Contacts of the helix formed by residues 379 - 390 (chain A) in PDB entry 1M6X
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 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A TYR* 4.5 11.1 + - - -
373A ALA* 5.3 9.3 - - - +
376A ASP 4.9 1.1 - - - +
377A GLU 2.9 10.4 + - - +
378A THR* 1.3 73.4 - - - +
380A PRO* 1.3 70.7 - - - +
381A ILE* 2.9 33.7 + - - +
382A GLU* 3.1 37.3 + - - +
383A GLU* 3.3 9.7 + - - +
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Residues in contact with PRO 380 (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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210A TYR 3.8 19.5 - - - +
211A LEU* 3.8 24.4 - - + +
234A SER* 5.2 6.5 - - - +
361A TYR* 3.2 54.3 - - + +
362A TYR* 4.4 3.6 - - + +
378A THR* 3.4 3.5 - - + +
379A ASN* 1.3 86.0 - - - +
381A ILE* 1.3 64.7 + - - +
383A GLU* 3.1 11.5 + - + +
384A TRP* 3.0 21.5 + - - +
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Residues in contact with ILE 381 (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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209A LYS* 3.4 26.9 - - - +
210A TYR 3.7 17.3 - - - +
211A LEU 4.2 0.8 + - - -
212A GLY* 3.7 23.8 - - - +
362A TYR* 4.2 7.0 - - - +
379A ASN* 2.9 19.5 + - - +
380A PRO* 1.3 72.7 - - - +
382A GLU* 1.3 66.8 + - + +
384A TRP* 2.9 20.8 + - + +
385A GLN* 3.2 27.3 + - - +
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Residues in contact with GLU 382 (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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377A GLU 6.1 0.2 - - - -
379A ASN* 3.1 30.5 + - + +
381A ILE* 1.3 80.7 - - + +
383A GLU* 1.3 62.1 + - - +
385A GLN* 3.1 33.9 + - - +
386A HIS* 3.4 19.6 + - + +
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A SER* 5.0 2.3 + - - -
361A TYR* 5.2 1.9 + - - -
378A THR* 4.7 18.1 - - + +
379A ASN 3.3 7.4 + - - +
380A PRO* 3.1 13.3 + - + +
382A GLU* 1.3 79.5 - - - +
384A TRP* 1.3 62.8 + - - +
386A HIS* 3.7 10.5 + - - +
387A ILE* 3.2 25.5 + - + +
418A TYR* 4.0 20.4 - - - -
421A ARG* 3.2 39.4 + - - +
422A ARG* 5.6 6.6 - - - +
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Residues in contact with TRP 384 (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 LEU* 5.9 2.4 - - - +
207A GLN* 2.9 30.7 - - + -
211A LEU 4.5 2.9 - - - +
212A GLY* 3.9 22.9 - - - -
213A VAL* 3.4 45.1 - - + +
380A PRO 3.0 10.6 + - - +
381A ILE* 2.9 13.0 + - + +
383A GLU* 1.3 73.1 - - - +
385A GLN* 1.3 91.4 + - - +
387A ILE* 3.0 9.0 + - - +
388A GLU* 2.8 58.7 + - + +
414A TYR* 3.7 22.4 - + + +
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Residues in contact with GLN 385 (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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381A ILE* 3.2 30.9 + - - +
382A GLU* 3.1 25.3 + - - +
384A TRP* 1.3 94.3 - - - +
386A HIS* 1.3 69.4 + - + +
388A GLU* 2.9 12.0 + - - +
389A GLN* 2.8 44.4 + - + +
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Residues in contact with HIS 386 (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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382A GLU* 3.4 20.5 + - + +
383A GLU* 3.8 6.5 - - - +
384A TRP 3.3 0.4 - - - -
385A GLN* 1.3 82.9 - - + +
387A ILE* 1.3 62.6 + - - +
389A GLN* 3.3 21.9 + - + +
390A LEU* 3.7 8.5 + - - +
421A ARG* 2.7 37.0 + - - +
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Residues in contact with ILE 387 (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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383A GLU* 3.2 23.6 - - + +
384A TRP* 3.0 9.3 + - + +
386A HIS* 1.3 76.8 - - - +
388A GLU* 1.3 61.8 + - - +
389A GLN 3.5 0.5 + - - -
390A LEU 4.0 12.6 - - - +
414A TYR* 4.0 29.8 - - + +
417A SER* 3.4 31.1 + - - +
418A TYR* 3.6 40.6 - - + +
421A ARG* 3.9 24.9 - - + -
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Residues in contact with GLU 388 (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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384A TRP* 2.8 57.5 + - + +
385A GLN* 2.9 9.5 + - - +
387A ILE* 1.3 76.9 - - - +
389A GLN* 1.3 83.7 + - - +
391A LYS* 3.1 30.5 + - - +
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Residues in contact with GLN 389 (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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385A GLN* 2.8 51.4 + - + +
386A HIS* 3.4 13.2 - - + +
387A ILE 3.2 1.0 - - - -
388A GLU* 1.3 100.4 + - - +
390A LEU* 1.3 60.1 + - - +
391A LYS* 2.6 43.5 + - - +
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Residues in contact with LEU 390 (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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386A HIS 3.7 8.7 + - - +
387A ILE 4.0 11.1 - - - +
388A GLU 4.9 0.2 - - - -
389A GLN* 1.3 76.0 - - + +
391A LYS* 1.3 85.8 + - - +
392A GLY 5.4 0.7 - - - +
393A SER* 4.9 5.9 - - - -
417A SER* 5.7 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