Contacts of the helix formed by residues 215 - 224 (chain A) in PDB entry 5H8N
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A THR* 3.4 4.3 + - - +
134A GLY 2.8 33.1 + - - +
136A SER* 3.2 30.1 - - - +
213A TYR 3.3 1.2 + - - -
214A ASP* 1.4 69.6 - - - +
216A ALA* 1.4 58.2 + - - +
218A LEU* 3.3 1.9 + - - +
219A ASN* 2.9 38.1 + - - +
238A ILE* 3.8 20.6 - - + -
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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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18A PHE* 4.1 9.6 - - + -
131A VAL* 3.9 26.9 - - + -
132A GLU 3.9 7.0 - - - +
133A THR* 3.1 13.3 + - - +
214A ASP* 3.2 8.5 + - - +
215A ALA* 1.4 74.6 - - - +
217A VAL* 1.3 61.0 + - - +
219A ASN* 3.9 5.0 - - - +
220A TYR* 3.1 23.6 + - - +
244A TYR* 3.6 11.2 - - + +
302A 5YD 6.0 1.1 - - + -
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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
----------------------------------------------------------
15A GLU* 3.7 34.3 - - + +
16A ALA 4.6 8.3 - - - +
18A PHE* 3.9 11.0 - - + -
196A VAL* 4.3 22.2 - - + -
213A TYR* 3.9 23.3 - - + -
214A ASP* 3.0 12.4 + - - +
216A ALA* 1.3 70.5 - - - +
218A LEU* 1.3 60.0 + - + +
220A TYR* 3.2 7.1 + - + +
221A LYS* 2.9 35.8 + - + +
244A TYR* 3.5 18.6 - - - +
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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
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136A SER* 3.4 35.4 - - - +
137A VAL 4.3 0.2 - - - -
138A MET* 3.3 35.5 - - + +
196A VAL* 5.4 4.5 - - + -
200A LEU* 5.3 2.5 - - + -
211A PHE* 3.7 40.6 - - + +
213A TYR* 3.6 23.3 - - + +
214A ASP 3.0 18.9 + - - +
215A ALA 3.3 3.1 + - - +
217A VAL* 1.3 77.1 - - - +
219A ASN* 1.3 56.0 + - - +
221A LYS* 3.4 2.3 + - + -
222A ALA* 2.9 26.0 + - - +
232A THR* 3.8 12.8 - - + -
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Residues in contact with ASN 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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136A SER* 4.1 12.9 + - - -
215A ALA* 2.9 32.9 + - - +
216A ALA* 4.1 4.2 - - - +
218A LEU* 1.3 72.8 - - - +
220A TYR* 1.3 62.8 + - - +
222A ALA* 4.0 5.3 - - - +
223A GLY* 3.2 18.9 + - - -
232A THR* 2.9 26.1 + - - +
236A GLY* 4.0 18.3 + - - -
238A ILE* 4.8 4.8 - - - +
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Residues in contact with TYR 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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16A ALA* 4.4 8.4 - - + +
17A PRO* 3.6 44.7 - - + +
18A PHE* 5.5 1.3 - - + -
216A ALA 3.1 17.9 + - - +
217A VAL* 3.2 7.6 + - - +
219A ASN* 1.3 76.9 - - - +
221A LYS* 1.3 86.2 + - + +
223A GLY* 3.4 9.8 + - - -
224A ARG* 3.4 57.5 + - + +
278A TRP 3.5 19.1 - - - -
279A LEU* 3.8 24.9 - - + +
281A GLY* 5.7 0.2 - - - -
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Residues in contact with LYS 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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16A ALA* 4.9 13.2 + - - +
138A MET* 4.3 8.5 - - + -
196A VAL* 4.1 24.5 - - + -
197A GLU* 3.0 27.6 + - - -
200A LEU* 3.8 29.3 - - + +
217A VAL* 2.9 25.8 + - + +
218A LEU* 3.9 5.2 - - + +
220A TYR* 1.3 94.7 - - + +
222A ALA* 1.4 64.0 + - - +
224A ARG* 3.5 5.5 + - + +
225A ASP* 3.2 24.3 + - - +
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Residues in contact with ALA 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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138A MET* 3.6 15.1 - - + +
218A LEU 2.9 17.4 + - - +
219A ASN* 4.0 9.2 - - - +
221A LYS* 1.4 74.8 - - - +
223A GLY* 1.3 60.4 + - - +
224A ARG 3.5 0.7 + - - -
225A ASP* 3.5 13.8 + - - +
228A CYS* 5.2 0.2 - - - -
230A LEU 3.7 20.9 - - - +
231A VAL* 4.5 7.6 - - - -
232A THR* 4.6 8.3 - - + +
283A CYS* 3.5 14.6 - - - +
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Residues in contact with GLY 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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219A ASN 3.2 12.2 + - - -
220A TYR 3.4 4.4 + - - -
221A LYS 3.3 0.2 - - - -
222A ALA* 1.3 80.2 - - - +
224A ARG* 1.3 57.5 + - - +
225A ASP 3.5 0.2 - - - -
281A GLY* 3.9 8.3 - - - -
282A ILE* 2.8 14.4 + - - +
283A CYS* 2.8 41.4 + - - -
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Residues in contact with ARG 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 TYR* 3.4 47.4 + - + +
221A LYS* 3.5 6.0 + - - +
222A ALA 3.3 0.2 - - - -
223A GLY* 1.3 76.6 - - - +
225A ASP* 1.3 62.7 + - - +
226A GLU* 3.5 2.8 + - - +
277A LEU 4.2 13.5 + - - -
278A TRP* 3.8 16.4 + - - +
280A THR* 3.1 26.0 + - - -
281A GLY* 4.1 9.3 - - - -
282A ILE* 4.9 11.6 - - + +
283A CYS* 4.9 0.4 - - - -
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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