8 - - - +
219A GLY* 1.3 74.6 - - - +
221A TYR* 1.3 65.7 + - - +
223A LEU* 3.2 5.4 + - - +
224A TYR* 3.0 18.4 + - - +
232A TYR* 3.6 33.9 - - + +
235A LYS* 3.9 6.7 - - + -
236A ALA* 3.9 12.3 - - + +
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Residues in contact with TYR 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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217A VAL* 3.1 17.2 + - + +
218A TRP* 3.7 4.7 - - - +
219A GLY 3.3 0.2 - - - -
220A ALA* 1.3 77.8 - - - +
222A TRP* 1.3 82.9 + + - +
224A TYR* 3.0 23.7 + + - +
225A LYS* 3.0 47.8 + - + +
233A LEU* 5.1 2.0 - - + +
236A ALA* 4.1 10.2 - - + +
267A THR* 5.9 3.4 - - + -
270A LEU* 3.6 66.7 + - + +
271A LEU* 4.0 21.3 - - + -
273A LYS* 5.2 4.9 - - - +
274A GLU* 3.5 23.6 + - + -
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Residues in contact with TRP 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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71A THR* 3.8 8.2 - - + +
75A TRP* 3.7 54.1 - + + -
78A ILE* 3.8 24.9 - - + -
158A ALA* 3.9 35.9 - - + +
161A ALA* 3.7 4.8 - - + +
162A ALA* 3.8 17.7 - - + -
165A ILE* 4.4 4.9 - - + +
218A TRP* 3.2 53.1 + + - +
219A GLY 4.0 2.9 - - - +
221A TYR* 1.3 100.3 - + - +
223A LEU* 1.3 57.4 + - - +
225A LYS* 3.3 13.3 + - + +
226A ALA* 3.0 28.4 + - - +
270A LEU* 4.0 12.4 - - + +
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Residues in contact with LEU 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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157A ALA* 4.9 3.4 - - + +
161A ALA* 4.1 11.4 - - + -
179A VAL* 4.5 3.4 - - + +
182A ALA* 3.8 30.7 - - + +
183A LYS* 4.1 17.7 - - + +
186A TYR* 3.4 40.2 - - + -
219A GLY 3.0 17.5 + - - +
220A ALA 3.7 4.3 - - - +
222A TRP* 1.3 73.6 - - - +
224A TYR* 1.3 55.8 + - - +
226A ALA* 4.5 0.4 - - + -
227A THR* 2.7 51.0 + - + +
232A TYR* 3.7 27.6 - - + +
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Residues in contact with TYR 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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220A ALA 3.0 13.6 + - - +
221A TYR* 3.0 14.6 + + - +
223A LEU* 1.3 77.2 - - - +
225A LYS* 1.3 67.6 + - + +
227A THR* 3.9 2.7 - - - -
228A GLY* 2.6 42.4 + - - -
229A ASP 3.3 17.5 - - - -
230A ASP* 3.8 23.0 + - - -
232A TYR* 3.8 13.9 - - + +
233A LEU* 3.7 50.2 - - + +
274A GLU* 3.5 30.8 + - + -
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Residues in contact with LYS 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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165A ILE* 3.7 22.6 - - + +
221A TYR* 3.0 51.7 + - + +
222A TRP* 3.6 13.9 - - + +
224A TYR* 1.3 86.3 - - + +
226A ALA* 1.3 59.6 + - - +
227A THR 4.9 0.2 - - - -
228A GLY* 4.5 1.9 + - - -
274A GLU* 3.3 28.5 + - - +
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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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161A ALA* 3.4 22.4 - - + +
164A SER* 3.4 23.7 + - - +
165A ILE* 3.9 9.6 - - + +
179A VAL* 4.1 15.8 - - + +
222A TRP 3.0 14.6 + - - +
223A LEU* 3.3 3.8 + - + +
225A LYS* 1.3 80.4 - - - +
227A THR* 1.3 61.3 + - + +
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Residues in contact with THR 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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179A VAL* 3.7 28.0 - - + -
183A LYS* 3.9 19.1 - - - +
223A LEU* 2.7 35.5 + - + +
225A LYS 4.9 0.2 - - - -
226A ALA* 1.3 80.8 - - - +
228A GLY* 1.3 59.1 + - - -
229A ASP* 3.1 26.5 + - - +
232A TYR* 3.6 7.7 - - + -
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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