Contacts of the helix formed by residues 218 - 228 (chain B) in PDB entry 5X6E
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 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ASP* 3.3 21.4 - - + +
145B GLY* 3.7 30.1 - - - +
148B LEU* 4.2 7.2 - - + +
214B LEU 2.9 13.3 + - - +
215B LYS* 3.2 7.0 - - - +
217B TYR* 1.3 79.4 - - - +
219B PRO* 1.3 65.2 - - - +
221B LEU* 4.1 6.7 - - + -
222B ASP* 3.5 18.5 + - - +
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Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER* 5.2 14.8 - - - -
132B ASN* 5.2 0.9 - - - +
133B ASP* 3.3 14.1 - - + +
136B ILE* 4.7 12.8 - - + -
137B ASN* 5.6 0.7 - - - +
215B LYS* 3.1 13.4 - - + +
216B ARG* 4.3 7.0 - - - +
217B TYR 3.5 7.2 - - - +
218B ALA* 1.3 89.4 - - - +
220B LYS* 1.3 69.0 + - + +
222B ASP* 3.6 4.5 + - + +
223B GLU* 3.4 23.4 + - - +
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 6.0 1.6 - - - +
50A SER* 3.2 26.0 - - - +
51A ILE 5.3 5.4 - - - +
52A SER* 5.9 5.8 - - - +
82A TYR* 3.0 25.7 + - - +
83A TYR* 3.6 25.3 - - + +
129B ALA* 3.5 19.5 - - - +
132B ASN* 3.8 17.5 - - + +
133B ASP* 3.2 18.3 + - - +
219B PRO* 1.3 83.3 - - + +
221B LEU* 1.3 65.4 + - - +
223B GLU* 2.3 45.4 + - - +
224B TRP* 3.3 15.2 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 4.2 22.2 - - + -
129B ALA* 3.8 12.6 - - + +
130B LYS* 3.8 26.0 - - + +
133B ASP* 2.6 26.7 + - + +
134B PHE* 4.4 11.4 - - + -
145B GLY* 3.6 39.7 - - - +
148B LEU* 4.4 7.2 - - + -
149B ILE* 3.9 14.1 - - + -
218B ALA* 3.8 8.1 - - + +
219B PRO 3.3 0.4 - - - -
220B LYS* 1.3 76.0 - - - +
222B ASP* 1.3 61.0 + - - +
224B TRP* 3.2 17.2 - - + +
225B PHE* 3.4 16.9 + - + -
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU* 4.2 14.5 - - + +
152B TYR* 2.4 32.2 + - - -
215B LYS* 2.7 28.0 + - + +
218B ALA 3.5 12.8 + - - +
219B PRO* 4.1 3.8 - - + +
220B LYS 3.4 0.4 - - - -
221B LEU* 1.3 75.6 - - - +
223B GLU* 1.3 60.2 + - - +
224B TRP 3.0 4.9 - - - -
225B PHE* 2.8 8.4 + - - +
226B TYR* 2.8 24.6 + - - +
233B TRP* 2.5 22.4 + - - -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLY* 4.4 2.7 - - - -
82A TYR* 3.3 43.6 + - + +
83A TYR* 5.3 0.7 + - - -
219B PRO 3.4 11.6 + - - +
220B LYS* 2.3 50.7 + - - +
222B ASP* 1.3 82.5 + - - +
224B TRP* 1.3 60.4 + - - +
226B TYR* 3.2 10.8 - - + +
227B LEU* 3.0 37.7 + - + +
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Residues in contact with TRP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL 4.1 7.6 - - - -
81A GLY* 6.2 0.7 - - - -
122B LYS* 3.1 25.2 + - + -
125B SER* 3.2 37.8 - - - -
126B TYR* 3.2 34.1 - + + +
129B ALA* 4.2 6.3 - - + -
220B LYS 3.3 9.6 + - - +
221B LEU* 3.2 12.3 - - + +
222B ASP 3.0 0.4 - - - -
223B GLU* 1.3 82.2 - - - +
225B PHE* 1.3 110.1 + + - +
227B LEU* 3.0 6.5 + - + +
228B ALA* 2.5 55.5 + - + +
229B CYS* 4.0 18.2 - - - -
301B GSH 3.8 23.8 - - + -
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 4.8 4.0 - + - -
148B LEU* 4.7 2.0 - - + -
149B ILE* 4.3 27.6 - - + -
152B TYR* 3.4 34.5 - + + -
153B VAL* 3.6 33.0 - - + -
221B LEU* 3.4 22.4 + - + -
222B ASP 2.8 8.3 + - - +
224B TRP* 1.3 108.7 - + - +
226B TYR* 1.3 59.0 + - - +
228B ALA 2.8 21.6 - - - +
229B CYS* 3.1 21.5 - - + +
232B THR* 5.1 6.3 - - + -
233B TRP* 3.1 34.4 - - + +
301B GSH 4.5 3.1 - - - -
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Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 5.1 5.4 - + - -
222B ASP* 2.8 12.1 + - - +
223B GLU* 3.2 17.5 - - + +
224B TRP 3.0 0.2 - - - -
225B PHE* 1.3 76.9 - - - +
227B LEU* 1.3 76.2 + - + +
230B PRO* 3.3 24.1 - - - +
233B TRP* 3.4 40.8 - + - +
10F LYS* 3.7 9.8 - - + +
11F TYR* 4.0 25.4 - + - -
14F THR* 4.0 21.3 + - + +
15F ASN* 5.4 1.3 + - - -
109F ASN* 5.8 2.1 + - - +
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Residues in contact with LEU 227 (chain B).
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* 4.3 5.2 - - - -
78A THR* 5.5 1.1 - - - +
79A SER* 3.5 28.0 - - - +
80A VAL* 4.0 4.5 - - - +
81A GLY* 3.6 35.7 - - - +
82A TYR* 3.6 32.5 - - + +
223B GLU* 3.0 20.3 + - + +
224B TRP* 3.9 3.4 - - + +
226B TYR* 1.3 98.0 - - + +
228B ALA* 1.3 59.6 + - + +
230B PRO* 3.8 3.7 - - - +
10F LYS* 2.4 37.2 + - + +
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Residues in contact with ALA 228 (chain B).
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* 4.0 15.5 - - + -
80A VAL 6.0 0.2 - - - +
122B LYS* 3.6 27.1 - - + +
224B TRP* 2.5 41.1 + - + +
225B PHE* 2.8 26.5 - - - +
227B LEU* 1.3 74.0 - - + +
229B CYS* 1.3 64.4 + - - +
230B PRO* 3.4 1.3 - - - -
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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