Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 4IQJ
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 ASP 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 5.7 1.5 - - + +
215A TYR* 3.7 19.3 - - + +
216A VAL* 3.5 8.8 + - - +
217A ARG* 2.9 31.5 + - - +
219A GLU* 1.3 82.3 - - - +
221A ALA* 1.3 58.3 + - - +
222A ARG 3.4 1.1 - - - -
223A ALA* 3.6 11.8 - - + +
224A HIS* 2.8 31.9 + - - +
564A ARG* 2.7 52.4 + - + +
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Residues in contact with ALA 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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215A TYR* 4.1 17.5 - - + +
218A LYS 3.4 14.8 + - - +
219A GLU 3.2 2.6 - - - -
220A ASP* 1.3 78.5 - - - +
222A ARG* 1.3 55.3 + - + +
224A HIS* 3.2 4.5 + - - +
225A GLU* 2.7 34.7 + - - +
247A ASP* 3.7 37.5 - - + +
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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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219A GLU 4.5 3.6 + - - +
220A ASP 3.4 0.2 - - - -
221A ALA* 1.3 80.3 - - + +
223A ALA* 1.3 58.0 + - - +
225A GLU* 3.8 22.4 + - - +
226A VAL* 2.7 45.0 + - + +
236A LEU* 5.4 15.9 - - - +
247A ASP* 6.1 0.7 - - - +
557A GLN* 3.9 28.2 + - - +
561A VAL* 5.2 6.7 - - + -
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 5.4 2.2 - - + -
219A GLU 4.9 2.7 + - - +
220A ASP* 3.6 14.7 - - + +
221A ALA 3.3 0.2 - - - -
222A ARG* 1.3 77.8 - - - +
224A HIS* 1.3 58.6 + - - +
226A VAL* 2.9 26.7 - - - +
227A LEU* 3.2 6.2 + - - +
561A VAL* 3.9 13.2 - - + +
564A ARG* 3.8 24.7 - - + -
565A LEU* 3.4 27.6 - - + +
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Residues in contact with HIS 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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20A ASP 2.9 30.7 + - - -
22A ALA* 3.6 24.4 - - + +
214A HIS* 3.8 8.8 - - + +
215A TYR* 3.4 30.0 - + + -
220A ASP 2.8 17.5 + - - +
221A ALA 3.5 3.7 + - - +
223A ALA* 1.3 74.3 - - - +
225A GLU* 1.3 65.9 + - - +
227A LEU* 3.2 17.0 + - + +
228A LEU* 3.2 30.4 + - + +
244A PHE* 3.6 43.3 - + - +
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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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221A ALA 2.7 19.5 + - - +
222A ARG* 3.0 28.0 + - - +
224A HIS* 1.3 78.5 + - - +
226A VAL* 1.3 61.1 + - + +
228A LEU* 3.4 18.2 + - + +
229A ALA* 3.4 10.0 + - - +
236A LEU* 5.2 9.1 - - + +
241A ARG* 3.2 40.6 + - - +
242A TRP 4.6 2.3 - - - +
243A ARG* 3.8 17.1 + - + +
244A PHE 5.9 1.6 - - - +
247A ASP* 5.7 2.8 - - - +
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Residues in contact with VAL 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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222A ARG* 2.7 25.8 + - + +
223A ALA 2.9 25.1 - - - +
225A GLU* 1.3 71.6 - - + +
227A LEU* 1.3 63.9 + - - +
229A ALA* 3.3 12.0 + - + +
230A ILE* 3.2 26.1 + - + +
236A LEU* 4.3 24.5 - - + -
507A VAL* 6.0 4.4 - - + +
561A VAL* 3.3 30.1 - - + -
565A LEU* 3.7 8.5 - - + -
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Residues in contact with LEU 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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18A LEU 5.7 2.2 - - - +
19A LEU 4.5 5.6 - - - +
20A ASP 4.9 2.2 - - - -
21A GLY 3.3 30.7 - - - +
22A ALA* 3.6 20.0 - - + -
223A ALA 3.2 13.9 + - - +
224A HIS* 3.2 12.2 + - + +
226A VAL* 1.3 77.6 - - - +
228A LEU* 1.3 63.1 + - + +
230A ILE* 3.1 22.9 + - + +
231A GLN* 2.8 41.1 - - - +
565A LEU* 4.3 13.5 - - + -
568A LEU* 4.0 14.6 - - + -
569A ASN 5.8 4.7 - - - +
570A ARG 6.4 0.2 - - - +
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Residues in contact with LEU 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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19A LEU 4.3 2.2 - - - +
20A ASP* 4.0 22.9 - - + -
224A HIS* 3.2 23.0 + - + +
225A GLU* 3.6 9.4 - - - +
226A VAL 3.3 0.2 - - - -
227A LEU* 1.3 78.8 - - + +
229A ALA* 1.3 55.9 + - - +
231A GLN* 3.6 3.6 + - - -
232A SER* 2.9 30.5 + - - -
242A TRP* 3.3 70.6 - - + +
243A ARG* 4.2 4.7 - - - -
244A PHE* 3.4 31.6 - - + +
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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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225A GLU 3.4 7.1 + - - +
226A VAL* 3.3 16.5 + - + +
227A LEU 3.2 0.2 - - - -
228A LEU* 1.3 76.2 - - - +
230A ILE* 1.3 57.3 + - + +
232A SER* 4.2 6.3 - - - -
233A LYS* 2.6 32.8 + - - -
234A THR* 3.3 27.5 + - - +
235A THR 4.6 6.5 - - - +
236A LEU* 5.9 3.6 - - + -
241A ARG* 5.5 7.2 - - - +
242A TRP 4.8 1.5 + - - -
507A VAL* 5.3 8.9 - - + +
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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 VAL* 3.2 15.0 + - + +
227A LEU* 3.1 15.7 + - + +
229A ALA* 1.3 78.7 - - + +
231A GLN* 1.3 70.8 + - - +
233A LYS* 3.4 26.7 - - - +
506A ASP* 3.4 50.3 - - + +
507A VAL* 5.0 7.2 - - + +
509A ARG* 5.9 4.5 - - - +
510A VAL* 4.5 9.3 - - + +
565A LEU* 4.0 18.2 - - + -
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Residues in contact with GLN 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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18A LEU 4.4 5.7 + - - -
19A LEU* 2.9 46.3 - - + +
227A LEU* 2.8 34.9 + - - +
228A LEU* 4.2 3.7 - - - +
230A ILE* 1.3 92.4 - - - +
232A SER* 1.3 60.8 + - - +
233A LYS* 3.3 9.1 + - - +
242A TRP* 5.1 8.3 - - + -
570A ARG 5.8 2.2 - - - +
571A HIS* 4.2 25.8 + - + +
20E A 3.2 21.5 + - - -
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Residues in contact with SER 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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228A LEU 2.9 21.1 + - - -
229A ALA* 4.2 0.4 - - - -
231A GLN* 1.3 74.9 - - - +
233A LYS* 1.3 71.5 + - - +
234A THR* 4.0 20.5 + - - +
240A GLU 5.3 0.5 + - - -
241A ARG* 4.4 1.0 - - - -
242A TRP* 3.8 31.9 + - - +
19E C 5.5 1.2 - - - +
20E A 4.2 5.7 + - - -
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Residues in contact with LYS 233 (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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229A ALA 2.6 17.1 + - - -
230A ILE* 3.4 20.6 - - - +
231A GLN* 3.9 7.9 + - - +
232A SER* 1.3 76.3 - - - +
234A THR* 1.3 60.9 + - - +
510A VAL* 3.6 32.5 - - + -
19E C 3.7 15.0 + - + +
20E A 2.6 91.1 + - + +
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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