Contacts of the helix formed by residues 390 - 400 (chain E) in PDB entry 6F0X
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 LYS 390 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386E ARG* 2.9 19.8 + - + +
387E VAL* 2.9 17.6 + - + +
389E ARG* 1.3 78.5 - - - +
391E LEU* 1.3 65.0 + - - +
392E PRO* 3.2 3.8 - - - +
393E PHE* 3.3 21.2 + - + +
394E LEU* 4.0 32.2 + - + +
421E GLN* 6.0 2.0 - - - +
170F THR* 3.5 28.3 - - + +
314F ASP 3.1 26.8 + - - -
315F ILE* 4.1 16.4 - - - +
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E TYR* 4.0 33.0 - - + +
383E LEU* 5.6 3.8 - - + -
387E VAL* 2.9 27.0 + - + +
388E LEU* 3.1 27.4 + - + +
390E LYS* 1.3 75.8 - - - +
392E PRO* 1.3 70.5 - - + +
393E PHE 3.1 1.0 + - - -
394E LEU* 3.3 5.5 + - - +
395E ALA* 3.0 20.3 + - - +
414E LEU* 3.9 13.5 - - + -
417E ALA* 5.0 4.6 - - + +
418E VAL* 3.6 35.9 - - + +
421E GLN* 4.9 8.7 - - + +
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Residues in contact with PRO 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E CYS* 4.8 19.1 - - + -
338E LEU* 4.6 11.4 - - + -
388E LEU 4.2 4.9 - - - +
389E ARG* 4.4 8.1 - - - +
390E LYS 3.4 5.2 - - - +
391E LEU* 1.3 96.3 - - + +
393E PHE* 1.3 63.9 + - + +
395E ALA* 3.4 7.7 - - + +
396E HIS* 2.9 26.9 + - - +
410E PHE* 3.9 21.5 - - + -
414E LEU* 4.1 8.7 - - + -
159F PHE* 4.7 9.8 - - + -
169F ILE* 4.9 8.1 - - + -
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Residues in contact with PHE 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390E LYS* 3.5 17.7 - - + +
391E LEU 3.1 0.4 + - - -
392E PRO* 1.3 78.1 - - + +
394E LEU* 1.3 65.4 + - + +
396E HIS* 3.3 2.6 + - - +
397E ALA* 2.8 28.7 + - - +
155F THR* 4.2 10.4 - - + +
156F THR* 5.9 2.2 - - - -
159F PHE* 3.3 44.0 - + + -
169F ILE* 3.3 21.5 - - + -
170F THR* 2.9 48.7 - - - +
171F TRP* 3.3 32.8 - + + -
315F ILE* 5.2 13.2 - - + -
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Residues in contact with LEU 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390E LYS* 4.0 36.9 + - + +
391E LEU* 3.3 7.1 + - - +
393E PHE* 1.3 79.7 - - - +
395E ALA* 1.3 58.4 + - - +
397E ALA* 3.2 11.1 - - + +
398E LEU* 2.9 43.3 + - + +
399E TYR* 4.2 0.2 - - - -
417E ALA* 4.8 4.7 - - + -
421E GLN* 4.9 14.4 - - - +
424E GLU* 5.3 2.5 - - - +
151F ASP* 4.7 7.2 - - - +
315F ILE* 4.6 24.7 - - + -
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Residues in contact with ALA 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E LEU 3.0 13.8 + - - +
392E PRO* 3.4 8.7 - - + +
393E PHE 3.1 0.2 - - - -
394E LEU* 1.3 75.8 - - - +
396E HIS* 1.3 64.9 + - - +
397E ALA 2.9 0.3 + - - -
399E TYR* 2.9 33.9 + - - +
400E VAL* 5.5 0.2 - - - -
410E PHE* 5.0 5.6 - - + -
413E ALA* 5.6 1.6 - - + -
414E LEU* 3.6 35.2 - - + +
417E ALA* 3.8 20.3 - - + +
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Residues in contact with HIS 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E ILE* 5.9 0.4 - - + -
392E PRO 2.9 18.9 + - - +
393E PHE 3.8 2.5 - - - +
395E ALA* 1.3 73.6 - - - +
397E ALA* 1.3 56.7 + - - +
400E VAL* 3.1 27.5 + - + -
401E GLN* 2.6 38.3 + - - -
402E ALA 2.9 45.9 + - - -
403E PRO 4.6 0.2 - - - -
405E VAL* 4.3 9.6 - - + -
410E PHE* 4.7 14.6 - + + -
154F MET 4.4 4.0 - - - -
155F THR* 2.7 38.7 + - + +
158F LEU* 3.5 24.5 - - + +
159F PHE* 5.1 2.2 - - + -
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Residues in contact with ALA 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E PHE 2.8 17.8 + - - +
394E LEU* 3.2 15.5 - - + +
395E ALA 2.9 1.0 - - - -
396E HIS* 1.3 80.8 - - - +
398E LEU* 1.3 60.0 + - + +
399E TYR 3.1 5.2 + - - -
400E VAL 4.1 0.5 + - - -
401E GLN* 3.3 22.9 + - - +
151F ASP* 2.9 41.3 - - + +
155F THR* 4.2 6.5 - - - +
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Residues in contact with LEU 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E LEU* 2.9 25.4 + - + +
397E ALA* 1.3 76.1 - - + +
399E TYR* 1.3 88.3 + - + +
417E ALA* 5.9 1.6 - - + -
420E LYS* 3.0 46.9 - - + +
148F HIS* 4.6 24.2 - - + +
151F ASP* 4.9 7.0 - - - +
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Residues in contact with TYR 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E LEU 4.5 0.2 - - - -
395E ALA* 2.9 27.3 + - - +
397E ALA 3.1 0.8 - - - -
398E LEU* 1.3 104.7 - - + +
400E VAL* 1.3 65.4 + - + +
413E ALA* 3.6 32.8 - - + -
416E LEU* 3.0 44.3 + - + +
417E ALA* 3.4 30.4 - - + -
420E LYS* 4.3 12.1 - - - +
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Residues in contact with VAL 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E HIS* 3.1 24.6 + - + +
397E ALA 4.1 0.2 + - - -
399E TYR* 1.3 90.9 - - + +
401E GLN* 1.3 69.9 + - - +
402E ALA* 3.3 39.3 + - + +
404E THR 4.9 0.2 - - - +
405E VAL* 3.9 25.6 - - + -
409E GLY 6.0 0.9 - - - +
410E PHE* 5.5 7.2 - - + -
413E ALA* 4.8 10.5 - - + -
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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