Contacts of the helix formed by residues 426 - 435 (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 SER 426 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262E ARG 5.3 4.9 - - - -
263E ILE* 4.6 8.9 - - - +
424E ASN 3.9 1.3 + - - -
425E LEU* 1.3 75.5 - - - +
427E ILE* 1.3 64.6 + - - +
428E TRP* 2.7 40.9 + - - +
429E HIS* 2.9 25.7 + - - +
430E TYR* 3.2 16.1 - - - -
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Residues in contact with ILE 427 (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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426E SER* 1.3 74.6 + - - +
428E TRP* 1.3 58.6 + - + +
430E TYR* 3.2 15.5 + - + -
431E THR* 2.9 41.2 + - - +
449E GLN* 4.0 34.8 - - + +
450E ILE* 4.4 3.1 - - + -
452E GLU* 4.3 11.7 - - - +
453E PHE* 3.6 40.8 - - + -
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Residues in contact with TRP 428 (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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244E LYS* 3.5 40.6 - - + -
261E ILE* 3.7 35.6 - - + +
262E ARG 5.8 0.4 - - - -
263E ILE* 3.7 27.8 - - + -
382E LEU* 4.2 8.7 - - + -
426E SER* 2.7 33.4 + - - +
427E ILE* 1.3 73.7 - - + +
429E HIS* 1.3 56.9 + - + +
431E THR* 4.3 1.6 - - - -
432E ALA* 2.7 33.6 + - - +
453E PHE* 3.9 30.2 - + - -
457E LYS* 4.7 10.5 - - + -
560E SER* 4.6 0.4 - - - -
561E LEU* 3.3 42.4 - - + +
564E ILE* 4.1 10.5 - - + -
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Residues in contact with HIS 429 (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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263E ILE* 3.2 26.2 - - + +
264E ASN* 4.6 4.4 + - + +
266E SER* 3.6 23.6 - - - -
382E LEU* 3.7 28.5 - - + +
383E CYS* 5.2 0.3 - - - +
385E VAL* 3.4 24.6 - - + +
386E VAL* 3.7 13.5 + - + +
424E ASN 5.0 1.2 + - - -
425E LEU* 3.8 31.9 - - + +
426E SER* 2.9 42.0 + - - +
428E TRP* 1.3 72.1 - - + +
430E TYR* 1.3 58.6 + - + +
432E ALA* 3.8 2.1 + - - +
433E PHE* 3.2 22.2 + - - +
566E ALA* 5.7 1.3 - - - -
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Residues in contact with TYR 430 (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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386E VAL* 4.2 7.4 - - + -
422E GLU 4.2 6.2 + - - -
425E LEU* 3.5 38.8 + - + +
426E SER* 3.2 29.8 - - - -
427E ILE* 3.2 15.2 + - + +
429E HIS* 1.3 74.9 - - - +
431E THR* 1.3 67.6 + - - +
432E ALA 3.3 0.2 - - - -
433E PHE* 3.1 10.9 + - - +
434E PHE 3.1 9.7 + - - -
442E MET* 3.5 37.1 - - + +
446E LYS* 3.6 34.2 - - + -
450E ILE* 3.7 16.0 - - + +
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Residues in contact with THR 431 (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* 2.9 24.4 + - - +
428E TRP 3.7 3.4 - - - -
430E TYR* 1.3 75.1 - - - +
432E ALA* 1.3 58.3 + - - +
434E PHE* 2.8 23.0 + - - +
435E PHE* 3.1 38.9 + - + -
450E ILE* 4.3 18.4 + - + +
453E PHE* 3.3 31.7 - - + -
454E CYS* 5.1 4.0 - - + -
557E LEU* 6.0 0.4 - - + -
561E LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 432 (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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382E LEU* 3.6 30.7 - - + -
383E CYS* 3.0 31.0 - - + +
428E TRP 2.7 23.8 + - - +
429E HIS 3.9 2.0 - - - +
431E THR* 1.3 72.3 - - - +
433E PHE* 1.3 61.1 + - - +
435E PHE* 4.1 10.5 - - - +
436E TYR 4.0 6.2 + - - -
561E LEU* 3.6 15.7 - - + +
562E LEU* 4.6 2.3 - - + +
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Residues in contact with PHE 433 (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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383E CYS 3.0 24.5 - - - +
384E PHE* 5.6 1.8 - + - -
386E VAL* 3.7 27.1 - - + -
387E PRO* 3.5 31.6 - - + -
390E LEU* 5.3 4.7 - - + -
429E HIS 3.2 12.8 + - - +
430E TYR 3.1 9.7 + - - +
431E THR 3.0 1.2 - - - -
432E ALA* 1.3 77.8 - - - +
434E PHE* 1.3 65.7 + - - +
436E TYR* 3.1 33.3 + + + +
438E PRO 6.0 0.2 - - - -
439E ALA* 3.6 7.2 - - + +
441E HIS* 4.3 23.3 - + - -
442E MET* 3.4 29.8 - - + -
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Residues in contact with PHE 434 (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 3.1 10.0 + - - +
431E THR* 2.8 10.2 + - - +
433E PHE* 1.3 74.6 - - - +
435E PHE* 1.3 66.4 + + + +
436E TYR 2.9 19.4 + - - +
437E PRO* 4.1 1.5 - - - +
439E ALA* 3.9 27.3 - - + +
442E MET* 4.8 6.3 - - + +
447E VAL* 4.8 4.3 - - + -
450E ILE* 3.9 30.5 - - + -
524E PHE* 3.4 31.6 - + - -
527E TYR* 3.4 32.1 + + - -
528E ARG* 3.6 35.2 - - + -
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Residues in contact with PHE 435 (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* 3.1 36.0 + - + +
432E ALA* 4.3 9.2 - - - +
433E PHE 3.3 0.6 - - - -
434E PHE* 1.3 91.7 - + + +
436E TYR* 1.3 56.1 + - - +
437E PRO* 4.0 0.2 - - - +
450E ILE* 5.7 0.2 - - + -
454E CYS* 4.3 24.2 - - + -
524E PHE* 5.9 1.6 - + - -
527E TYR* 4.1 19.1 - + - -
540E VAL* 4.2 0.7 - - - +
544E TRP* 3.1 31.6 + + - +
554E LEU* 5.0 11.4 - - + -
557E LEU* 3.9 16.8 - - + -
558E ALA* 3.3 45.1 - - + -
561E LEU* 4.1 12.6 - - + -
562E LEU* 3.7 16.9 - - + +
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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