Contacts of the helix formed by residues 445 - 455 (chain F) 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 LYS 445 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208F TRP* 4.2 14.1 - - + +
215F GLU* 5.1 15.5 - - - +
441F VAL* 2.4 47.4 + - - +
442F SER* 3.4 18.1 - - - +
443F GLU 3.2 2.2 - - - -
444F ASN* 1.3 79.6 - - - +
446F LEU* 1.3 61.8 + - - +
447F ARG 3.2 1.6 - - - -
448F GLU* 2.8 22.2 + - - +
449F ILE* 2.9 31.2 + - + +
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Residues in contact with LEU 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F TRP* 3.4 53.1 - - + +
211F LYS* 5.2 2.2 - - - +
280F ASP* 3.3 36.1 - - - +
281F GLY* 3.7 21.0 - - - +
284F ALA* 3.7 12.1 - - + -
285F LYS* 6.1 2.0 - - + -
288F PHE* 4.9 9.6 - - + -
442F SER 4.7 1.2 + - - -
443F GLU 4.5 1.6 + - - -
445F LYS* 1.3 79.1 - - - +
447F ARG* 1.3 57.2 + - - +
448F GLU 3.1 0.2 - - - -
449F ILE* 4.1 23.8 - - + +
450F SER* 2.9 34.7 + - - -
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Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F LYS* 3.5 37.5 - - + +
288F PHE* 4.2 5.8 - - + -
292F ARG* 3.7 22.2 - - - +
443F GLU* 2.9 42.4 + - - +
444F ASN* 3.3 37.1 - - - +
446F LEU* 1.3 76.3 - - - +
448F GLU* 1.3 57.4 + - + +
450F SER* 4.6 1.8 - - - -
451F LEU* 3.3 18.7 - - - +
480F SER* 3.1 33.8 + - - +
502F GLU* 6.2 1.8 - - + -
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Residues in contact with GLU 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444F ASN* 4.1 9.9 - - - +
445F LYS* 2.8 9.5 + - - +
447F ARG* 1.3 77.9 - - + +
449F ILE* 1.3 76.1 + - - +
450F SER 3.3 1.6 - - - -
451F LEU* 3.2 9.0 + - - +
452F ASN* 2.4 59.9 + - - +
480F SER* 5.3 0.4 - - - -
481F GLY* 4.8 15.5 - - - -
482F VAL 4.5 8.1 - - - +
484F ASP* 4.3 4.2 - - - +
502F GLU* 6.1 4.0 - - + -
504F LYS* 5.8 8.5 - - + +
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Residues in contact with ILE 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F LYS* 5.8 2.2 - - - +
277F ASP* 5.5 8.5 - - + +
280F ASP* 5.8 1.8 - - - +
445F LYS* 2.9 44.1 + - + +
446F LEU* 4.1 22.9 - - + +
448F GLU* 1.3 90.9 - - - +
450F SER* 1.3 59.2 + - - +
452F ASN* 3.3 12.1 + - + +
453F HIS* 2.9 26.9 + - + +
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Residues in contact with SER 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F GLY* 4.8 17.8 - - - -
282F GLU* 5.4 3.8 + - - +
446F LEU* 2.9 18.2 + - - +
447F ARG* 5.2 2.0 - - - -
449F ILE* 1.3 78.5 - - - +
451F LEU* 1.3 59.9 + - - +
453F HIS* 2.9 22.1 + - - +
454F GLU* 2.8 42.4 + - - +
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Residues in contact with LEU 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447F ARG 3.3 22.4 - - - +
448F GLU* 3.2 9.2 + - - +
450F SER* 1.3 77.2 - - - +
452F ASN* 1.3 62.4 + - - +
454F GLU* 3.8 14.8 - - - +
455F TRP* 3.2 37.3 + - - +
478F MET* 4.8 9.6 - - + +
479F LEU* 3.7 26.5 - - + -
480F SER* 3.4 21.5 - - - +
481F GLY* 3.4 30.7 - - - +
482F VAL 5.0 4.7 - - - +
483F PRO* 4.6 4.7 - - + +
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Residues in contact with ASN 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448F GLU* 2.4 47.5 + - - +
449F ILE* 3.5 11.1 - - - +
451F LEU* 1.3 76.2 - - - +
453F HIS* 1.3 64.6 + - - +
455F TRP 3.9 12.2 - - - +
456F THR* 5.2 1.0 - - - +
482F VAL 4.1 1.1 - - - +
483F PRO* 3.9 4.5 - - - +
484F ASP* 2.9 45.8 + - + +
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Residues in contact with HIS 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ASP* 5.8 1.8 - - + +
278F LYS* 3.4 39.7 + - + +
449F ILE* 2.9 17.2 + - + +
450F SER* 2.9 16.1 + - - +
452F ASN* 1.3 80.7 - - - +
454F GLU* 1.3 72.9 + - + +
456F THR* 3.4 16.3 - - - +
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Residues in contact with GLU 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F SER* 2.8 49.0 + - - +
451F LEU* 3.8 19.1 - - - +
453F HIS* 1.3 84.4 - - + +
455F TRP* 1.3 79.4 + - + +
456F THR* 2.8 0.4 + - - -
459F LYS* 2.5 37.0 + - - +
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Residues in contact with TRP 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F LEU* 3.2 36.8 + - - +
452F ASN* 3.9 11.9 - - - +
453F HIS 3.4 0.6 - - - -
454F GLU* 1.3 90.5 + - + +
456F THR* 1.3 64.6 + - - +
459F LYS* 4.4 17.0 - - + -
460F LEU* 4.3 25.8 - - + -
463F HIS* 3.9 32.3 - + - -
474F LEU* 5.5 5.4 - - + -
475F HIS 5.6 1.3 - - - -
478F MET* 5.9 4.7 - - + +
479F LEU* 3.7 43.7 - - + +
483F PRO* 4.3 16.2 - - + +
484F ASP 5.5 0.2 + - - -
485F ALA* 3.5 16.1 + - - +
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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