Contacts of the helix formed by residues 368 - 376 (chain A) in PDB entry 6DMY
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 THR 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLU* 5.1 8.7 + - + +
150A GLU 5.2 5.8 - - - +
152A MET* 4.4 2.4 + - - -
153A PHE* 3.7 37.4 - - - +
154A ASN* 3.8 13.9 - - + +
366A LEU 3.7 0.2 + - - -
367A MET* 1.3 74.7 - - - +
369A PRO* 1.3 69.0 - - + +
370A LYS* 4.1 5.7 + - - +
371A GLN* 2.9 28.3 + - - +
372A MET* 2.9 24.8 + - - +
396A LEU* 4.0 0.4 - - - -
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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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154A ASN* 4.9 6.3 - - - +
368A THR* 1.3 86.9 - - - +
370A LYS* 1.3 56.2 + - - +
372A MET* 3.8 4.3 - - + +
373A TYR* 2.9 27.9 + - - +
389A GLU* 3.6 17.2 - - + +
392A ALA* 4.1 2.8 - - + +
393A ALA* 3.7 35.2 - - + +
396A LEU* 3.7 24.0 - - + -
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Residues in contact with LYS 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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147A ILE 5.7 2.7 - - - +
148A GLY* 4.9 11.3 + - - -
149A GLU* 3.3 44.3 + - - +
368A THR* 3.2 4.2 + - - +
369A PRO* 1.3 75.6 - - - +
371A GLN* 1.3 65.1 + - + +
373A TYR* 3.4 8.9 + - + +
374A GLU* 2.9 56.5 + - + +
389A GLU* 4.2 25.5 - - - +
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Residues in contact with GLN 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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147A ILE* 5.7 2.8 - - - +
152A MET* 4.0 41.2 - - - +
204A TYR* 4.4 16.3 - - + -
367A MET* 3.8 22.2 - - + +
368A THR* 2.9 25.9 + - - +
370A LYS* 1.3 81.1 - - + +
372A MET* 1.3 58.5 + - - +
374A GLU* 3.5 7.9 + - - +
375A HIS* 2.9 27.5 + - - +
942A ARG* 5.6 0.3 + - - -
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Residues in contact with MET 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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197A TRP* 3.7 24.9 - - + +
202A LEU* 3.7 31.4 - - + -
367A MET* 4.2 16.8 - - + +
368A THR 2.9 13.8 + - - +
369A PRO* 4.0 5.8 - - + +
371A GLN* 1.3 75.9 - - - +
373A TYR* 1.3 64.0 + - - +
375A HIS* 3.6 4.8 - - - +
376A PHE* 3.2 42.2 + - + -
387A TRP* 3.8 18.4 + - + -
392A ALA* 3.9 19.1 - - + +
395A ILE* 4.2 10.3 - - + -
396A LEU* 4.1 15.5 - - + -
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Residues in contact with TYR 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 2.9 20.6 + - - +
370A LYS* 3.7 10.1 - - + +
372A MET* 1.3 77.7 - - - +
374A GLU* 1.3 79.9 + - + +
376A PHE 3.1 22.3 - - - +
377A LYS* 4.7 16.2 + - - -
387A TRP* 3.2 51.2 + + + +
388A ASN* 3.7 9.8 + - - -
389A GLU* 3.5 37.7 - - + -
392A ALA* 4.5 1.5 - - - +
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Residues in contact with GLU 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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370A LYS* 2.9 36.1 + - + +
371A GLN* 3.7 9.4 - - - +
373A TYR* 1.3 96.0 - - - +
375A HIS* 1.3 65.8 + - - +
376A PHE 4.8 0.2 - - - -
377A LYS* 3.9 28.7 + - - +
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Residues in contact with HIS 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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201A HIS* 4.8 1.7 + - - -
205A LYS* 5.6 9.9 - - + -
367A MET* 4.3 21.8 - - + +
371A GLN 2.9 18.0 + - - +
372A MET* 3.2 9.1 + - - +
374A GLU* 1.3 80.3 - - - +
376A PHE* 1.3 91.0 + + - +
377A LYS* 3.2 9.4 + - - +
379A TYR* 3.5 45.0 + + - -
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Residues in contact with PHE 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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197A TRP* 4.3 3.8 - - - -
201A HIS* 3.7 41.7 - + + -
372A MET* 3.2 30.8 + - + -
373A TYR 3.1 15.0 - - - +
375A HIS* 1.3 95.4 - + - +
377A LYS* 1.3 60.8 + - - +
378A GLY 3.8 1.1 - - - -
379A TYR* 3.8 34.8 - + + -
381A TYR* 3.9 27.6 - + + -
382A VAL* 4.6 6.5 - - + -
387A TRP* 3.2 45.2 - + + -
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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