Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 5IJ7
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 SER 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ASP* 3.3 25.6 + - - -
219A PRO* 1.4 74.7 - - - +
221A ASP* 1.4 64.7 + - - +
222A LYS* 3.3 26.0 + - - +
223A ILE* 3.2 27.4 + - - +
224A PHE* 3.2 15.6 - - - -
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Residues in contact with ASP 221 (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 PRO 3.7 2.0 + - - +
220A SER* 1.4 67.9 + - - +
222A LYS* 1.3 56.3 + - - +
223A ILE 3.0 10.5 + - - -
224A PHE* 3.2 11.3 + - - +
225A GLU* 3.1 33.5 + - - +
237A ALA* 5.5 0.7 - - - +
241A LYS* 2.8 36.8 + - + +
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Residues in contact with LYS 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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9A GLU* 3.5 18.4 - - + +
10A LYS 3.3 32.3 - - - +
15A TRP* 3.5 55.3 - - + +
194A ASP* 3.4 25.8 + - - -
197A ASP* 4.2 5.5 + - - +
220A SER* 3.3 19.5 + - - +
221A ASP* 1.3 75.6 - - - +
223A ILE* 1.3 57.0 + - + +
225A GLU* 3.6 26.3 + - - +
226A ALA* 3.8 1.7 - - - +
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Residues in contact with ILE 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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15A TRP* 3.7 21.3 - - + -
175A VAL* 4.5 15.0 - - + +
178A LEU* 3.6 56.8 - - + +
179A GLY* 3.8 6.3 - - - +
194A ASP* 3.9 22.4 - - + +
219A PRO 5.8 1.6 - - - -
220A SER* 3.2 21.7 + - - +
221A ASP 3.0 0.6 - - - -
222A LYS* 1.3 76.9 - - - +
224A PHE* 1.3 62.0 + - + +
225A GLU 3.3 0.9 - - - -
226A ALA* 3.2 7.4 + - - +
227A ILE* 3.0 36.5 + - + +
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Residues in contact with PHE 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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171A PHE* 4.6 5.4 - + - -
175A VAL* 4.2 17.3 - - + -
219A PRO* 3.2 31.2 - - + -
220A SER 3.2 22.2 - - - -
221A ASP* 3.2 7.7 + - - +
223A ILE* 1.3 79.8 - - + +
225A GLU* 1.4 55.5 + - - +
227A ILE* 3.3 7.1 + - + -
228A SER* 3.0 30.3 + - - -
237A ALA* 3.6 20.6 - - + +
240A LEU* 3.4 45.4 - - + +
241A LYS* 3.6 23.6 - - + -
244A TYR* 3.7 32.5 - + + -
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Residues in contact with GLU 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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12A PRO* 4.4 22.4 - - + +
221A ASP* 3.1 25.1 + - - +
222A LYS* 3.6 25.0 - - - +
224A PHE* 1.4 74.6 - - - +
226A ALA* 1.3 56.3 + - + +
228A SER* 3.9 2.5 - - - -
229A SER* 2.8 36.4 + - - -
237A ALA* 4.0 18.5 - - + +
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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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12A PRO 5.3 0.4 - - - +
15A TRP* 3.7 31.0 - - + -
16A ARG* 4.1 5.6 - - + +
19A VAL* 3.5 23.3 - - + -
222A LYS 3.8 4.7 - - - +
223A ILE* 3.2 9.7 + - - +
225A GLU* 1.3 79.5 - - + +
227A ILE* 1.4 63.1 + - - +
229A SER* 3.3 6.1 + - - -
230A MET* 3.2 28.8 + - - +
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Residues in contact with ILE 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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19A VAL* 4.2 6.5 - - + -
166A ILE* 4.9 1.8 - - + -
171A PHE* 4.1 17.0 - - + -
174A LEU* 4.0 17.5 - - + -
175A VAL* 3.7 30.7 - - + -
178A LEU* 3.8 26.9 - - + -
223A ILE* 3.0 28.9 + - + +
224A PHE* 3.3 5.1 + - + +
226A ALA* 1.4 75.6 - - - +
228A SER* 1.4 57.6 + - - +
230A MET 3.2 1.6 + - - -
231A PHE* 2.8 47.7 + - + +
234A LYS* 6.0 1.1 - - + -
240A LEU* 3.8 16.8 - - + -
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Residues in contact with SER 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 PHE 3.0 17.5 + - - -
225A GLU 4.0 4.3 - - - -
227A ILE* 1.4 74.1 - - - +
229A SER* 1.3 57.8 + - - +
231A PHE 4.2 2.5 - - - -
232A PRO* 3.1 28.2 - - - +
235A GLY 2.7 26.2 + - - -
236A THR* 3.4 9.7 + - - -
237A ALA* 3.6 16.7 + - - -
240A LEU* 3.4 10.4 - - - +
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Residues in contact with SER 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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16A ARG* 3.6 31.4 + - - +
225A GLU 2.8 22.6 + - - -
226A ALA* 3.5 6.5 - - - -
227A ILE 3.2 0.6 - - - -
228A SER* 1.3 75.9 - - - +
230A MET* 1.3 67.8 + - - +
232A PRO* 3.8 9.1 - - - +
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Residues in contact with MET 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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16A ARG* 3.1 53.2 - - + +
19A VAL* 3.8 15.5 - - + -
20A LYS* 5.0 10.1 - - + +
226A ALA 3.2 16.6 + - - +
229A SER* 1.3 94.3 - - - +
231A PHE* 1.3 88.1 + - + +
232A PRO* 3.6 5.7 - - - +
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Residues in contact with PHE 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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19A VAL* 4.0 15.3 - - + -
20A LYS* 6.5 0.2 - - - -
23A TYR* 3.8 41.3 - + - -
166A ILE* 3.6 37.7 - - + -
174A LEU* 4.4 3.6 - - + -
227A ILE* 2.8 30.9 + - + +
228A SER* 3.5 4.8 - - - +
230A MET* 1.3 96.6 - - + +
232A PRO* 1.4 66.3 - - - +
233A ASP* 3.3 3.4 - - - -
234A LYS* 3.1 29.9 + - + +
235A GLY 3.8 5.5 + - - +
240A LEU* 5.5 0.2 - - - +
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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