Contacts of the helix formed by residues 213 - 229 (chain A) in PDB entry 3RQ5
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 GLY 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.6 22.6 - - - +
212A GLY* 1.3 72.6 - - - -
214A THR* 1.3 64.1 + - - +
216A ASP* 3.2 10.4 + - - +
217A THR* 3.1 24.4 + - - -
261A ALA* 3.3 8.0 - - - +
277A COA 2.9 20.2 + - - -
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Residues in contact with THR 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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149A HIS* 5.5 5.2 - - - -
208A ALA 4.5 5.2 - - - +
209A LEU* 2.7 41.1 + - + +
211A LYS* 3.4 17.8 + - + +
212A GLY 4.8 0.7 - - - +
213A GLY* 1.3 77.6 - - - +
215A GLY* 1.3 60.0 + - - +
217A THR* 3.5 3.5 + - - -
218A LEU 3.0 12.5 + - - -
243A HIS* 2.8 35.5 + - - -
259A LEU* 5.0 2.5 - - + +
261A ALA* 3.8 21.8 - - + +
264A LEU* 4.1 11.4 - - + -
277A COA 5.5 0.3 + - - -
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Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.8 5.2 - - - +
149A HIS* 4.8 1.9 + - - -
186A LYS* 3.6 19.8 + - - -
214A THR* 1.3 80.3 + - - +
216A ASP* 1.3 59.3 + - - +
218A LEU* 3.3 6.5 + - - +
219A THR* 3.0 31.9 + - - -
243A HIS* 5.5 0.4 - - - -
277A COA 2.9 22.1 + - - -
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.4 33.1 - - + +
45A LEU* 3.7 17.6 - - + +
46A ALA* 3.3 14.6 - - - +
103A PRO* 3.6 19.4 - - + +
104A GLY 4.6 0.9 + - - -
128A ASP* 4.4 7.6 - - - +
129A ALA* 5.2 1.9 - - - +
213A GLY* 3.2 15.6 + - - +
215A GLY* 1.3 75.9 - - - +
217A THR* 1.3 62.1 + - - +
219A THR* 3.3 3.5 + - - -
220A GLY 3.2 16.8 + - - -
277A COA 3.2 24.5 + - - -
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Residues in contact with THR 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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45A LEU* 3.8 23.0 + - - +
49A GLY* 4.1 1.8 - - - -
213A GLY 3.1 12.8 + - - -
214A THR* 3.6 10.8 - - - -
216A ASP* 1.3 76.8 - - - +
218A LEU* 1.3 63.7 + - - +
220A GLY* 3.2 3.6 + - - -
221A MET* 2.9 35.8 + - + +
243A HIS* 4.2 2.9 - - + -
261A ALA* 3.6 17.6 + - - +
264A LEU* 4.1 21.8 - - + -
265A SER* 3.6 23.1 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 5.4 3.4 - - + -
184A VAL* 4.5 4.9 - - + -
186A LYS* 3.9 30.1 - - + +
190A THR* 5.9 0.2 - - + -
214A THR 3.0 9.1 + - - +
215A GLY* 3.3 8.0 + - - +
217A THR* 1.3 76.3 - - - +
219A THR* 1.3 62.3 + - - +
221A MET* 3.0 4.3 + - + +
222A ILE* 2.9 40.0 + - + +
239A ALA* 3.8 26.5 - - + +
240A VAL* 3.9 25.4 - - + +
243A HIS* 3.7 36.3 - - + +
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Residues in contact with THR 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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46A ALA* 5.1 2.0 - - + -
100A ALA* 4.0 22.9 - - + -
101A ILE 5.6 0.2 - - - +
103A PRO* 3.8 22.9 - - + -
126A ILE* 3.8 15.1 - - + +
128A ASP* 2.7 32.5 + - + +
147A THR* 3.6 8.3 + - - +
215A GLY 3.0 12.3 + - - -
216A ASP 3.7 4.5 - - - -
217A THR 3.3 0.4 - - - -
218A LEU* 1.3 77.5 - - - +
220A GLY* 1.3 63.8 + - - +
222A ILE* 3.4 11.2 + - - +
223A LEU* 3.0 21.3 + - - +
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Residues in contact with GLY 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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32A LEU* 5.8 0.2 - - - -
46A ALA* 3.2 29.7 - - - +
50A ALA* 3.0 19.0 - - - -
216A ASP 3.2 5.1 + - - -
217A THR 3.2 6.9 + - - -
219A THR* 1.3 80.0 - - - +
221A MET* 1.3 56.3 + - - +
223A LEU* 3.1 6.7 + - - +
224A GLY 2.9 25.3 + - - -
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Residues in contact with MET 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 3.7 12.1 - - - +
53A SER* 3.5 18.4 - - - +
217A THR* 2.9 23.4 + - + +
218A LEU* 3.5 7.9 - - + +
220A GLY* 1.3 76.7 - - - +
222A ILE* 1.3 57.2 + - - +
224A GLY 3.4 0.3 + - - -
225A MET* 2.9 43.3 + - + +
239A ALA* 3.6 16.2 - - + +
242A LEU 4.0 0.7 - - - -
243A HIS* 3.5 53.8 - - - +
246A CYS* 5.3 0.7 - - - -
264A LEU* 5.5 5.6 - - - +
265A SER* 5.6 1.1 - - - -
268A LEU* 3.9 33.7 - - + -
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Residues in contact with ILE 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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126A ILE* 3.6 19.7 - - + -
145A ILE* 4.6 2.5 - - + -
147A THR* 3.8 29.4 - - + -
184A VAL* 4.6 12.3 - - + -
218A LEU* 2.9 36.8 + - + +
219A THR* 3.8 7.0 - - - +
221A MET* 1.3 75.5 - - - +
223A LEU* 1.3 62.2 + - - +
225A MET* 3.2 2.6 + - - +
226A LEU* 2.9 33.4 + - + +
235A ALA 5.0 0.2 - - - -
236A VAL* 3.9 27.8 - - + +
239A ALA* 3.6 21.1 - - + -
240A VAL* 4.7 3.4 - - + -
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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
----------------------------------------------------------
30A ALA* 3.8 17.5 - - + -
31A LEU 3.8 14.6 - - - +
32A LEU* 4.0 19.7 - - + -
50A ALA* 4.0 14.1 - - + -
58A LEU* 4.2 0.4 - - + -
98A ALA* 3.6 38.6 - - + +
99A ILE 3.6 2.5 - - - +
100A ALA* 3.6 26.2 - - + +
126A ILE* 3.4 10.9 - - + +
219A THR 3.0 14.0 + - - +
220A GLY* 3.3 9.4 - - - +
222A ILE* 1.3 78.1 - - - +
224A GLY* 1.3 64.4 + - - +
226A LEU* 3.4 14.3 + - - +
227A CYS* 3.6 10.7 - - - -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.6 19.8 - - - +
53A SER* 3.0 20.6 - - - +
55A LEU* 3.9 13.1 + - - -
220A GLY 2.9 11.5 + - - -
221A MET 3.9 1.8 - - - -
223A LEU* 1.3 76.6 - - - +
225A MET* 1.3 57.1 + - - +
227A CYS* 2.9 25.3 + - - +
228A CYS* 3.5 3.6 + - - -
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Residues in contact with MET 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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15A LEU* 5.0 0.2 - - - -
53A SER* 3.3 21.5 + - - +
221A MET* 2.9 27.4 + - + +
222A ILE 3.9 1.8 - - - +
224A GLY* 1.3 75.3 - - - +
226A LEU* 1.3 62.4 + - - +
227A CYS 3.1 0.3 + - - -
228A CYS* 3.2 3.4 + - - -
229A HIS* 2.9 44.2 + - + +
235A ALA* 3.5 18.4 - - - +
238A ASN* 3.7 12.1 - - - -
239A ALA* 3.4 36.3 - - + -
242A LEU* 3.6 26.9 - - + -
268A LEU* 4.8 0.2 - - + -
272A TRP* 3.6 22.4 - - + -
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Residues in contact with LEU 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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97A ARG* 4.1 10.9 - - - +
98A ALA* 3.8 18.6 - - + -
124A PRO* 4.0 23.0 - - + +
126A ILE* 3.7 26.0 - - + -
145A ILE* 3.9 17.0 - - + -
222A ILE* 2.9 26.5 + - + +
223A LEU* 3.5 7.6 - - - +
224A GLY 3.2 0.2 - - - -
225A MET* 1.3 75.8 - - - +
227A CYS* 1.3 60.4 + - - +
228A CYS 3.4 0.2 - - - -
229A HIS 3.6 13.8 - - - +
232A PRO* 3.5 41.6 - - + +
235A ALA* 3.7 10.5 - - + -
236A VAL* 4.6 0.9 - - + -
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Residues in contact with CYS 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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26A THR 4.5 0.2 - - - +
27A TYR* 3.7 5.2 - - - -
28A GLY 3.2 32.5 + - - +
30A ALA* 3.8 24.7 - - - -
54A GLY 4.6 0.9 - - - -
55A LEU* 3.8 16.6 - - + -
97A ARG* 3.3 37.5 + - - -
98A ALA* 4.3 5.6 - - - -
223A LEU 3.6 14.8 - - - -
224A GLY 2.9 11.4 + - - +
226A LEU* 1.3 80.2 - - - +
228A CYS* 1.3 56.7 + - - +
229A HIS 4.9 0.7 - - - -
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Residues in contact with CYS 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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16A PRO* 3.2 33.5 - - + +
18A ARG* 4.7 2.0 - - - +
27A TYR* 4.1 18.2 - - + -
53A SER 3.5 24.5 - - - -
54A GLY* 3.4 21.8 - - - +
225A MET* 3.2 14.2 + - - -
227A CYS* 1.3 77.2 - - - +
229A HIS* 1.3 69.5 + - - +
230A GLU* 4.2 3.1 + - - +
272A TRP* 4.2 11.0 - - - -
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Residues in contact with HIS 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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14A THR 3.6 19.1 - - - -
15A LEU* 3.8 4.9 - - + +
16A PRO* 3.5 25.7 - - + +
225A MET* 2.9 55.3 + - + +
226A LEU* 3.6 14.0 - - - +
227A CYS 4.9 0.7 - - - -
228A CYS* 1.3 84.0 - - - +
230A GLU* 1.3 64.9 + - - +
231A ASP 3.7 17.7 - - - +
232A PRO* 4.8 1.4 - - - +
234A HIS* 3.9 6.1 - - + -
235A ALA* 3.8 18.4 - - + -
238A ASN* 3.0 26.9 + - - +
272A TRP* 5.1 0.9 - + - -
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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