Contacts of the helix formed by residues 224 - 230 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B VAL 3.9 0.8 + - - -
223B VAL* 1.3 77.9 - - - +
225B ALA* 1.3 65.5 + - - -
226B ALA 3.2 2.9 - - - -
227B ALA* 3.2 20.3 + - - +
228B ILE* 4.1 1.7 + - - +
250B THR* 3.9 6.3 - - - -
253B ALA* 3.9 5.4 - - - +
294B VAL 3.0 10.9 + - - +
295B GLY 3.9 9.1 + - - -
296B TYR* 5.6 1.5 - - - +
300B GLU* 3.5 19.1 - - - -
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Residues in contact with ALA 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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69B ARG* 5.9 0.2 - - - +
98B ASP 5.9 0.9 - - - +
224B GLY* 1.3 69.0 - - - -
226B ALA* 1.3 59.9 + - - +
228B ILE* 2.9 30.5 + - - +
229B ARG* 3.1 28.2 + - - +
252B ILE* 3.4 36.6 - - + -
253B ALA* 4.1 1.6 - - - +
300B GLU* 2.8 16.4 + - + +
427B PHE* 4.4 8.9 - - + -
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Residues in contact with ALA 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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159B GLU* 4.6 4.9 - - - +
224B GLY 3.2 0.8 + - - -
225B ALA* 1.3 77.9 - - - +
227B ALA* 1.3 56.0 + - - +
229B ARG* 3.4 32.5 + - - +
230B SER* 3.0 28.1 + - - -
295B GLY* 3.7 25.0 + - - +
296B TYR 5.6 0.9 - - - +
297B ASP* 5.8 3.8 - - + -
300B GLU* 4.9 1.4 + - - -
319B SER* 5.8 0.2 - - - +
320B PRO* 4.6 17.5 - - + +
339B VAL* 4.3 3.3 - - + +
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Residues in contact with ALA 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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223B VAL* 3.8 11.4 - - + -
224B GLY 3.2 12.9 + - - +
225B ALA 3.1 0.4 - - - -
226B ALA* 1.3 79.4 - - - +
228B ILE* 1.3 59.3 + - + +
230B SER* 3.5 3.5 + - - -
232B ALA* 3.0 30.2 + - - +
233B VAL* 5.0 2.2 - - + -
236B ILE* 3.7 27.6 - - + -
294B VAL 4.0 8.1 - - - +
295B GLY* 4.3 1.0 - - - -
339B VAL* 3.8 21.1 - - + +
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Residues in contact with ILE 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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224B GLY 4.5 2.0 - - - +
225B ALA* 2.9 13.9 + - - +
227B ALA* 1.3 75.7 - - + +
229B ARG* 1.3 59.9 + - - +
231B GLY* 2.8 22.3 + - - -
232B ALA 4.8 0.2 - - - +
233B VAL* 3.7 24.9 - - + +
252B ILE 4.3 0.7 - - - +
253B ALA* 4.0 22.7 - - + -
256B VAL* 3.9 20.4 - - + -
426B PRO* 4.0 23.6 - - + -
427B PHE* 3.5 43.5 - - + -
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Residues in contact with ARG 229 (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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69B ARG* 5.9 3.9 - - + +
98B ASP 4.8 1.8 + - - -
99B ARG* 3.8 35.0 + - - +
101B PRO* 5.8 2.5 - - - -
159B GLU* 2.9 44.9 + - - +
160B PRO* 5.1 1.2 - - - +
161B VAL* 3.5 23.9 - - - +
193B LYS* 3.7 7.8 - - - +
194B PRO* 3.7 28.1 - - + +
225B ALA* 3.1 19.2 + - - +
226B ALA* 3.6 35.7 - - - +
228B ILE* 1.3 74.3 - - - +
230B SER* 1.3 60.9 + - - +
231B GLY* 3.2 1.2 + - - -
297B ASP* 4.9 4.8 + - - +
427B PHE* 5.2 9.4 - - + -
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Residues in contact with SER 230 (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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159B GLU* 5.5 0.2 + - - -
193B LYS* 2.8 35.1 + - - +
194B PRO* 5.3 1.3 - - - -
226B ALA 3.0 17.3 + - - -
227B ALA 3.6 8.1 - - - -
228B ILE 3.1 0.4 - - - -
229B ARG* 1.3 75.1 - - - +
231B GLY* 1.3 60.9 + - - +
232B ALA* 4.4 0.7 - - - -
320B PRO* 6.6 0.2 - - - -
338B ASP* 2.7 26.6 + - - -
339B VAL* 3.5 14.7 + - - -
340B LEU* 3.0 24.0 + - - +
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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