Contacts of the helix formed by residues 230 - 240 (chain A) in PDB entry 4IM3
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 ASN 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A PRO* 3.6 20.6 - - + +
224A PHE* 3.2 28.3 + - - +
225A GLU* 3.8 12.0 + - - +
226A GLY 2.9 6.0 + - - +
227A PRO 2.9 7.2 - - - +
229A ARG* 1.3 81.4 - - - +
231A LYS* 1.3 65.0 + - - +
232A GLU* 2.9 21.4 - - - +
233A VAL* 3.2 20.6 + - + +
234A MET* 3.0 19.1 + - - +
250A GLN* 4.3 2.8 + - - -
253A GLU* 6.1 2.0 - - - +
254A ASN* 5.9 1.6 + - - +
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Residues in contact with LYS 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 PRO 2.9 10.8 + - - +
228A ARG* 2.8 28.3 + - - +
229A ARG* 2.7 29.7 + - - +
230A ASN* 1.3 71.6 - - - +
232A GLU* 1.3 72.3 + - - +
234A MET* 3.4 6.4 - - - +
235A TYR* 3.2 22.0 + - - +
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Residues in contact with GLU 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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229A ARG 4.4 1.0 - - - +
230A ASN* 2.9 25.7 - - - +
231A LYS* 1.3 96.1 + - - +
233A VAL* 1.3 74.4 + - + +
235A TYR* 3.4 6.3 + - - +
236A LYS* 3.3 27.2 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 3.9 7.9 - - + -
230A ASN* 3.2 37.6 + - + +
232A GLU* 1.3 84.8 - - + +
234A MET* 1.3 56.7 + - - +
236A LYS* 3.4 12.0 + - + +
237A ILE* 3.0 42.0 + - + +
250A GLN* 3.3 32.3 - - + +
254A ASN* 5.6 5.2 - - - +
257A ILE* 5.6 3.1 - - + -
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Residues in contact with MET 234 (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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205A TRP* 6.0 0.7 - - + +
221A PHE* 3.7 42.4 - - + +
223A PRO* 3.8 18.3 - - + +
227A PRO* 4.2 18.4 - - + +
230A ASN 3.0 12.5 + - - +
231A LYS* 3.4 13.9 - - - +
233A VAL* 1.3 75.4 - - - +
235A TYR* 1.3 60.1 + - - +
237A ILE* 3.2 6.9 + - - +
238A ILE* 3.0 52.6 + - + +
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Residues in contact with TYR 235 (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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231A LYS 3.2 13.5 + - - +
232A GLU* 3.9 6.3 - - - +
233A VAL 3.4 0.2 - - - -
234A MET* 1.3 77.8 - - - +
236A LYS* 1.3 72.4 + - + +
238A ILE* 3.2 7.7 + - + -
239A THR* 2.9 59.9 + - + +
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Residues in contact with LYS 236 (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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232A GLU 3.3 13.5 + - - +
233A VAL* 3.6 11.7 - - + +
234A MET 3.3 0.4 - - - -
235A TYR* 1.3 84.2 - - + +
237A ILE* 1.3 55.1 + - + +
239A THR* 3.4 6.0 + - - -
240A GLY* 2.6 35.9 + - - -
257A ILE* 5.7 2.7 - - + -
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Residues in contact with ILE 237 (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 PHE* 4.0 31.2 - - + -
222A ARG 4.3 7.0 - - - +
223A PRO* 4.1 28.7 - - + -
233A VAL* 3.0 31.8 + - + +
234A MET* 3.2 9.4 + - - +
236A LYS* 1.3 76.6 - - + +
238A ILE* 1.3 57.2 + - - +
241A LYS* 3.1 30.1 + - - +
248A GLY* 4.4 9.2 - - - +
250A GLN* 5.1 1.6 - - + -
257A ILE* 3.6 28.5 - - + -
259A TRP* 3.4 19.7 - - + -
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Residues in contact with ILE 238 (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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205A TRP* 3.5 43.1 - - + +
221A PHE* 4.5 8.5 - - + -
234A MET* 3.0 56.0 + - + +
235A TYR* 4.0 8.5 - - + +
237A ILE* 1.3 76.7 - - - +
239A THR* 1.3 66.7 - - + +
241A LYS* 3.6 24.0 + - - +
287A ALA* 4.1 6.3 - - + +
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Residues in contact with THR 239 (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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235A TYR* 2.9 59.6 + - + +
236A LYS* 3.4 7.1 + - - -
238A ILE* 1.3 79.5 - - + +
240A GLY* 1.3 60.4 + - - +
241A LYS 3.1 12.8 + - - +
287A ALA* 4.3 12.9 - - - +
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Residues in contact with GLY 240 (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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236A LYS 2.6 22.7 + - - -
237A ILE 3.8 2.5 - - - -
239A THR* 1.3 74.0 + - - +
241A LYS* 1.3 62.4 + - - +
242A PRO* 3.3 8.1 - - - +
259A TRP* 4.1 8.6 - - - -
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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