Contacts of the helix formed by residues 200 - 216 (chain A) in PDB entry 5TQW
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 ALA 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS* 3.5 34.7 - - + +
141A ILE* 4.2 10.8 - - + +
199A THR* 1.3 81.8 + - - +
201A THR* 1.3 55.5 + - + -
202A VAL 3.2 0.9 - - - -
203A ASP 3.3 4.8 + - - -
204A TYR* 3.0 47.7 + - + +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 2.6 22.6 + - - +
199A THR* 3.2 24.5 - - + +
200A ALA* 1.3 73.0 - - + +
202A VAL* 1.3 59.8 + - - +
204A TYR* 3.5 19.7 - - + -
205A TRP* 2.9 29.5 + - - +
284A PRO* 3.2 26.7 - - - +
287A ARG* 3.3 33.2 + - - +
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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
----------------------------------------------------------
141A ILE* 4.7 5.2 - - + -
143A ARG* 3.9 20.4 - - + +
187A TYR 4.8 3.1 - - - +
189A ALA* 3.7 16.8 - - + +
191A GLU* 3.0 29.3 + - + +
192A LEU* 3.9 31.6 - - + -
198A TYR* 3.8 16.4 - - + -
199A THR 3.5 15.3 - - - +
200A ALA 3.2 0.4 - - - -
201A THR* 1.3 77.6 + - - +
203A ASP* 1.3 58.0 + - - +
205A TRP* 3.4 1.7 + - - +
206A SER* 2.8 31.9 + - - -
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.8 4.6 - - + +
136A HIS* 3.6 16.2 + - + +
141A ILE* 3.1 12.0 - - - +
142A HIS* 2.4 35.3 + - - +
143A ARG* 2.7 27.6 + - - -
144A ASP 3.7 0.9 + - - -
145A LEU* 3.3 24.1 - - + +
199A THR 4.8 0.2 + - - -
200A ALA 3.3 9.5 + - - +
202A VAL* 1.3 76.0 - - - +
204A TYR* 1.3 55.9 + - - +
206A SER* 3.4 3.7 + - - -
207A PHE* 2.6 39.1 + - - +
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Residues in contact with TYR 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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132A ILE* 5.2 5.2 - - + -
136A HIS* 3.3 30.5 + + - +
200A ALA* 3.0 35.8 + - + +
201A THR* 3.5 27.1 - - + -
203A ASP* 1.3 78.4 - - - +
205A TRP* 1.3 57.9 + - - +
207A PHE* 3.3 2.3 + - - +
208A GLY* 3.0 24.9 + - - -
279A MET* 3.1 39.6 - - + +
287A ARG* 4.8 4.5 - - + -
288A GLY* 4.0 20.0 - - - -
289A GLY 6.1 0.2 - - - -
298A PRO* 4.0 24.5 - - + +
300A CYS* 5.4 1.8 - - + -
301A PHE* 4.3 17.9 - + - -
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Residues in contact with TRP 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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186A GLN 3.4 17.7 - - - -
187A TYR* 3.4 27.6 - - - -
188A LEU 3.5 15.5 - - - -
189A ALA* 3.6 16.8 - - + -
190A PRO* 4.7 7.8 - - + +
201A THR 2.9 20.1 + - - +
202A VAL 3.7 1.8 - - - +
204A TYR* 1.3 77.6 - - - +
206A SER* 1.3 68.0 + - - +
208A GLY* 3.8 0.5 - - - -
209A THR* 2.3 46.7 + - + -
221A PHE* 3.4 31.2 - + - -
230A TRP* 3.5 13.7 - + - -
231A HIS* 5.2 1.8 - + - -
234A ILE* 5.7 3.2 - - + +
279A MET 3.7 20.2 - - - -
280A LEU* 3.5 23.7 + - + +
281A ASN 4.8 0.4 - - - -
282A TRP* 5.8 1.2 - - - +
287A ARG* 3.3 32.2 - - - +
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Residues in contact with SER 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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143A ARG 5.6 0.4 - - - -
144A ASP 5.0 0.3 + - - -
145A LEU* 3.3 26.2 + - - +
187A TYR* 3.4 36.8 - - - -
202A VAL* 2.8 27.8 + - - +
203A ASP* 3.4 9.2 + - - -
205A TRP* 1.3 76.8 - - - +
207A PHE* 1.3 61.5 + - - +
209A THR* 4.0 4.9 - - - -
210A MET* 2.9 30.4 + - - +
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 6.4 0.4 - - + -
125A LEU* 4.1 13.2 - - + -
128A ILE* 3.5 33.0 - - + -
129A GLY* 3.8 19.3 - - - -
132A ILE* 3.6 22.2 - - + -
145A LEU* 3.7 15.0 - - + -
203A ASP 2.6 23.6 + - - +
204A TYR* 3.4 5.4 - - - +
205A TRP 3.2 0.2 - - - -
206A SER* 1.3 77.8 + - - +
208A GLY* 1.3 58.2 + - - +
210A MET* 3.2 13.4 + - + +
211A VAL* 2.9 41.5 + - + +
275A TRP* 3.4 38.1 - + - -
279A MET* 4.6 4.7 - - + -
304A MET* 3.8 12.3 - - + -
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Residues in contact with GLY 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 TYR 3.0 15.0 + - - -
205A TRP 4.0 0.4 - - - -
207A PHE* 1.3 77.3 - - - +
209A THR* 1.3 56.9 + - - +
211A VAL* 3.3 8.5 + - - +
212A PHE* 2.9 29.1 + - - +
275A TRP* 4.3 10.8 - - - -
276A LEU* 3.9 21.6 - - - +
279A MET* 4.4 6.7 - - - -
280A LEU* 5.7 2.7 - - - -
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLN 3.8 10.8 - - - +
187A TYR* 3.5 25.8 - - + -
205A TRP* 2.3 46.4 + - + -
206A SER* 3.9 1.1 - - - -
208A GLY* 1.3 75.4 - - - +
210A MET* 1.3 60.6 + - - +
212A PHE* 3.4 1.0 + - - -
213A GLU* 2.9 36.8 + - - +
220A PRO* 3.7 31.9 - - + +
221A PHE* 5.2 1.6 - - + -
230A TRP* 5.2 2.0 - - + -
280A LEU* 4.1 8.9 - - - +
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Residues in contact with MET 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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103A LEU* 5.4 1.3 - - + -
107A LEU* 5.5 0.2 - - - +
124A LEU* 5.5 7.9 - - + -
128A ILE* 3.9 31.0 - - + -
145A LEU* 3.7 7.9 - - + +
146A LYS 3.5 37.0 - - - +
147A PRO* 3.8 19.7 - - + -
150A ILE* 4.5 9.6 - - + -
187A TYR* 3.3 16.9 + - + +
206A SER 2.9 20.7 + - - +
207A PHE* 3.5 19.1 - - + +
209A THR* 1.3 74.9 - - - +
211A VAL* 1.3 60.6 + - + +
213A GLU* 3.3 2.6 + - - +
214A CYS* 3.0 40.6 + - - -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.4 9.9 - - + -
124A LEU* 5.3 9.4 - - + -
125A LEU* 4.2 23.8 - - + -
207A PHE* 2.9 48.6 + - + +
208A GLY* 3.6 8.7 - - - +
209A THR 3.2 0.2 - - - -
210A MET* 1.3 80.8 - - + +
212A PHE* 1.3 57.5 + - - +
214A CYS* 2.9 11.3 + - - +
215A ILE* 2.9 42.9 + - + +
272A MET* 4.4 8.5 - - + -
275A TRP* 4.4 3.6 - - + -
276A LEU* 5.7 1.6 - - + -
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Residues in contact with PHE 212 (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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208A GLY 2.9 16.2 + - - +
211A VAL* 1.3 72.7 - - - +
213A GLU* 1.3 57.9 + - - +
214A CYS 3.1 5.6 - - - -
215A ILE* 3.9 23.3 - - + +
216A ALA* 2.9 52.8 + - + +
217A GLY 3.5 1.0 + - - -
218A TYR* 4.0 5.8 - + - -
219A ARG 4.8 0.4 - - - -
220A PRO* 3.5 44.9 - - + -
242A ILE 5.4 2.2 - - - -
243A PHE* 4.2 13.5 - + + -
258A LEU* 3.6 30.7 - - + -
259A PRO* 3.5 28.3 - - + -
276A LEU* 4.4 16.6 - - + -
280A LEU* 6.2 1.3 - - + -
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Residues in contact with GLU 213 (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 LEU* 3.9 16.1 - - + +
186A GLN* 2.9 35.4 - - - +
187A TYR* 2.4 40.1 + - - +
209A THR* 2.9 19.1 + - - +
210A MET 3.5 2.7 - - - +
212A PHE* 1.3 75.5 - - - +
214A CYS* 1.3 58.5 + - - +
217A GLY* 3.2 24.2 - - - +
218A TYR* 3.2 24.2 - - - +
219A ARG* 3.3 18.8 - - - +
220A PRO* 3.5 11.1 - - + +
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Residues in contact with CYS 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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103A LEU* 4.5 9.0 - - - -
107A LEU* 3.7 30.2 - - - +
115A GLY* 3.6 3.0 - - - -
116A LEU* 3.3 37.9 + - + +
121A ILE* 3.4 17.0 - - + +
124A LEU* 3.7 23.6 - - + -
210A MET* 3.0 20.5 + - - -
211A VAL 2.9 10.8 + - - +
213A GLU* 1.3 79.6 - - - +
215A ILE* 1.3 60.9 + - - +
217A GLY 4.1 1.3 - - - -
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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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114A CYS 3.0 14.0 - - - +
115A GLY* 3.2 8.8 - - - -
116A LEU 4.1 1.6 + - - +
121A ILE* 3.9 23.7 - - + +
211A VAL* 2.9 34.2 + - + +
212A PHE* 3.0 29.8 + - + +
214A CYS* 1.3 77.6 - - - +
216A ALA* 1.3 61.6 + - + +
258A LEU* 5.5 7.0 - - + -
262A ASN* 5.1 11.9 - - + +
264A LEU* 4.2 37.0 - - + +
272A MET* 4.8 11.9 - - + -
276A LEU* 5.4 6.1 - - + -
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Residues in contact with ALA 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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113A CYS 3.5 6.9 - - - +
114A CYS* 3.0 26.8 - - - +
115A GLY 4.1 0.2 - - - -
212A PHE* 2.9 40.3 + - + +
215A ILE* 1.3 76.0 - - + +
217A GLY* 1.3 58.9 + - - +
218A TYR* 3.4 27.2 + - + +
259A PRO* 4.9 8.3 - - + -
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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
------------------------------------------------------------
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