Contacts of the helix formed by residues 357 - 363 (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 ALA 357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D GLN* 5.9 4.0 - - + -
350D ILE* 3.2 31.0 - - + +
352D SER* 4.0 9.0 - - - -
353D VAL 3.9 9.8 + - - +
356D LEU* 1.3 82.5 - - + +
358D GLU* 1.3 68.8 + - - +
359D VAL 2.5 7.2 + - - -
360D HIS* 2.8 28.4 + - + +
361D ARG 3.2 1.6 + - - -
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Residues in contact with GLU 358 (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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295D MET* 6.2 0.7 - - + -
298D HIS* 3.2 32.9 - - + +
299D MET* 3.4 21.4 - - + +
302D SER* 3.9 3.6 + - - +
309D ARG* 3.1 7.1 + - - -
350D ILE 3.5 2.6 - - - -
351D SER* 1.4 38.7 - - - +
352D SER* 1.6 68.6 + - - +
353D VAL* 3.9 6.7 - - - -
354D ASN 4.7 0.4 - - - +
355D SER* 4.5 6.8 - - - +
356D LEU 3.6 3.8 - - - +
357D ALA* 1.3 80.9 - - - +
359D VAL* 1.4 52.6 + - - +
361D ARG* 2.6 32.8 + - - +
362D LEU 3.3 3.5 + - - -
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Residues in contact with VAL 359 (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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298D HIS* 4.9 4.0 - - + -
355D SER* 4.3 15.9 - - - +
356D LEU 4.0 12.8 - - - +
357D ALA 2.5 12.5 + - - -
358D GLU* 1.4 68.2 - - - +
360D HIS* 1.4 72.2 - - - +
361D ARG 2.5 1.6 - - - -
362D LEU* 3.5 5.4 - - - +
363D TYR* 2.9 27.0 + - + +
364D VAL 2.8 13.5 + - - +
367D PRO* 4.4 17.5 - - + -
403D THR* 5.4 3.1 - - - -
406D VAL* 3.1 40.8 - - + -
407D PHE* 5.7 0.7 - - + -
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Residues in contact with HIS 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D GLN* 3.6 29.7 + - + +
350D ILE* 4.4 24.0 - - + -
356D LEU 4.0 3.1 + - - -
357D ALA* 2.8 34.0 + - + +
359D VAL* 1.4 78.6 - - - +
361D ARG* 1.4 56.8 + - - +
364D VAL* 2.7 41.5 + - + +
367D PRO* 5.1 6.0 - - - +
368D PRO* 4.7 20.5 - - + +
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Residues in contact with ARG 361 (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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298D HIS* 3.7 11.5 + - - -
301D ILE* 4.3 14.1 - - - +
302D SER* 3.1 26.8 - - - +
349D ASP* 2.6 48.2 - - + +
350D ILE* 2.6 31.6 + - - +
351D SER* 3.1 11.0 - - - +
357D ALA 3.2 1.4 + - - -
358D GLU* 2.6 17.9 + - - +
359D VAL 2.5 1.2 - - - -
360D HIS* 1.4 84.9 - - - +
362D LEU* 1.3 107.5 + - - +
364D VAL* 4.3 3.8 - - - +
411D LEU* 5.3 0.6 - - - +
414D PHE* 6.1 1.8 - - - +
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Residues in contact with LEU 362 (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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298D HIS* 3.0 43.1 - - + +
301D ILE* 5.7 0.9 - - + -
358D GLU 3.3 3.7 + - - +
359D VAL* 3.1 8.8 + - - -
361D ARG* 1.3 108.6 - - - +
363D TYR* 1.3 59.8 + - + +
364D VAL* 4.6 1.2 - - - +
406D VAL* 4.3 10.3 - - + +
407D PHE* 4.5 0.9 - - - +
410D GLN* 3.7 36.8 + - + -
411D LEU* 4.0 14.6 - - + +
414D PHE* 4.0 23.4 - - + -
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Residues in contact with TYR 363 (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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359D VAL* 2.9 22.9 + - + +
362D LEU* 1.3 78.6 - - + +
364D VAL* 1.3 71.4 - - - +
365D GLY* 3.2 34.9 + - - -
367D PRO* 5.9 1.1 - - + -
406D VAL* 3.9 30.1 - - + -
410D GLN* 4.8 15.9 - - + +
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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