Contacts of the helix formed by residues 434 - 455 (chain E) in PDB entry 6C3P
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 LEU 434 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E TRP* 3.0 13.2 + - + +
431E PHE* 3.2 8.9 - - + +
433E PHE* 1.3 77.1 - - + +
435E CYS* 1.3 66.0 + - - +
436E PRO* 3.6 1.8 - - - -
437E ASN* 3.9 9.5 + - + +
438E LEU* 3.9 11.1 + - - +
592E LEU* 4.1 26.2 - - + -
595E SER* 3.8 11.7 - - - +
596E VAL* 3.6 53.7 - - + +
599E SER* 3.8 23.1 - - - +
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Residues in contact with CYS 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU* 3.7 40.6 - - + -
303E SER* 5.7 0.7 - - - -
431E PHE* 2.8 12.8 + - + +
432E PHE* 3.5 33.2 - - + +
433E PHE 3.1 3.6 - - - -
434E LEU* 1.3 79.3 - - - +
436E PRO* 1.3 71.0 - - + +
438E LEU* 3.1 6.3 + - - +
439E TRP* 3.0 43.3 - - - -
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Residues in contact with PRO 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU* 4.8 1.6 - - + +
302E SER* 4.0 17.5 - - - +
303E SER* 3.4 41.4 + - - +
306E ARG* 3.8 24.2 - - + +
376E SER* 4.3 2.2 - - - +
380E ALA* 4.0 11.2 - - + -
433E PHE 3.3 13.2 - - - +
434E LEU* 3.7 0.4 - - - -
435E CYS* 1.3 93.3 - - + +
437E ASN* 1.3 69.6 + - - +
438E LEU 3.0 0.5 + - - -
439E TRP* 3.3 5.2 + - + -
440E ALA* 2.9 23.5 + - - +
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Residues in contact with ASN 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ARG* 3.6 23.0 + - - +
434E LEU* 4.0 14.1 - - + +
435E CYS 3.2 0.4 + - - -
436E PRO* 1.3 82.0 - - + +
438E LEU* 1.3 64.2 + - - +
440E ALA* 3.0 5.3 + - - +
441E MET* 2.9 33.8 + - - +
444E GLN* 5.6 0.7 - - - +
589E PRO* 4.6 14.6 + - - +
592E LEU* 3.6 32.3 - - + +
593E LEU* 4.7 3.7 - - - +
596E VAL* 3.7 20.3 - - + +
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Residues in contact with LEU 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E PHE* 5.6 9.0 - - + -
434E LEU 3.9 6.7 + - - +
435E CYS* 3.1 13.1 + - - +
436E PRO 3.0 0.8 - - - -
437E ASN* 1.3 77.0 - - - +
439E TRP* 1.3 89.7 + - + +
441E MET* 4.4 1.9 - - - +
442E PRO* 3.0 23.5 - - + +
593E LEU* 5.3 9.9 - - + -
596E VAL* 5.0 17.4 - - + +
600E THR* 5.4 12.6 - - + +
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Residues in contact with TRP 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU* 5.9 1.8 - - + -
303E SER* 4.6 15.3 - - - +
307E ILE* 4.6 5.4 - - + +
431E PHE* 5.6 9.2 - + - -
432E PHE* 6.3 0.2 - + - -
435E CYS* 3.0 55.0 - - - -
436E PRO* 3.3 6.9 + - + +
438E LEU* 1.3 103.1 - - + +
440E ALA* 1.3 60.0 + - - +
442E PRO* 3.8 9.0 - - - +
443E VAL* 4.1 14.2 - - - +
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Residues in contact with ALA 440 (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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306E ARG* 3.5 33.0 - - + -
307E ILE* 4.0 16.3 - - + +
310E ASP* 4.1 10.0 - - - +
436E PRO 2.9 17.5 + - - +
437E ASN* 3.0 8.0 + - - +
439E TRP* 1.3 78.7 - - - +
441E MET* 1.3 66.3 + - - +
443E VAL* 3.4 8.7 + - - +
444E GLN* 3.2 17.2 + - - +
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Residues in contact with MET 441 (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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437E ASN* 2.9 26.8 + - - +
438E LEU* 4.4 1.1 - - - +
440E ALA* 1.3 73.0 - - - +
442E PRO* 1.3 65.9 - - + +
444E GLN* 2.8 16.9 + - + +
445E ILE* 2.7 47.1 + - + +
467E ILE* 4.9 1.8 - - + -
586E LEU* 4.9 4.5 - - + +
589E PRO* 4.2 23.6 - - + +
590E LEU* 3.5 36.6 - - + -
593E LEU* 4.0 31.4 - - + -
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Residues in contact with PRO 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E LEU* 3.0 21.5 - - + +
439E TRP* 3.8 7.4 - - - +
440E ALA 3.6 2.9 - - - -
441E MET* 1.3 90.6 - - + +
443E VAL* 1.3 62.7 + - + +
445E ILE* 3.0 13.8 - - + +
446E ILE* 2.9 31.9 + - + +
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Residues in contact with VAL 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ILE* 4.2 30.5 - - + -
310E ASP* 6.0 0.9 - - - +
311E LEU* 6.1 4.9 - - + -
439E TRP 4.1 14.1 - - - +
440E ALA 3.4 7.3 + - - +
441E MET 3.3 0.2 - - - -
442E PRO* 1.3 76.5 - - + +
444E GLN* 1.3 62.1 + - - +
446E ILE* 3.9 4.7 - - - +
447E VAL* 3.2 32.6 + - + +
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Residues in contact with GLN 444 (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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310E ASP* 3.4 45.8 + - + +
311E LEU* 6.4 1.3 - - - +
314E PHE* 5.0 12.1 - - + -
437E ASN* 5.6 0.9 - - - +
440E ALA 3.2 4.2 + - - +
441E MET* 2.8 18.3 + - + +
443E VAL* 1.3 76.6 - - - +
445E ILE* 1.3 60.7 + - - +
447E VAL* 3.3 6.9 + - - +
448E GLY* 2.9 24.8 + - - -
585E ILE* 4.2 13.7 + - - +
586E LEU* 4.7 13.0 - - + +
589E PRO* 3.2 39.4 - - - +
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Residues in contact with ILE 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E MET* 2.7 25.9 + - + +
442E PRO* 3.0 31.9 - - + +
444E GLN* 1.3 72.9 - - - +
446E ILE* 1.3 72.1 + - + +
448E GLY* 3.2 1.8 + - - +
449E VAL* 2.9 37.3 + - + +
467E ILE* 3.7 27.8 - - + -
586E LEU* 3.4 42.6 - - + -
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Residues in contact with ILE 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442E PRO* 2.9 26.0 + - + +
443E VAL* 3.9 5.6 - - - +
445E ILE* 1.3 84.5 - - + +
447E VAL* 1.3 59.2 + - + +
449E VAL* 3.2 10.6 + - + +
450E ILE* 2.9 51.1 + - + +
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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
----------------------------------------------------------
311E LEU* 3.6 27.8 - - + -
314E PHE* 3.4 28.5 - - + -
443E VAL* 3.2 26.1 + - + +
444E GLN* 3.7 5.2 - - - +
446E ILE* 1.3 77.1 - - + +
448E GLY* 1.3 58.8 + - - +
450E ILE* 3.3 12.8 + - + +
451E LEU* 2.9 28.8 + - + +
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Residues in contact with GLY 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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314E PHE* 3.3 22.8 - - - -
444E GLN 2.9 13.6 + - - -
445E ILE* 3.2 5.3 + - - -
447E VAL* 1.3 77.2 - - - +
449E VAL* 1.3 61.3 + - - +
451E LEU* 3.3 1.6 + - - +
452E LEU* 3.0 33.4 + - - +
582E LEU* 5.1 3.6 - - - -
586E LEU* 5.5 9.2 - - - -
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Residues in contact with VAL 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445E ILE* 2.9 27.3 + - + +
446E ILE* 3.2 12.5 + - + +
448E GLY* 1.3 74.4 - - - +
450E ILE* 1.3 67.8 + - + +
452E LEU* 3.1 9.3 + - - +
453E TYR* 3.0 22.6 + - + +
461E LEU* 4.7 5.6 - - + +
464E ALA* 4.9 21.3 - - + -
467E ILE* 5.8 2.5 - - + -
468E ILE* 5.3 15.9 - - + -
586E LEU* 6.3 0.9 - - + -
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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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446E ILE* 2.9 37.3 + - + +
447E VAL* 3.8 11.7 - - + +
449E VAL* 1.3 77.9 - - + +
451E LEU* 1.3 58.3 + - - +
453E TYR* 3.2 11.2 + - + +
454E TYR* 2.9 28.3 + - + +
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Residues in contact with LEU 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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314E PHE* 3.3 37.2 - - + +
317E PRO* 5.8 2.5 - - + -
318E LEU* 4.1 33.4 - - + -
447E VAL* 2.9 7.6 + - + +
448E GLY 3.7 0.7 - - - +
450E ILE* 1.3 76.0 - - - +
452E LEU* 1.3 53.7 + - - +
454E TYR* 2.9 16.8 + - + +
455E ILE* 2.4 66.2 + - + +
582E LEU* 3.6 20.4 - - + -
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Residues in contact with LEU 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E GLY 3.0 27.6 + - - +
449E VAL* 3.5 10.5 - - - +
451E LEU* 1.3 75.1 - - - +
453E TYR* 1.3 57.6 + - - +
455E ILE* 2.7 35.4 - - + +
457E GLY* 3.1 18.8 - - - -
461E LEU* 3.3 31.4 - - + -
464E ALA* 5.7 3.8 - - + -
558E THR* 6.1 0.4 - - + -
579E SER* 3.8 24.2 - - - +
582E LEU* 3.5 37.9 - - + -
583E PHE* 4.3 14.1 - - + -
586E LEU* 6.1 0.7 - - + -
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Residues in contact with TYR 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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449E VAL* 3.0 14.4 + - + +
450E ILE* 3.5 13.0 - - + +
451E LEU 3.1 0.2 - - - -
452E LEU* 1.3 77.2 - - - +
454E TYR* 1.3 62.2 + + + +
455E ILE 3.4 0.2 - - - -
458E VAL* 3.0 56.3 - - + +
459E SER* 5.1 6.5 - - - -
461E LEU* 3.4 9.8 - - + +
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Residues in contact with TYR 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E LEU* 6.5 0.2 - - + -
450E ILE* 2.9 16.4 + - + +
451E LEU* 2.9 18.6 + - + +
453E TYR* 1.3 78.9 - - + +
455E ILE* 1.3 66.4 + - + +
458E VAL* 4.1 8.3 - - + +
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Residues in contact with ILE 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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318E LEU* 3.9 24.9 - - + -
321E PHE* 4.8 23.1 - - + -
451E LEU* 2.4 55.0 + - + +
452E LEU* 2.7 22.5 - - + +
454E TYR* 1.3 79.9 - - + +
456E LEU* 1.3 79.7 + - + +
457E GLY 2.5 18.3 + - - +
458E VAL* 2.5 21.7 + - - +
579E SER* 6.0 1.3 - - - -
582E LEU* 5.3 1.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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