Contacts of the helix formed by residues 219 - 232 (chain A) in PDB entry 2HVY
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 THR 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 1.3 - - - -
55A ASP* 4.2 15.5 - - + +
218A ILE* 1.3 79.2 - - - +
220A LEU* 1.3 59.4 + - - +
221A HIS* 3.6 14.6 + - - +
222A ASP* 3.2 29.7 + - - +
223A LEU* 3.0 27.7 + - - +
32C PRO* 3.9 28.7 - - + -
33C PRO* 5.0 4.5 - - + -
62D GLU* 5.1 5.7 + - - +
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Residues in contact with LEU 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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54A LEU* 4.0 18.2 - - + +
55A ASP 4.6 2.4 + - - -
57A PRO* 3.7 29.4 - - + -
65A VAL* 4.2 11.0 - - + +
68A TRP* 4.1 13.7 - - + -
69A ILE* 3.8 31.0 - - + -
72A ILE* 6.0 0.9 - - + -
219A THR* 1.3 73.4 - - - +
221A HIS* 1.3 58.1 + - + +
223A LEU* 3.5 9.0 - - + +
224A VAL* 3.0 37.6 + - + +
35C PHE* 3.6 50.7 - - + -
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Residues in contact with HIS 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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219A THR* 3.2 11.8 - - - +
220A LEU* 1.3 77.5 - - - +
222A ASP* 1.3 62.4 + - - +
224A VAL* 3.3 7.6 - - - +
225A ASP* 3.1 30.0 + - - -
32C PRO* 6.1 0.4 - - + -
33C PRO* 3.6 34.5 + - + +
34C ARG 3.0 31.8 + - - -
35C PHE* 3.7 20.8 - + + -
36C SER 5.3 0.4 - - - -
39C ASP* 4.9 2.0 - - - -
45C ARG* 3.6 36.2 + - - +
49C LYS* 4.0 7.9 - - - +
62D GLU* 4.7 15.2 - - + +
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Residues in contact with ASP 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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218A ILE* 3.7 20.7 - - + +
219A THR* 3.2 19.1 + - - +
221A HIS* 1.3 76.9 - - - +
223A LEU* 1.3 60.7 + - - +
225A ASP* 4.5 0.9 - - - -
226A TYR* 2.9 57.3 + - + -
49C LYS* 2.7 38.1 + - - +
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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
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52A ILE* 3.8 38.4 - - + -
54A LEU* 4.1 13.2 - - + -
69A ILE* 4.0 22.2 - - + -
73A LEU* 4.3 13.9 - - + -
218A ILE* 3.7 10.9 - - + +
219A THR 3.0 18.0 + - - +
220A LEU* 3.5 10.1 - - + +
222A ASP* 1.3 78.0 - - - +
224A VAL* 1.3 61.4 + - + +
226A TYR* 3.9 3.0 - - - +
227A TYR* 3.1 26.5 + - - +
239A PHE* 3.9 20.3 - - + -
242A ALA* 4.1 14.8 - - + -
243A ILE* 5.2 0.4 - - + -
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Residues in contact with VAL 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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72A ILE* 3.7 31.6 - - + -
73A LEU* 5.1 1.3 - - + -
220A LEU* 3.0 18.7 + - + +
221A HIS 3.3 11.9 - - - +
223A LEU* 1.3 83.7 - - + +
225A ASP* 1.3 61.0 + - - +
227A TYR* 3.4 8.0 - - - +
228A TYR* 3.0 38.3 + - + -
35C PHE* 3.7 27.4 - - + -
39C ASP* 4.3 5.2 - - - +
45C ARG* 3.5 20.4 - - - +
46C ARG* 4.6 3.4 - - - +
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Residues in contact with ASP 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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221A HIS 3.1 14.5 + - - +
222A ASP 4.0 2.7 - - - +
224A VAL* 1.3 76.7 - - - +
226A TYR* 1.3 59.6 + - - +
228A TYR* 3.2 2.8 + - - +
229A PHE* 2.9 41.5 + - + -
45C ARG* 2.7 35.7 + - - +
46C ARG* 3.1 31.1 + - + +
49C LYS* 2.8 43.3 + - + +
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Residues in contact with TYR 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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218A ILE* 3.6 26.7 - - + -
222A ASP* 2.9 45.4 + - + +
223A LEU* 3.9 3.6 - - - +
225A ASP* 1.3 72.8 - - + +
227A TYR* 1.3 65.4 + - - +
229A PHE* 3.4 30.1 + + - +
230A TRP* 3.2 16.3 + - - +
235A ILE 4.5 0.7 - - - +
238A TYR* 3.4 43.0 - + + +
239A PHE* 3.5 30.7 + - + +
241A LYS* 6.1 1.3 - - + -
242A ALA* 4.4 0.7 - - + -
49C LYS* 4.7 3.4 - - + -
53C LEU* 4.2 13.5 - - + +
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Residues in contact with TYR 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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72A ILE* 3.6 24.0 + - + -
73A LEU* 3.6 36.8 + - + -
74A ASN* 4.7 5.5 - - - +
223A LEU 3.1 14.3 + - - +
224A VAL 3.4 11.2 - - - +
226A TYR* 1.3 75.7 - - - +
228A TYR* 1.3 70.3 + + - +
230A TRP* 3.2 17.9 + + - +
231A LYS* 3.0 66.0 + - + +
239A PHE* 3.6 33.3 - + + -
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ILE* 5.4 6.3 - - + -
224A VAL* 3.0 30.6 + - + -
225A ASP 3.2 8.0 + - - +
227A TYR* 1.3 87.8 - + - +
229A PHE* 1.3 60.4 + - - +
231A LYS* 4.4 5.2 - - + +
232A GLU* 3.0 65.8 + - + +
43C GLU* 4.0 7.9 - - - -
46C ARG* 3.3 52.9 + - - +
50C ARG* 4.3 1.2 + - - +
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Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ASP* 2.9 25.9 + - + -
226A TYR* 3.7 29.8 - + - +
227A TYR 3.3 0.6 - - - -
228A TYR* 1.3 76.1 - - + +
230A TRP* 1.3 58.1 + - - +
233A ASP* 3.2 33.7 - - - +
234A GLY 3.3 1.6 + - - -
235A ILE* 3.0 32.4 + - + +
238A TYR* 4.4 8.7 - + + -
46C ARG* 4.2 10.5 - - + -
49C LYS* 4.0 28.5 - - + -
50C ARG* 3.6 37.0 - - + -
53C LEU* 3.7 23.8 - - + -
55C ILE* 4.1 13.7 - - + -
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Residues in contact with TRP 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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43A ILE* 3.7 19.2 - - + +
44A GLU* 3.7 27.8 - - + -
47A ILE* 3.7 31.4 - - + -
226A TYR 3.2 11.3 + - - +
227A TYR* 3.4 17.9 - + - +
228A TYR 3.1 0.8 - - - -
229A PHE* 1.3 76.4 - - - +
231A LYS* 1.3 103.2 + - + +
234A GLY* 3.2 22.4 + - - -
235A ILE 3.2 12.5 + - - +
236A GLU* 3.7 28.5 + - + +
239A PHE* 3.6 25.1 - + + -
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TYR* 3.0 48.0 + - + +
228A TYR* 4.3 5.6 - - + +
230A TRP* 1.3 122.2 - - + +
232A GLU* 1.3 65.1 + - + +
234A GLY 4.7 0.2 - - - -
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Residues in contact with GLU 232 (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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228A TYR* 3.0 45.2 + - + +
231A LYS* 1.3 84.4 - - + +
233A ASP* 1.3 72.2 + - - +
234A GLY 3.5 0.7 - - - -
43C GLU* 4.4 10.9 - - - +
46C ARG* 5.0 0.5 - - - -
50C ARG* 3.2 20.8 + - - +
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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