Contacts of the helix formed by residues 215 - 230 (chain A) in PDB entry 2L6X
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 SER 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU 5.6 0.2 + - - -
207A GLY 4.6 3.2 + - - +
211A GLY* 6.2 0.6 - - - -
212A ASP* 5.0 16.1 - - - +
213A GLY 4.9 0.2 - - - +
214A GLY* 1.3 75.1 - - - +
216A ALA* 1.3 64.3 + - - +
217A LEU* 3.3 30.3 + - - +
218A ASN* 3.7 16.2 + - - +
219A LEU* 3.9 12.4 + - - +
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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
----------------------------------------------------------
84A ILE* 3.8 18.7 - - + +
214A GLY 3.7 3.2 + - - -
215A SER* 1.3 71.3 + - - +
217A LEU* 1.3 69.3 + - + +
219A LEU* 3.0 19.0 + - + +
220A ASN 2.9 19.1 + - - -
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Residues in contact with LEU 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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23A LEU 3.5 9.0 - - - +
24A ASP 3.0 32.1 - - - +
25A ALA* 3.5 24.9 - - + +
28A TYR* 3.4 27.8 - - + -
29A THR* 4.6 7.6 - - - +
84A ILE* 4.7 10.8 - - + -
215A SER* 3.1 19.4 - - - +
216A ALA* 1.3 81.3 - - + +
218A ASN* 1.3 64.9 + - - +
219A LEU 3.0 0.9 + - - -
220A ASN* 3.0 3.4 + - - +
221A LEU* 2.9 25.5 + - - +
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Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 4.5 16.0 + - - -
28A TYR* 4.0 29.4 + - - -
206A THR* 4.0 12.5 + - - +
207A GLY* 4.4 16.8 - - - -
211A GLY* 5.7 6.4 - - - -
215A SER* 3.7 12.6 + - - +
216A ALA 3.4 0.2 - - - -
217A LEU* 1.3 79.3 - - - +
219A LEU* 1.3 56.4 + - - +
221A LEU* 4.4 6.8 - - - +
222A ILE* 2.9 63.0 + - + +
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Residues in contact with LEU 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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80A ARG* 5.3 2.2 - - - +
204A TYR* 3.6 35.7 - - + +
207A GLY 3.4 27.1 - - - +
208A TYR* 4.7 2.0 - - - -
214A GLY 6.4 0.2 - - - -
215A SER 3.9 7.1 + - - +
216A ALA* 3.0 21.9 + - + +
217A LEU 3.0 0.2 + - - -
218A ASN* 1.3 79.2 - - - +
220A ASN* 1.3 57.5 + - - +
222A ILE* 3.9 3.7 - - - +
223A TYR* 2.9 48.8 + - + -
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 5.7 7.5 + - - +
32A SER* 4.7 9.9 + - - -
80A ARG* 3.3 37.1 + - - +
81A GLY* 4.8 0.3 - - - -
84A ILE* 2.9 61.5 - - + +
216A ALA 2.9 5.9 + - - -
217A LEU* 3.7 4.9 + - - +
219A LEU* 1.3 71.4 - - - +
221A LEU* 1.3 63.4 + - - +
223A TYR* 3.1 2.6 + - - +
224A ASN* 2.7 36.7 + - - +
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Residues in contact with LEU 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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28A TYR* 3.8 37.5 - - + +
32A SER* 3.5 30.5 - - - +
35A LEU* 6.5 0.7 - - + -
36A VAL* 6.1 0.9 - - + -
217A LEU 2.9 15.3 + - - +
218A ASN* 3.9 5.4 - - - +
220A ASN* 1.3 83.7 - - - +
222A ILE* 1.3 73.4 + - + +
224A ASN* 3.2 3.8 + - + -
225A LEU* 2.8 48.3 + - + +
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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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199A ILE 5.7 0.2 - - - +
200A TYR* 4.2 14.8 - - + +
203A GLY* 3.0 36.3 - - - +
204A TYR* 3.7 32.8 - - + +
206A THR* 4.2 3.4 - - + -
207A GLY* 4.5 2.0 - - - +
218A ASN* 2.9 54.4 + - + +
219A LEU* 3.9 4.0 - - - +
221A LEU* 1.3 82.8 - - + +
223A TYR* 1.3 59.2 + - + +
225A LEU* 3.3 10.3 + - + +
226A ALA* 3.0 28.4 + - - +
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Residues in contact with TYR 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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76A TYR* 5.4 5.9 - + + -
80A ARG* 3.1 46.4 - - - +
94A ARG* 5.9 0.4 - - - -
137A PHE* 4.6 20.3 - + - -
200A TYR* 3.6 39.6 + + - -
204A TYR* 4.0 21.7 + + - -
219A LEU* 2.9 46.9 + - + +
220A ASN 3.3 0.7 - - - +
222A ILE* 1.3 77.6 - - + +
224A ASN* 1.3 62.8 + - - +
226A ALA* 3.2 6.6 + - + +
227A ASP* 3.0 24.1 + - - +
301A RET 5.8 0.2 - - + -
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Residues in contact with ASN 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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32A SER* 5.1 6.3 - - - +
36A VAL* 3.9 31.3 - - + +
73A PHE* 5.9 0.4 - - - -
77A MET* 4.2 17.8 - - - +
80A ARG* 3.2 31.5 - - + +
81A GLY* 4.3 4.2 + - - -
220A ASN* 2.7 23.0 + - - +
221A LEU* 3.7 5.8 - - + +
223A TYR* 1.3 73.4 - - - +
225A LEU* 1.3 53.9 + - - +
227A ASP* 4.1 4.1 - - - +
228A PHE* 2.7 47.7 + - - +
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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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35A LEU* 5.9 7.6 - - + -
199A ILE* 5.3 14.1 - - + -
221A LEU* 2.8 36.4 + - + +
222A ILE* 3.5 12.6 - - + +
224A ASN* 1.3 76.9 - - - +
226A ALA* 1.3 57.3 + - - +
228A PHE* 3.3 7.3 + - + +
229A VAL* 3.0 48.1 + - + +
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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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196A GLY 5.7 1.6 - - - +
199A ILE* 6.4 1.3 - - + -
200A TYR* 4.4 35.0 - - + +
222A ILE* 3.0 17.2 + - + +
223A TYR* 3.6 5.4 - - + +
225A LEU* 1.3 80.4 - - + +
227A ASP* 1.3 57.7 + - - +
229A VAL* 3.8 2.8 - - - -
230A ASN* 2.8 44.9 + - - +
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Residues in contact with ASP 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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73A PHE* 4.9 4.0 - - - -
76A TYR* 2.9 61.6 - - + +
77A MET* 4.7 2.3 + - - -
223A TYR 3.0 15.3 + - - +
224A ASN* 4.1 4.3 - - - +
226A ALA* 1.3 77.5 - - - +
228A PHE* 1.3 63.3 + - - +
230A ASN* 3.7 6.7 - - - +
231A LYS* 2.8 51.7 + - - +
301A RET 3.0 9.3 - - + +
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Residues in contact with PHE 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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36A VAL* 4.2 22.4 - - + -
39A ALA* 3.4 33.4 - - + -
40A LEU 4.1 8.3 - - - -
43A SER* 5.3 0.2 - - - -
73A PHE* 3.4 31.0 - + - -
224A ASN* 2.7 28.0 + - - +
225A LEU* 3.5 8.1 - - + +
226A ALA 3.2 0.2 - - - -
227A ASP* 1.3 77.4 - - - +
229A VAL* 1.3 67.5 + - + +
231A LYS 3.3 0.2 + - - -
232A ILE* 2.7 70.8 + - + +
233A LEU* 5.6 3.8 - - + -
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Residues in contact with VAL 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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192A ILE* 5.1 8.6 - - + +
196A GLY* 5.6 7.9 - - - -
199A ILE* 6.4 1.1 - - + -
225A LEU* 3.0 31.5 + - + +
226A ALA* 4.1 3.1 - - - +
228A PHE* 1.3 83.0 - - + +
230A ASN* 1.3 61.8 + - - +
231A LYS 3.0 9.5 + - - -
233A LEU* 2.8 58.0 + - + +
234A PHE* 3.5 2.8 + - - -
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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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105A LEU* 5.9 2.1 - - - +
192A ILE* 6.1 1.3 - - - +
196A GLY* 4.0 22.0 + - - -
197A TRP* 3.9 21.1 - - - +
200A TYR* 5.6 1.8 - - - +
226A ALA* 2.8 35.5 + - - +
227A ASP 3.9 4.0 - - - +
228A PHE 3.2 0.2 - - - -
229A VAL* 1.3 81.6 - - - +
231A LYS* 1.3 63.3 + - - +
234A PHE* 3.8 13.9 - - - +
301A RET 3.6 51.3 - - + +
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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
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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