Contacts of the helix formed by residues 222 - 232 (chain A) in PDB entry 1B43
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 ARG 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A LEU 4.4 5.6 - - - +
177A LEU* 2.9 17.2 + - - +
178A PHE 3.0 19.6 + - - -
179A GLY* 3.0 24.3 - - - +
211A LEU* 4.3 11.9 - - + -
215A LEU* 3.7 25.5 - - + +
221A THR* 1.3 74.0 - - - +
223A GLU* 1.3 61.7 - - - +
225A LEU* 3.2 5.2 + - + +
226A ILE* 3.0 32.1 + - + +
278A PHE 2.7 29.7 + - - -
279A LEU* 3.4 34.4 + - + +
281A PRO* 4.9 0.6 - - - +
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Residues in contact with GLU 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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221A THR* 3.1 9.5 - - - +
222A ARG* 1.3 80.4 - - - +
224A LYS* 1.3 58.6 + - + +
226A ILE* 3.4 12.8 + - - +
227A GLU* 3.1 29.1 + - - +
275A LYS* 2.8 39.1 + - - +
279A LEU* 4.2 19.8 - - + +
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Residues in contact with LYS 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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219A LYS 5.6 0.4 - - - +
220A LEU* 4.3 11.0 - - + -
221A THR* 3.1 31.9 + - + +
223A GLU* 1.3 78.3 - - + +
225A LEU* 1.3 60.1 + - - +
227A GLU* 3.2 20.2 + - - +
228A LEU* 2.8 29.5 + - - +
253A VAL* 2.7 46.6 + - + +
254A ARG* 4.7 5.4 + - - +
256A SER 2.9 21.0 + - - -
257A LYS* 4.5 8.5 + - - +
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Residues in contact with LEU 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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4A ILE* 4.3 18.6 - - + -
7A ILE* 5.0 1.3 - - + -
8A ILE* 4.7 5.2 - - + -
176A LEU* 4.9 10.5 - - + +
177A LEU* 3.9 18.8 - - + -
211A LEU* 4.2 16.4 - - + -
214A VAL* 4.7 8.7 - - + -
215A LEU* 4.1 19.5 - - + -
218A LEU* 4.2 23.6 - - + -
220A LEU* 4.4 10.3 - - + +
221A THR 3.0 12.7 + - - +
222A ARG* 3.2 11.6 + - + +
224A LYS* 1.3 76.0 - - - +
226A ILE* 1.3 57.6 + - + +
228A LEU* 3.3 14.1 + - + +
229A ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 226 (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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177A LEU* 3.4 36.3 - - + +
222A ARG* 3.0 22.2 + - + +
223A GLU* 3.4 6.7 - - - +
224A LYS 3.2 0.2 - - - -
225A LEU* 1.3 76.3 - - - +
227A GLU* 1.3 57.0 + - - +
229A ALA* 3.1 9.7 + - - +
230A ILE* 2.9 29.5 + - + +
275A LYS* 4.0 22.0 - - + +
278A PHE* 3.5 35.9 - - + -
279A LEU* 3.5 37.2 - - + +
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Residues in contact with GLU 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 GLU* 3.1 15.9 + - - +
224A LYS* 3.2 27.5 + - - +
226A ILE* 1.3 75.2 - - - +
228A LEU* 1.3 65.1 + - - +
230A ILE* 3.4 8.9 + - - +
231A LEU* 3.1 27.9 + - - +
253A VAL* 3.9 8.6 - - + +
257A LYS 4.7 3.6 - - - +
258A ASP* 4.9 3.5 - - - +
259A PRO* 3.3 36.8 - - + +
260A LEU* 4.0 19.1 - - + +
275A LYS* 2.7 41.1 + - + +
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Residues in contact with LEU 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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4A ILE* 3.8 10.5 - - + -
7A ILE* 3.7 22.0 - - + -
220A LEU* 4.0 12.3 - - + -
224A LYS 2.8 13.6 + - - +
225A LEU* 3.5 12.1 - - + +
227A GLU* 1.3 76.5 - - - +
229A ALA* 1.3 64.5 + - - +
231A LEU* 3.2 6.5 + - - +
232A VAL* 3.0 26.4 + - + +
246A LEU* 3.6 28.9 - - + -
249A ALA* 4.0 14.4 - - + +
250A LEU* 3.8 30.5 - - + -
253A VAL* 3.6 13.8 - - + +
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Residues in contact with ALA 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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2A VAL* 3.7 17.5 - - + +
4A ILE* 4.3 9.0 - - + -
177A LEU* 3.6 32.8 - - + -
225A LEU 2.9 13.9 + - - +
226A ILE* 3.3 9.4 - - + +
228A LEU* 1.3 77.8 - - - +
230A ILE* 1.3 52.1 + - + +
232A VAL 4.7 0.2 - - - +
233A GLY 2.7 31.9 + - - +
234A THR* 3.3 11.7 - - + +
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Residues in contact with ILE 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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226A ILE* 2.9 24.2 + - + +
227A GLU* 3.7 7.6 - - - +
228A LEU 3.3 0.2 - - - -
229A ALA* 1.3 75.4 - - - +
231A LEU* 1.3 65.7 + - + +
233A GLY 3.6 2.8 + - - -
234A THR* 4.0 11.4 - - + -
237A ASN* 2.8 36.8 + - - +
240A GLY* 3.7 1.2 - - - -
241A ILE* 4.4 2.0 + - + +
260A LEU* 4.0 19.1 - - + -
271A LEU* 3.7 31.0 - - + +
274A ILE* 3.9 18.6 - - + -
275A LYS* 3.6 40.2 - - + +
278A PHE* 4.7 0.9 - - + -
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Residues in contact with LEU 231 (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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227A GLU 3.1 20.0 + - - +
228A LEU 3.2 6.7 + - - +
230A ILE* 1.3 74.8 - - + +
232A VAL* 1.3 61.1 + - - +
241A ILE* 2.8 42.8 + - + +
244A ILE* 4.2 9.8 - - + +
249A ALA* 4.0 31.9 - - + +
252A ILE* 4.0 25.4 - - + -
253A VAL* 4.2 7.9 - - + -
259A PRO* 4.7 4.3 - - + +
260A LEU* 4.1 17.9 - - + -
263A PHE* 3.4 35.7 - - + -
271A LEU* 5.5 0.2 - - + -
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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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3A PRO* 3.5 38.7 - - + +
4A ILE* 4.7 4.3 - - + -
228A LEU* 3.0 18.3 + - + +
229A ALA 4.0 3.1 - - - +
231A LEU* 1.3 74.2 - - - +
233A GLY* 1.3 57.9 + - - +
239A GLY* 3.4 19.6 - - - +
241A ILE 5.3 0.2 - - - +
244A ILE 4.2 10.0 - - - +
245A GLY* 4.3 1.8 - - - +
246A LEU* 3.7 33.7 - - + +
249A ALA* 3.6 20.9 - - + -
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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