Contacts of the helix formed by residues 223 - 234 (chain B) in PDB entry 4IA4
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 PRO 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ASN* 3.5 16.6 - - - +
102B PRO* 3.9 10.8 - - + -
103B ALA 3.8 8.5 - - - +
222B ASN* 1.4 80.4 - - - +
224B ALA* 1.3 57.0 + - - +
225B ARG 3.0 2.1 + - - -
226B SER* 3.0 3.5 + - - +
227B PHE* 2.7 37.5 + - - +
245B PHE 3.6 17.3 - - - +
246B TRP* 3.9 28.1 + - + -
249B PRO* 3.8 14.6 - - + -
250B PHE* 3.7 23.6 - - + -
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Residues in contact with ALA 224 (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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48B THR* 4.7 4.3 - - + -
52B LEU* 5.3 0.4 - - - -
100B ILE 5.1 0.7 - - - +
102B PRO* 3.2 32.7 - - + +
126B GLN* 3.7 30.7 - - + +
127B CYS* 3.9 13.4 - - - +
130B ALA* 2.8 28.9 - - + +
222B ASN* 4.0 2.7 - - - +
223B PRO* 1.3 78.9 - - - +
225B ARG* 1.3 53.7 + - - +
227B PHE* 3.9 1.1 - - - +
228B GLY 3.1 11.8 + - - -
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Residues in contact with ARG 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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51B PHE* 4.3 13.5 - - + -
52B LEU* 3.7 32.0 - - + +
56B VAL* 4.8 3.2 - - - +
59B VAL* 5.5 4.0 - - - +
81B PHE* 3.8 33.4 - - + -
151B GLY* 3.2 29.9 + - - -
152B ALA* 4.8 0.6 - - - +
153B ASN* 3.4 34.7 + - - +
218B GLY 4.7 4.6 + - - -
219B THR 4.7 6.4 + - - -
220B GLY 3.9 16.1 + - - -
222B ASN* 3.2 27.3 + - + +
223B PRO 3.0 0.6 - - - -
224B ALA* 1.3 76.3 - - - +
226B SER* 1.3 68.2 + - - +
227B PHE 3.2 0.2 - - - -
228B GLY 3.6 0.3 + - - -
229B ALA* 3.4 20.6 + - - +
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Residues in contact with SER 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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153B ASN* 3.1 29.8 + - - +
220B GLY* 4.2 1.4 - - - -
222B ASN 2.8 20.3 + - - -
223B PRO 3.0 5.5 + - - -
225B ARG* 1.3 81.1 - - - +
227B PHE* 1.3 58.4 + - - +
229B ALA* 3.7 1.6 + - - +
230B ALA* 3.0 29.8 + - - +
242B GLN* 3.7 9.6 + - - -
245B PHE* 3.6 30.2 - - - +
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Residues in contact with PHE 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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127B CYS* 3.2 33.2 - - + -
131B ILE* 3.9 19.1 - - + -
223B PRO 2.7 17.0 + - - +
224B ALA 3.9 3.4 - - - +
226B SER* 1.3 74.7 - - - +
228B GLY* 1.3 66.7 + - - +
230B ALA* 3.1 2.0 + - - +
231B VAL* 2.8 47.1 + - + +
239B TRP* 3.7 23.3 - + - -
242B GLN* 3.6 12.5 + - + +
246B TRP* 3.9 22.0 - + + -
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Residues in contact with GLY 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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130B ALA* 3.8 8.3 - - - -
131B ILE* 3.6 32.3 - - - -
134B VAL* 3.8 7.4 - - - -
224B ALA 3.1 11.9 + - - -
225B ARG 4.1 0.7 - - - -
227B PHE* 1.3 77.5 - - - +
229B ALA* 1.3 56.4 + - - +
231B VAL* 3.4 2.1 - - - +
232B ILE* 3.1 33.1 + - - +
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Residues in contact with ALA 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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56B VAL* 5.0 0.9 - - + -
134B VAL* 3.8 20.0 - - + +
145B TYR* 4.1 0.7 + - - -
150B GLY 4.1 5.4 - - - +
151B GLY 3.1 30.7 - - - +
152B ALA* 3.8 10.3 - - - -
225B ARG* 3.4 17.6 + - - +
226B SER 4.2 1.6 - - - +
227B PHE 3.2 0.6 - - - -
228B GLY* 1.3 73.7 - - - +
230B ALA* 1.3 58.7 + - - +
233B PHE* 2.7 37.9 + - - +
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Residues in contact with ALA 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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152B ALA* 4.4 1.5 - - + +
226B SER 3.0 20.3 + - - +
227B PHE 3.1 3.8 + - - +
229B ALA* 1.3 71.8 - - - +
231B VAL* 1.3 67.6 + - - +
233B PHE* 4.8 0.2 - - - -
234B ASN* 2.8 25.5 + - - -
235B SER 4.5 0.5 + - - -
238B VAL* 4.0 22.4 - - + +
239B TRP* 3.8 24.8 - - + -
242B GLN* 3.6 20.6 - - - +
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Residues in contact with VAL 231 (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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131B ILE* 3.7 36.1 - - + -
227B PHE* 2.8 57.9 + - + +
228B GLY 3.4 4.7 - - - +
230B ALA* 1.3 80.7 - - - +
232B ILE* 1.3 64.8 + - + +
234B ASN* 3.6 15.4 - - - +
239B TRP* 3.8 12.6 - - + -
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Residues in contact with ILE 232 (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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131B ILE* 3.5 39.5 - - + +
134B VAL* 3.6 13.5 - - + -
135B GLY* 3.8 17.5 - - - +
138B LYS* 3.8 36.3 + - + -
145B TYR* 3.5 19.3 - - + +
146B ASN* 5.4 0.2 - - - +
228B GLY 3.1 15.0 + - - +
231B VAL* 1.3 78.6 - - + +
233B PHE* 1.3 66.9 + - - +
234B ASN* 4.2 2.1 - - - +
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Residues in contact with PHE 233 (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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138B LYS* 5.7 0.3 + - - -
145B TYR* 3.5 15.5 + + - +
146B ASN* 3.5 35.5 - - + +
149B GLY* 3.7 35.4 - - - +
150B GLY* 3.8 12.3 - - - -
152B ALA* 4.1 7.6 - - + -
229B ALA 2.7 23.1 + - - +
230B ALA* 4.2 1.3 - - - +
232B ILE* 1.3 74.8 - - - +
234B ASN* 1.3 68.8 + - - +
235B SER* 3.6 31.9 - - - +
238B VAL* 3.8 18.4 - - + -
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Residues in contact with ASN 234 (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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230B ALA 2.8 17.6 + - - -
231B VAL 3.6 12.8 - - - +
232B ILE 4.2 2.5 - - - +
233B PHE* 1.3 82.1 - - - +
235B SER* 1.3 57.5 + - - +
236B ASN 4.4 0.2 + - - -
239B TRP* 3.1 23.6 + - - +
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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