Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 1RXV
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 THR 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.0 6.3 - - - -
220A LEU* 1.3 78.5 - - - +
222A ARG* 1.3 67.0 + - - +
223A GLU* 3.6 15.9 + - - +
224A GLN* 2.9 44.5 + - - +
225A LEU* 3.1 11.4 + - - +
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Residues in contact with ARG 222 (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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176A LEU 3.6 8.7 - - - +
177A LEU 2.6 35.2 + - - +
178A PHE 3.4 8.2 + - - -
179A GLY* 3.3 32.9 - - - +
211A LEU* 4.0 10.3 - - + -
215A LEU* 3.7 17.3 - - + +
221A THR* 1.3 73.1 - - - +
223A GLU* 1.3 62.5 + - - +
225A LEU* 3.2 12.2 + - + +
226A ILE* 3.0 35.2 + - + +
279A PHE 3.1 17.2 + - - -
280A LEU* 3.0 37.1 + - + +
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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* 3.0 13.5 + - - +
222A ARG* 1.3 80.1 - - + +
224A GLN* 1.3 61.9 + - + +
226A ILE* 3.4 11.8 + - - +
227A ASP* 3.2 26.2 + - - +
276A ARG* 4.3 20.6 + - - +
280A LEU* 3.5 37.5 - - + +
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Residues in contact with GLN 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 GLY 4.4 2.5 + - - +
220A LEU* 3.4 23.8 - - + +
221A THR* 2.9 44.1 + - - +
223A GLU* 1.3 75.1 - - + +
225A LEU* 1.3 66.1 + - - +
227A ASP* 3.2 7.5 + - - +
228A ILE* 2.9 29.3 + - - +
252A ILE* 3.8 23.8 + - + +
253A LYS* 5.0 7.3 + - - +
256A GLY* 3.7 28.4 + - - +
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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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5A ILE* 4.8 5.3 - - + +
8A LEU* 4.6 20.0 - - + -
9A PHE* 4.2 24.5 - - + -
176A LEU 4.6 6.1 - - - +
177A LEU* 3.8 21.8 - - + -
211A LEU* 3.7 29.4 - - + -
215A LEU* 3.9 15.5 - - + -
218A LEU* 5.3 4.9 - - + -
220A LEU* 4.7 9.5 - - + +
221A THR 3.1 11.5 + - - +
222A ARG* 3.3 14.8 - - + +
224A GLN* 1.3 77.1 - - - +
226A ILE* 1.3 62.0 + - + +
228A ILE* 3.1 9.8 + - - +
229A ALA* 3.0 21.3 + - - +
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Residues in contact with ILE 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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177A LEU* 3.5 35.4 - - + +
222A ARG* 3.0 35.2 + - - +
223A GLU* 3.5 7.9 - - - +
224A GLN 3.2 0.2 - - - -
225A LEU* 1.3 73.4 - - - +
227A ASP* 1.3 60.4 + - - +
229A ALA* 3.2 8.5 + - - +
230A ILE* 3.0 28.9 + - + +
276A ARG* 3.9 22.7 - - + -
279A PHE* 3.7 40.2 - - + -
280A LEU* 3.8 17.7 - - + +
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Residues in contact with ASP 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 3.2 13.3 + - - +
224A GLN* 3.2 11.9 + - - +
226A ILE* 1.3 74.1 - - - +
228A ILE* 1.3 64.7 + - - +
230A ILE* 4.4 1.5 - - - +
231A LEU* 3.1 21.5 + - - +
252A ILE* 3.6 20.6 - - + -
256A GLY 4.7 0.2 - - - +
257A ASP* 3.8 7.6 - - - -
258A ILE* 3.1 36.6 + - + +
276A ARG* 2.7 49.6 + - - +
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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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5A ILE* 4.0 8.1 - - + -
8A LEU* 3.9 24.7 - - + -
220A LEU* 3.7 18.8 - - + -
224A GLN 2.9 17.4 + - - +
225A LEU* 3.1 8.9 + - + +
227A ASP* 1.3 75.0 - - - +
229A ALA* 1.3 66.4 + - - +
231A LEU* 3.3 4.2 + - - +
232A VAL* 3.2 23.2 + - + +
245A VAL* 5.0 2.7 - - - +
248A ALA* 3.7 24.0 - - + +
249A LEU* 3.4 38.4 - - + +
252A ILE* 3.7 24.0 - - + -
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Residues in contact with ALA 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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5A ILE* 4.0 22.6 - - + +
177A LEU* 3.7 31.0 - - + -
225A LEU 3.0 12.2 + - - +
226A ILE 3.2 8.5 + - - +
228A ILE* 1.3 77.5 - - - +
230A ILE* 1.3 63.0 + - + +
232A VAL* 3.2 6.2 + - - +
233A GLY 3.0 25.5 + - - +
234A THR* 3.8 9.9 - - + -
279A PHE* 5.7 0.7 - - + -
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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* 3.0 23.2 + - + +
227A ASP* 4.5 2.7 - - - +
228A ILE 3.2 0.2 - - - -
229A ALA* 1.3 75.9 - - - +
231A LEU* 1.3 55.2 + - - +
233A GLY* 2.7 21.2 + - - +
234A THR* 4.3 3.8 - - + -
237A ASN* 2.9 38.6 + - - +
239A GLY* 4.1 0.3 - - - -
258A ILE* 3.5 26.9 - - + -
269A ILE* 3.6 13.4 - - + +
272A VAL* 4.5 10.8 - - + +
275A ILE* 3.6 33.7 - - + -
276A ARG* 3.9 28.0 - - + +
279A PHE* 4.8 5.8 - - + -
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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 ASP 3.1 12.0 + - - +
228A ILE 3.3 6.9 + - - +
230A ILE* 1.3 77.3 - - - +
232A VAL* 1.3 58.5 + - - +
239A GLY* 3.1 0.7 - - - -
240A VAL* 2.8 51.4 + - + +
243A VAL* 4.6 4.6 - - + +
248A ALA* 4.1 24.2 - - + +
251A TYR* 4.7 5.4 - - + -
252A ILE* 3.6 35.2 - - + -
258A ILE* 3.8 8.1 - - + -
261A ALA* 4.6 9.6 - - + -
262A LEU* 3.3 34.1 - - + -
265A LEU* 4.6 7.0 - - + -
269A ILE* 4.7 3.8 - - + -
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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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4A ASP* 4.3 28.7 - - + +
5A ILE* 5.3 6.5 - - + +
228A ILE* 3.2 15.2 + - + +
229A ALA* 3.2 9.0 + - - +
230A ILE 3.1 0.6 - - - -
231A LEU* 1.3 75.4 - - - +
233A GLY* 1.3 64.1 + - - +
239A GLY* 3.4 7.8 + - - -
243A VAL 4.3 13.7 - - - +
244A GLY* 3.9 20.0 - - - -
245A VAL* 4.0 9.2 - - + +
248A ALA* 3.7 20.2 - - + -
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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