Contacts of the helix formed by residues 224 - 230 (chain A) in PDB entry 2IHU
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A VAL 3.9 1.0 + - - -
223A VAL* 1.3 76.8 - - - +
225A ALA* 1.3 65.2 + - - -
226A ALA 3.3 3.1 - - - -
227A ALA* 3.1 20.2 + - - +
228A ILE* 4.0 2.1 + - - +
250A THR* 3.8 6.1 - - - -
253A ALA* 3.9 6.0 - - - +
294A VAL 3.1 11.7 + - - -
295A GLY 3.9 8.3 - - - -
296A TYR* 5.7 1.1 - - - +
300A GLU* 3.4 19.3 - - - -
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Residues in contact with ALA 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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69A ARG* 5.8 0.7 - - - +
98A ASP 5.9 0.9 - - - +
224A GLY* 1.3 71.4 - - - -
226A ALA* 1.3 56.8 + - - +
228A ILE* 2.9 31.5 + - - +
229A ARG* 3.2 27.0 + - - +
252A ILE* 3.7 30.3 - - + -
253A ALA* 4.1 1.6 - - - +
300A GLU* 2.9 23.8 + - + +
427A PHE* 4.4 8.6 - - + -
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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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159A GLU* 5.0 1.7 - - - +
224A GLY 3.3 1.0 + - - -
225A ALA* 1.3 77.1 - - - +
227A ALA* 1.3 61.3 + - - +
229A ARG* 3.4 32.2 + - - +
230A SER* 3.1 23.7 + - - -
295A GLY* 3.6 24.8 + - - +
296A TYR 5.6 0.9 - - - +
297A ASP* 5.7 4.5 - - + +
300A GLU* 4.8 1.0 + - - -
320A PRO* 4.6 19.3 - - + +
339A VAL* 4.3 3.5 - - - +
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Residues in contact with ALA 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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223A VAL* 3.8 12.1 - - + -
224A GLY 3.1 13.8 + - - +
226A ALA* 1.3 78.5 - - - +
228A ILE* 1.3 59.4 + - + +
230A SER* 3.6 4.0 + - - -
232A ALA* 3.1 30.2 + - - +
233A VAL* 5.0 2.0 - - + -
236A ILE* 3.7 27.6 - - + -
294A VAL 4.0 8.5 - - - +
295A GLY* 4.3 2.6 - - - -
339A VAL* 3.8 19.3 - - + -
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Residues in contact with ILE 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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224A GLY 4.4 3.8 - - - +
225A ALA* 2.9 11.9 + - - +
227A ALA* 1.3 75.8 - - + +
229A ARG* 1.3 58.5 + - - +
231A GLY* 3.0 20.8 + - - -
233A VAL* 3.8 24.0 - - + +
252A ILE 4.0 1.1 - - - +
253A ALA* 3.8 32.3 - - + -
256A VAL* 3.9 13.7 - - + -
426A PRO* 3.9 24.5 - - + -
427A PHE* 3.6 42.4 - - + -
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Residues in contact with ARG 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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69A ARG* 5.9 5.4 - - + +
98A ASP 4.8 1.6 + - - -
99A ARG* 3.8 40.3 + - - +
101A PRO* 6.0 2.2 - - - -
159A GLU* 2.9 42.0 + - - +
160A PRO* 5.2 1.2 - - - +
161A VAL* 3.5 17.9 - - - +
193A LYS* 3.9 7.8 - - - +
194A PRO* 3.8 27.0 - - + +
225A ALA* 3.2 18.4 + - - +
226A ALA* 3.7 39.3 - - - +
228A ILE* 1.3 76.0 - - - +
230A SER* 1.3 61.1 + - - +
231A GLY* 3.1 1.3 + - - -
297A ASP* 4.9 3.6 + - - -
427A PHE* 5.2 10.7 - - + -
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Residues in contact with SER 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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193A LYS* 2.8 35.7 + - - +
194A PRO* 5.5 1.1 - - - -
226A ALA 3.1 14.3 + - - -
227A ALA 3.7 8.1 - - - -
229A ARG* 1.3 77.4 - - - +
231A GLY* 1.3 60.1 + - - +
232A ALA* 4.3 0.9 - - - -
338A ASP* 2.7 26.8 + - - -
339A VAL* 3.5 14.6 + - - -
340A LEU* 3.0 24.8 + - - +
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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