Contacts of the helix formed by residues 395 - 406 (chain E) in PDB entry 6M04
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 TYR 395 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391E PRO* 3.9 17.2 + - + +
392E LEU* 4.8 4.2 - - + +
394E GLU* 1.3 75.5 - - - +
396E SER* 1.3 59.0 + - - +
397E PHE 3.1 3.1 + - - -
398E GLU* 3.4 12.4 + - + +
399E LYS* 2.9 26.3 + - + +
421E HIS* 3.9 9.4 - - - +
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Residues in contact with SER 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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394E GLU 3.2 1.8 - - - -
395E TYR* 1.3 73.5 - - - +
397E PHE* 1.3 59.0 + - - +
399E LYS* 3.1 28.0 + - - +
400E VAL* 2.9 30.0 + - - +
414E ASN* 3.9 6.6 - - - +
415E ASP* 3.3 23.6 + - - +
418E PHE* 5.3 0.6 - - - -
420E LEU* 3.9 16.3 - - - +
421E HIS* 3.3 24.4 + - - -
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Residues in contact with PHE 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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394E GLU 4.3 7.9 - - - +
395E TYR 3.1 0.8 - - - -
396E SER* 1.3 77.3 - - - +
398E GLU* 1.3 58.6 + - - +
400E VAL* 3.2 2.4 + - - -
401E ARG* 2.9 24.0 + - - +
412E VAL 3.5 10.3 - - - +
413E LYS* 3.8 15.0 - - + -
414E ASN 3.4 27.1 - - - +
415E ASP* 3.6 13.8 + - - +
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Residues in contact with GLU 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E TYR* 3.4 12.0 + - + +
397E PHE* 1.3 76.2 - - - +
399E LYS* 1.3 62.0 + - - +
401E ARG* 3.5 12.0 - - + +
402E GLU* 2.8 43.8 + - - +
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Residues in contact with LYS 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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395E TYR 2.9 17.4 + - - +
396E SER* 3.1 32.1 + - - +
397E PHE 3.2 0.2 - - - -
398E GLU* 1.3 80.0 + - - +
400E VAL* 1.3 60.4 + - + +
402E GLU* 3.2 7.5 + - - +
403E GLU* 2.9 28.1 + - + +
420E LEU* 3.4 29.7 + - - +
421E HIS* 4.3 10.3 - - + +
424E ASP* 4.2 18.2 - - - +
428E GLN* 4.9 7.6 - - - +
431E SER* 3.1 29.5 + - - +
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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 SER* 2.9 22.3 + - - +
397E PHE 3.8 3.8 - - - +
399E LYS* 1.3 89.5 - - - +
401E ARG* 1.3 58.9 + - - +
403E GLU* 3.2 26.1 - - - +
404E SER* 2.9 35.3 + - - +
412E VAL* 3.7 31.6 - - + +
414E ASN* 4.1 14.4 - - + -
420E LEU* 4.5 9.6 - - + -
431E SER* 5.1 0.4 - - - +
435E GLY* 4.7 13.2 - - - +
438E LEU* 5.5 2.2 - - + -
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Residues in contact with ARG 401 (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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397E PHE 2.9 13.4 + - - +
398E GLU* 3.4 21.1 - - + +
399E LYS 3.2 0.2 - - - -
400E VAL* 1.3 77.7 - - - +
402E GLU* 1.3 51.3 + - - +
404E SER* 3.3 3.5 + - - -
405E SER* 2.5 36.4 + - - +
411E ASP* 3.7 29.0 - - + +
412E VAL 4.3 2.6 + - - +
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Residues in contact with GLU 402 (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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398E GLU* 2.8 31.6 + - - +
399E LYS* 3.6 7.6 - - - +
401E ARG* 1.3 73.0 - - - +
403E GLU* 1.3 65.6 + - - +
405E SER* 3.1 23.3 + - - -
406E PHE* 3.2 35.1 - - + -
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Residues in contact with GLU 403 (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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399E LYS* 2.9 13.4 + - + +
400E VAL* 3.2 34.8 - - - +
402E GLU* 1.3 77.9 - - - +
404E SER* 1.3 62.2 + - - +
405E SER 3.4 0.2 + - - -
406E PHE* 3.8 3.8 + - - -
407E SER* 3.5 11.1 + - - -
428E GLN* 6.0 1.8 - - - +
431E SER* 2.9 25.3 + - - +
432E LYS* 2.4 69.2 + - + +
435E GLY* 3.3 19.8 - - - -
436E VAL* 5.2 0.3 - - - +
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Residues in contact with SER 404 (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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400E VAL* 2.9 24.9 + - - +
401E ARG 3.6 5.6 - - - -
402E GLU 3.2 0.2 - - - -
403E GLU* 1.3 78.1 - - - +
405E SER* 1.3 62.6 + - - +
406E PHE 3.2 0.4 - - - -
407E SER* 3.3 14.8 + - - -
408E ASP* 3.4 8.5 + - - -
409E ILE* 3.3 42.5 + - - +
410E PRO 4.1 0.3 + - - -
411E ASP* 4.0 18.6 - - - -
412E VAL* 4.7 1.2 + - - +
435E GLY 5.4 2.1 + - - -
439E SER* 4.7 2.6 + - - -
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Residues in contact with SER 405 (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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401E ARG* 2.5 24.6 + - - +
402E GLU* 3.1 28.0 + - - -
404E SER* 1.3 77.2 - - - +
406E PHE* 1.3 57.7 + - - +
408E ASP* 4.8 1.9 + - - -
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Residues in contact with PHE 406 (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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402E GLU* 3.2 45.8 - - + -
403E GLU* 4.2 1.6 - - - -
404E SER 3.2 0.4 - - - -
405E SER* 1.3 77.4 - - - +
407E SER* 1.3 57.4 + - - +
408E ASP* 3.6 2.0 - - - +
428E GLN* 6.5 0.9 - - + -
432E LYS* 3.3 32.8 - - - -
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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