Contacts of the helix formed by residues 445 - 459 (chain E) in PDB entry 6DWZ
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 GLU 445 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444E GLN* 1.3 84.6 + - - +
446E LYS* 1.3 95.4 + - + +
447E VAL* 3.5 2.0 - - - -
448E ALA* 3.0 29.6 - - - +
449E GLN* 3.2 16.3 - - - +
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Residues in contact with LYS 446 (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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430E TYR* 3.6 42.1 - - + -
442E MET* 3.6 29.5 - - - +
443E GLN 3.0 2.4 + - - -
444E GLN* 3.5 20.6 - - + +
445E GLU* 1.3 108.0 + - + +
447E VAL* 1.3 52.1 + - - +
448E ALA 2.8 9.2 + - - -
449E GLN* 2.9 13.1 + - - +
450E ILE* 2.7 45.1 + - + +
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Residues in contact with VAL 447 (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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434E PHE* 4.8 4.7 - - + -
442E MET 4.8 0.2 + - - -
443E GLN* 3.1 43.8 + - - +
444E GLN 4.8 0.4 - - - +
445E GLU 5.0 0.4 - - - -
446E LYS* 1.3 77.7 - - - +
448E ALA* 1.3 68.6 + - - +
450E ILE* 3.5 13.9 - - + +
451E LYS* 3.1 18.8 + - + +
524E PHE* 3.6 31.4 - - + -
525E GLU* 5.5 1.3 - - - +
528E ARG* 4.8 12.1 - - - +
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Residues in contact with ALA 448 (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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445E GLU* 3.0 17.5 - - - +
446E LYS 2.8 0.4 + - - -
447E VAL* 1.3 88.6 - - + +
449E GLN* 1.3 68.7 + - + +
450E ILE 3.2 0.2 + - - -
451E LYS* 4.0 1.6 - - - +
452E GLU* 3.2 17.8 + - - +
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Residues in contact with GLN 449 (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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427E ILE* 4.0 23.6 - - + +
445E GLU* 3.2 36.8 - - - +
446E LYS* 2.9 11.9 + - - +
448E ALA* 1.3 79.2 - - + +
450E ILE* 1.3 55.5 + - - +
452E GLU* 3.5 17.2 - - - +
453E PHE* 2.8 35.5 + - - +
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Residues in contact with ILE 450 (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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427E ILE* 4.4 3.3 - - + +
430E TYR* 3.7 28.0 - - + +
431E THR* 4.4 18.6 - - + +
434E PHE* 3.9 26.2 - - + -
435E PHE* 5.7 0.2 - - + -
442E MET* 4.3 7.9 - - + +
446E LYS* 2.7 39.3 + - + +
447E VAL* 3.5 16.2 - - + +
449E GLN* 1.3 69.6 - - - +
451E LYS* 1.3 60.4 + - - +
453E PHE* 3.1 9.6 - - - +
454E CYS* 2.8 35.2 + - - -
524E PHE* 3.8 20.6 - - + -
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Residues in contact with LYS 451 (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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447E VAL* 3.1 14.9 + - + +
448E ALA 4.0 1.6 - - - +
450E ILE* 1.3 76.1 - - - +
452E GLU* 1.3 68.1 + - - +
454E CYS* 3.6 7.9 - - - -
455E LEU* 3.1 50.2 + - + +
521E SER* 3.6 15.9 + - - +
524E PHE* 3.3 47.6 - - + -
525E GLU* 3.6 31.9 + - - +
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Residues in contact with GLU 452 (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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427E ILE* 4.3 9.7 - - - +
448E ALA 3.2 11.6 + - - +
449E GLN* 3.5 27.8 - - - +
451E LYS* 1.3 75.7 - - - +
453E PHE* 1.3 60.9 + - - +
455E LEU* 4.8 0.7 - - - +
456E SER* 3.0 28.8 + - - -
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Residues in contact with PHE 453 (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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427E ILE* 3.6 26.5 - - + -
428E TRP* 3.9 51.8 - + - -
431E THR* 3.3 37.5 - - + -
449E GLN 2.8 17.9 + - - +
450E ILE 3.1 8.1 - - - +
451E LYS 3.1 0.2 - - - -
452E GLU* 1.3 70.5 + - - +
454E CYS* 1.3 69.5 + - - +
455E LEU 3.0 2.0 - - - -
456E SER* 2.4 40.3 + - - -
457E LYS* 3.5 16.8 + - + +
557E LEU* 5.6 4.3 - - + -
561E LEU* 4.9 3.4 - - + -
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Residues in contact with CYS 454 (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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431E THR* 5.1 1.1 - - - -
435E PHE* 4.3 18.4 - - + -
450E ILE* 2.8 47.1 + - - -
451E LYS* 3.2 10.3 + - - -
453E PHE* 1.3 81.6 - - + +
455E LEU* 1.3 60.3 + - + +
457E LYS* 3.9 1.6 + - - +
458E MET* 2.9 30.7 + - - +
524E PHE* 3.6 21.1 - - + -
554E LEU* 5.3 2.7 - - + -
557E LEU* 3.4 28.1 - - + +
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Residues in contact with LEU 455 (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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451E LYS* 3.1 47.9 + - + +
452E GLU* 4.8 0.9 - - - +
453E PHE 2.7 3.6 + - - -
454E CYS* 1.3 78.2 - - + +
456E SER* 1.3 63.9 + - - +
457E LYS 3.2 0.7 - - - -
458E MET* 3.1 44.8 + - + -
459E GLU* 3.2 22.4 - - + +
520E PRO* 3.9 16.4 - - + +
521E SER* 4.1 19.5 - - - +
524E PHE* 5.2 6.5 - - + -
554E LEU* 5.5 0.7 - - + -
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Residues in contact with SER 456 (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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452E GLU* 3.0 25.1 + - - -
453E PHE* 2.4 32.1 + - - -
455E LEU* 1.3 69.9 - - - +
457E LYS* 1.3 57.3 + - - +
459E GLU* 4.4 4.4 - - - +
460E ASP* 3.2 21.1 - - - +
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Residues in contact with LYS 457 (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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173E ASP* 3.2 28.7 + - - +
242E SER* 4.6 4.9 - - - +
244E LYS* 4.5 3.4 - - - +
261E ILE* 4.4 19.8 - - - +
428E TRP* 4.7 11.1 - - + -
453E PHE* 3.5 16.2 + - + +
454E CYS* 4.8 2.0 - - - +
455E LEU 3.2 0.2 - - - -
456E SER* 1.3 80.2 - - - +
458E MET* 1.3 67.2 + - - +
459E GLU 3.5 1.6 - - - -
460E ASP* 3.2 15.0 - - - +
461E LEU* 3.4 44.6 + - + +
557E LEU* 5.7 8.5 - - + -
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Residues in contact with MET 458 (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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454E CYS 2.9 20.8 + - - +
455E LEU* 3.1 20.7 + - + -
457E LYS* 1.3 80.4 - - - +
459E GLU* 1.3 62.1 + - - +
461E LEU 3.6 3.0 - - - +
462E GLU* 2.9 26.5 - - - +
520E PRO* 3.3 45.8 - - + +
523E GLU* 4.1 3.6 - - - -
553E LYS* 3.2 44.6 - - + +
554E LEU* 3.6 28.3 - - + +
557E LEU* 4.6 13.0 - - + -
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Residues in contact with GLU 459 (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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455E LEU* 3.2 22.0 - - + +
456E SER* 4.4 3.8 - - - +
458E MET* 1.3 79.9 - - - +
460E ASP* 1.3 82.8 + - + +
462E GLU* 4.0 13.2 - - - +
520E PRO* 4.8 19.3 - - + +
553E LYS* 5.5 7.1 + - - +
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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