Contacts of the strand formed by residues 225 - 232 (chain A) in PDB entry 1HMY
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 LYS 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A THR* 2.9 29.9 + - + +
224A PRO* 1.3 91.4 - - + +
226A THR* 1.3 66.7 + - - +
227A VAL* 3.6 9.9 + - + +
246A GLY* 3.7 6.6 - - - -
247A ILE* 3.2 24.6 + - - -
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Residues in contact with THR 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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162A LYS* 4.7 16.1 - - + +
225A LYS* 1.3 75.9 - - - +
227A VAL* 1.3 60.0 + - - +
228A ARG* 3.9 2.7 + - + +
242A TYR* 4.2 21.8 - - + -
247A ILE* 4.1 20.2 + - - +
248A ALA 4.7 0.2 + - - -
249A ILE* 3.9 22.6 - - + +
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Residues in contact with VAL 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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219A ILE* 4.0 29.2 - - + -
223A THR* 5.6 6.7 - - + -
225A LYS* 3.6 15.7 + - + +
226A THR* 1.3 75.1 - - - +
228A ARG* 1.3 63.1 + - - +
229A LEU* 3.3 3.0 + - + -
242A TYR* 3.6 9.3 - - - +
243A SER* 3.3 48.2 + - - +
246A GLY* 4.3 10.8 - - - -
247A ILE 5.3 1.4 + - - -
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Residues in contact with ARG 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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215A THR* 4.4 6.1 + - - +
216A ASN* 3.2 24.6 + - - +
226A THR* 3.9 3.4 + - + +
227A VAL* 1.3 70.4 - - - +
229A LEU* 1.3 63.2 + - - +
230A GLY 3.7 13.5 - - - +
231A ILE* 4.0 28.4 - - - +
235A GLY 4.8 1.0 + - - -
240A ARG* 3.5 45.1 - - + +
241A ILE 3.8 8.7 - - - +
242A TYR* 3.9 21.6 + - + -
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Residues in contact with LEU 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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214A MET* 3.9 9.0 - - + +
215A THR* 3.1 22.0 + - - -
216A ASN* 3.2 24.3 + - + +
217A GLN 3.8 31.2 - - - +
218A GLU* 4.0 15.7 - - - +
219A ILE* 4.8 5.6 - - + +
227A VAL* 3.3 4.3 + - + +
228A ARG* 1.3 75.6 - - - +
230A GLY* 1.3 56.0 + - - +
241A ILE* 2.8 18.5 + - + +
242A TYR 4.1 0.7 - - - -
243A SER* 3.6 42.4 - - - +
266A LEU* 3.9 34.3 - - + -
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Residues in contact with GLY 230 (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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212A LEU* 4.9 0.4 - - - -
213A VAL 3.6 11.7 - - - -
214A MET* 4.2 9.0 - - - -
215A THR* 4.0 7.2 + - - -
228A ARG* 3.7 8.4 - - - +
229A LEU* 1.3 80.1 - - - +
231A ILE* 1.3 75.0 + - - +
241A ILE* 3.3 28.2 + - - +
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Residues in contact with ILE 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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211A ASP 5.2 0.2 - - - +
212A LEU* 2.9 25.6 - - - +
213A VAL* 3.1 35.7 + - + +
215A THR* 5.8 7.2 - - + +
228A ARG* 4.0 25.8 - - - +
230A GLY* 1.3 80.0 - - - +
232A VAL* 1.3 70.1 + - - +
233A GLY 4.7 4.0 - - - +
234A LYS 5.2 0.7 - - - -
235A GLY* 3.1 38.6 - - - +
239A GLU 3.2 13.5 - - - +
240A ARG* 4.0 4.0 - - + -
241A ILE* 4.1 5.9 - - - +
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Residues in contact with VAL 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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209A ARG* 4.0 31.2 - - + +
211A ASP* 3.6 10.5 - - - +
212A LEU* 4.0 15.7 - - + -
231A ILE* 1.3 82.5 - - - +
233A GLY* 1.3 74.1 + - - +
235A GLY* 2.8 18.2 + - - -
239A GLU* 3.2 24.9 + - + +
241A ILE* 4.4 7.4 - - + -
258A ILE* 3.4 34.8 - - + -
259A PHE* 4.6 8.1 - - + -
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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