Contacts of the helix formed by residues 368 - 380 (chain A) in PDB entry 4MHG
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 ASP 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ASN 3.5 17.7 - - - +
353A PHE* 3.2 17.9 + - + +
366A ILE* 4.1 2.2 - - - -
367A VAL* 1.3 80.4 - - + +
369A PRO* 1.3 54.8 - - - +
370A ASN* 3.5 7.6 + - - +
371A GLY* 2.8 30.2 + - - -
372A LEU* 2.7 36.4 + - - +
374A ARG* 5.3 1.0 + - - -
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Residues in contact with PRO 369 (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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366A ILE* 3.5 14.3 - - + -
367A VAL 3.6 8.7 - - - +
368A ASP* 1.3 86.5 - - - +
370A ASN* 1.3 62.1 + - - +
372A LEU* 3.8 1.3 - - + +
373A ALA* 3.1 23.9 + - - +
387A TYR* 3.5 48.2 - - + -
411A LEU* 4.0 18.6 - - + -
3B C 3.6 31.9 - - - +
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Residues in contact with ASN 370 (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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368A ASP* 3.2 5.5 + - - +
369A PRO* 1.3 78.2 - - - +
371A GLY* 1.3 64.8 + - - +
373A ALA* 3.4 4.5 + - - +
374A ARG* 3.1 23.0 + - - +
387A TYR* 3.8 20.0 + - - +
3B C 4.3 17.0 + - - -
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Residues in contact with GLY 371 (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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353A PHE* 3.6 15.3 - - - -
368A ASP* 2.8 30.1 + - - -
370A ASN* 1.3 75.6 - - - +
372A LEU* 1.3 62.2 + - - +
374A ARG* 3.2 16.5 + - - +
375A LEU* 3.0 26.7 + - - +
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Residues in contact with LEU 372 (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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340A TYR* 5.0 4.7 - - + -
341A VAL* 5.5 8.3 - - + -
344A LEU* 3.5 31.9 - - + -
353A PHE* 3.9 12.5 - - + +
354A ILE* 4.0 25.6 - - + -
366A ILE* 3.7 31.0 - - + -
368A ASP 2.7 20.8 + - - +
369A PRO 3.8 6.1 - - - +
371A GLY* 1.3 72.8 - - - +
373A ALA* 1.3 62.1 + - - +
375A LEU* 3.2 6.0 + - + +
376A TRP* 3.0 22.7 + - - +
390A MET* 3.7 26.2 - - + -
394A LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 373 (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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369A PRO 3.1 16.0 + - - +
370A ASN* 3.8 4.9 - - - +
371A GLY 3.3 0.2 - - - -
372A LEU* 1.3 76.5 - - - +
374A ARG* 1.3 58.7 + - - +
376A TRP* 3.8 0.6 - - - +
377A GLY 3.0 23.0 + - - -
385A MET* 3.1 17.2 - - + +
386A THR* 3.4 39.0 - - - +
387A TYR* 3.4 7.9 - - + +
390A MET* 3.8 14.7 - - - -
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Residues in contact with ARG 374 (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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353A PHE* 3.8 29.9 - - - -
368A ASP* 5.3 0.8 + - - -
370A ASN 3.1 12.8 + - - +
371A GLY* 3.5 14.1 - - - +
373A ALA* 1.3 75.9 - - - +
375A LEU* 1.3 75.6 + - - +
377A GLY* 3.5 1.7 + - - -
378A ASN* 3.0 44.5 + - - +
385A MET* 5.3 4.3 - - - -
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Residues in contact with LEU 375 (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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340A TYR* 3.4 25.4 + - + +
344A LEU* 4.4 10.3 - - + -
350A TYR* 4.2 18.6 - - + -
353A PHE* 3.5 52.5 - - + -
371A GLY 3.0 12.6 + - - +
372A LEU* 3.6 7.9 - - + +
374A ARG* 1.3 98.2 - - - +
376A TRP* 1.3 56.3 + - - +
378A ASN* 3.2 13.5 - - - +
379A HIS* 2.8 23.9 + - - +
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Residues in contact with TRP 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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335A ARG 3.7 10.1 - - - -
337A LEU* 3.5 51.7 - - + +
340A TYR* 3.6 36.5 - + + -
372A LEU* 3.0 16.9 + - + +
373A ALA 3.8 2.0 - - - +
375A LEU* 1.3 74.5 - - - +
377A GLY* 1.3 63.7 + - - +
379A HIS* 3.1 11.0 + + - +
380A LYS* 3.0 43.2 + - + +
385A MET* 3.8 19.5 - - + -
390A MET* 3.6 32.6 - - + +
6C C 3.9 10.8 - - - -
7C T 2.9 40.9 + - - -
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Residues in contact with GLY 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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373A ALA 3.0 13.4 + - - -
374A ARG 3.9 1.6 - - - -
376A TRP* 1.3 77.5 - - - +
378A ASN* 1.3 61.7 + - - +
380A LYS* 3.4 1.5 + - - -
381A ASN 3.0 3.6 + - - -
382A ARG* 3.0 44.4 + - - +
385A MET* 3.6 25.5 - - - +
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Residues in contact with ASN 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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374A ARG* 3.0 39.4 + - - +
375A LEU* 3.2 16.8 - - - +
377A GLY* 1.3 76.9 - - - +
379A HIS* 1.3 63.8 + - - +
381A ASN* 2.9 21.5 + - - +
382A ARG 5.1 0.6 - - - +
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Residues in contact with HIS 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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335A ARG* 3.2 41.3 - - + +
340A TYR* 3.4 42.8 - + + +
343A GLN* 4.8 8.1 - - - -
375A LEU 2.8 14.5 + - - +
376A TRP* 3.1 26.9 + + + +
378A ASN* 1.3 76.9 - - - +
380A LYS* 1.3 60.7 + - + +
381A ASN* 3.5 8.5 + - - -
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Residues in contact with LYS 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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335A ARG 3.8 20.1 + - - +
376A TRP* 3.0 48.3 + - + +
379A HIS* 1.3 79.2 - - + +
381A ASN* 1.3 71.6 + - - +
382A ARG* 3.3 31.4 + - + +
13B A 4.8 11.0 + - - +
6C C 3.1 18.0 + - - -
7C T 2.8 32.9 + - - +
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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