Contacts of the helix formed by residues 375 - 385 (chain A) in PDB entry 6MOL
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 HIS 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ALA 3.2 23.1 - - - -
339A LEU 3.2 19.1 + - - -
340A ILE 4.3 3.4 - - - -
341A GLY* 3.5 23.3 + - - -
370A ALA* 3.3 10.3 + - + +
373A MET* 3.4 33.0 - - + +
374A GLY* 1.3 73.8 - - - +
376A LEU* 1.3 66.2 + - - +
377A GLU 3.3 1.8 - - - +
378A ILE* 3.3 24.2 + - + +
379A VAL* 3.1 24.9 + - - +
411A ILE* 4.0 1.1 - - - -
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Residues in contact with LEU 376 (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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374A GLY 3.1 8.6 + - - +
375A HIS* 1.3 72.7 - - - +
377A GLU* 1.3 63.6 + - - +
379A VAL* 3.4 2.1 + - + +
380A GLU* 3.2 42.5 + - - +
410A GLU* 4.0 27.4 - - + -
411A ILE* 4.0 23.6 - - + -
414A VAL* 3.9 28.0 - - + -
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Residues in contact with GLU 377 (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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343A LEU* 3.9 29.2 - - + -
375A HIS 3.3 0.6 - - - -
376A LEU* 1.3 80.4 - - - +
378A ILE* 1.3 67.5 + - + +
380A GLU* 3.5 14.3 + - - +
381A VAL* 3.3 26.5 + - - +
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Residues in contact with ILE 378 (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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338A ALA* 3.9 21.5 - - + -
341A GLY* 4.1 16.2 - - - +
342A HIS 4.5 1.3 - - - +
343A LEU* 4.0 34.3 - - + +
346A VAL* 4.0 24.5 - - + -
370A ALA* 3.9 6.5 - - + -
375A HIS* 3.3 26.2 + - + +
376A LEU 3.3 0.4 - - - -
377A GLU* 1.3 78.6 - - + +
379A VAL* 1.3 62.3 + - - +
381A VAL* 3.1 4.9 + - - +
382A LEU* 2.9 50.9 + - + +
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Residues in contact with VAL 379 (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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367A LEU* 3.7 22.0 - - + -
370A ALA* 3.6 25.8 - - + +
371A ALA* 4.1 1.8 - - + +
375A HIS 3.1 18.2 + - - +
376A LEU* 3.9 5.2 - - + +
377A GLU 3.4 0.2 - - - -
378A ILE* 1.3 76.5 - - - +
380A GLU* 1.3 62.0 + - + +
382A LEU* 3.6 0.5 + - - +
383A LEU* 3.2 37.6 + - + +
411A ILE* 3.8 38.8 - - + -
414A VAL* 4.6 8.3 - - + -
415A LEU* 4.6 4.7 - - + -
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Residues in contact with GLU 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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376A LEU* 3.2 37.2 + - - +
377A GLU* 3.6 12.2 - - - +
378A ILE 3.2 0.6 - - - -
379A VAL* 1.3 78.9 - - - +
381A VAL* 1.3 62.8 + - + +
383A LEU* 3.6 2.7 + - - +
384A LYS* 3.1 46.6 + - - +
414A VAL* 4.4 27.8 - - + +
418A TYR* 4.3 2.5 + - - -
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Residues in contact with VAL 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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343A LEU* 3.9 19.3 - - + -
346A VAL* 4.6 5.4 - - + -
347A GLU* 4.1 24.5 - - + +
350A LEU* 3.9 13.0 - - + -
377A GLU 3.3 15.0 - - - +
378A ILE* 3.1 8.1 + - - +
380A GLU* 1.3 75.4 - - + +
382A LEU* 1.3 67.1 + - - +
384A LYS* 3.2 25.1 + - + +
385A TYR* 3.2 42.0 - - + -
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Residues in contact with LEU 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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334A LEU* 4.3 15.5 - - + -
338A ALA* 4.5 2.0 - - + -
346A VAL* 4.3 8.1 - - + -
350A LEU* 3.8 23.1 - - + -
356A VAL* 3.6 20.4 - - + +
366A PRO* 3.6 36.6 - - + +
367A LEU* 3.8 24.0 - - + +
370A ALA* 4.0 2.2 - - + -
378A ILE* 2.9 36.1 + - + +
379A VAL 4.0 0.2 - - - +
381A VAL* 1.3 76.3 - - - +
383A LEU* 1.3 62.5 + - - +
385A TYR* 3.1 10.6 + - - -
386A GLY 3.3 1.0 + - - -
387A ALA* 3.3 21.6 + - + +
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Residues in contact with LEU 383 (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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367A LEU* 3.7 26.7 - - + -
379A VAL* 3.2 29.1 + - + +
380A GLU 4.1 1.1 - - - +
382A LEU* 1.3 77.5 - - - +
384A LYS* 1.3 60.7 + - - +
386A GLY* 3.3 11.3 + - - -
387A ALA* 3.8 20.3 + - + +
389A VAL* 4.3 8.7 - - + -
414A VAL* 3.8 16.2 - - + +
415A LEU* 4.2 11.2 - - + -
418A TYR* 3.5 64.3 - - + -
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Residues in contact with LYS 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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380A GLU* 3.1 40.1 + - - +
381A VAL* 3.2 20.7 + - + +
383A LEU* 1.3 77.1 - - - +
385A TYR* 1.3 67.0 + - + +
386A GLY 3.7 0.3 + - - -
418A TYR* 3.5 18.6 - - - +
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Residues in contact with TYR 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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347A GLU* 4.7 1.9 + - + -
350A LEU* 3.7 55.0 - - + -
351A LYS* 3.3 34.2 - - + +
356A VAL* 3.9 11.7 - - + +
381A VAL* 3.2 38.3 + - + +
382A LEU 3.1 8.5 + - - +
384A LYS* 1.3 84.1 - - + +
386A GLY* 1.3 58.9 + - - +
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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