Contacts of the helix formed by residues 382 - 390 (chain D) in PDB entry 3IKM
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 MET 382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D ALA* 4.8 16.2 - - + -
205D GLU 6.0 0.7 - - - +
228D LEU* 3.2 40.2 - - + +
229D VAL* 2.9 35.0 - - - +
231D GLU 4.6 4.5 - - - +
234D SER 4.1 15.3 - - - +
235D TRP* 5.7 3.4 - - + -
241D PRO* 3.6 35.4 - - + -
381D THR* 1.3 89.0 + - - +
383D LYS* 1.3 79.8 + - + +
384D ASP 3.6 1.3 - - - -
385D ILE* 3.0 18.9 - - - +
386D ARG* 3.3 0.5 - - - +
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Residues in contact with LYS 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D VAL* 4.0 20.0 - - + +
233D TYR 5.7 0.8 - - - -
234D SER* 4.7 21.6 - - - +
235D TRP* 5.7 12.2 - - + -
381D THR* 5.4 0.9 - - - +
382D MET* 1.3 98.0 - - + +
384D ASP* 1.3 61.9 + - + +
386D ARG* 2.5 35.2 + - - +
387D GLU* 4.3 1.2 + - - +
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Residues in contact with ASP 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D THR* 3.4 21.3 + - - +
383D LYS* 1.3 75.6 - - - +
385D ILE* 1.3 65.5 + - - +
386D ARG 2.9 3.4 + - - -
387D GLU* 3.3 4.5 + - - +
388D ASN* 2.4 42.7 + - - +
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Residues in contact with ILE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D CYS* 5.7 6.3 - - + -
211D LEU* 6.4 1.8 - - + -
225D SER* 5.3 4.9 - - - +
228D LEU* 4.1 17.7 - - + -
229D VAL* 4.8 0.2 - - + -
375D GLU* 4.1 11.7 - - - +
378D VAL* 3.8 18.4 - - + +
380D GLY* 2.9 28.9 - - - +
381D THR* 3.2 17.5 - - + +
382D MET 3.0 20.2 - - - +
384D ASP* 1.3 76.4 - - - +
386D ARG* 1.3 57.7 + - + +
388D ASN* 2.9 13.1 - - + +
389D PHE* 2.6 34.2 + - + +
393D MET* 3.8 18.7 - - + +
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D SER* 5.2 0.2 - - - +
229D VAL* 3.5 30.3 - - + +
382D MET 3.3 7.6 - - - +
383D LYS* 2.5 38.8 + - - +
385D ILE* 1.3 77.4 - - + +
387D GLU* 1.3 81.3 + - - +
388D ASN 2.8 0.9 - - - -
389D PHE* 2.5 75.5 + - + -
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D LYS 4.3 1.1 + - - +
384D ASP* 3.3 5.6 + - - +
386D ARG* 1.3 97.6 + - - +
388D ASN* 1.3 63.4 - - - +
389D PHE* 4.9 3.4 - - - -
390D GLN* 2.7 50.5 + - - +
391D ASP* 4.4 1.6 + - - +
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Residues in contact with ASN 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D VAL* 4.7 15.9 - - + +
384D ASP* 2.4 37.6 + - - +
385D ILE* 2.9 16.8 - - + +
386D ARG 2.8 0.2 - - - -
387D GLU* 1.3 84.5 - - - +
389D PHE* 1.3 57.5 + - - +
390D GLN 3.4 0.4 + - - -
391D ASP* 4.2 2.0 - - - +
392D LEU* 3.5 28.6 + - + +
393D MET* 2.9 25.1 - - + +
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ALA* 5.0 7.4 - - - +
221D TYR* 4.8 6.7 + - + -
225D SER* 3.4 33.7 - - - +
385D ILE* 2.6 8.7 + - + +
386D ARG* 2.5 72.5 + - + -
387D GLU* 4.9 3.1 - - - -
388D ASN* 1.3 65.3 - - - +
390D GLN* 1.3 98.2 + - + -
391D ASP 3.1 0.8 - - - -
393D MET* 2.7 41.9 - - + +
394D GLN 4.6 1.2 + - - -
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Residues in contact with GLN 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D TRP* 2.7 61.3 - - - +
170D ALA* 5.2 3.3 - - - +
387D GLU* 2.7 49.8 + - - +
389D PHE* 1.3 97.3 - - + +
391D ASP* 1.3 79.7 + - + +
394D GLN* 5.4 0.9 - - - +
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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