Contacts of the helix formed by residues 433 - 454 (chain A) in PDB entry 3S95
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 PRO 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLN 3.6 8.5 - - - +
432A TYR* 1.4 101.1 - - + +
434A TRP* 1.3 67.1 + - + +
435A SER* 4.1 14.4 - - - +
436A GLN* 3.1 23.3 + - + +
437A ARG* 3.1 12.6 + - - +
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Residues in contact with TRP 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A SER 4.6 6.2 + - - -
431A GLN* 6.1 1.3 - - - +
432A TYR 3.3 4.4 + - - -
433A PRO* 1.3 69.8 - - + +
435A SER* 1.3 66.3 + - - +
437A ARG* 3.1 47.7 + - + +
438A VAL* 2.9 29.5 + - - +
543A ILE* 3.7 13.0 - - - -
572A PRO* 3.4 34.1 - - + +
574A ASN* 3.4 34.6 + - + +
575A CYS* 3.8 14.1 - - + -
576A PRO* 3.4 27.4 - - + -
579A PHE* 3.9 26.2 - + - -
611A LEU* 4.1 12.3 - - + -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO* 4.1 10.9 - - - +
434A TRP* 1.3 76.0 - - - +
436A GLN* 1.3 59.1 + - - +
438A VAL* 3.8 3.1 - - - +
439A SER* 2.9 27.8 + - - -
608A ARG* 4.1 13.2 - - - +
611A LEU* 4.0 28.0 - - - +
612A ALA* 5.1 10.1 - - - -
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Residues in contact with GLN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 3.7 29.6 - - + +
433A PRO* 3.1 20.8 + - + +
435A SER* 1.3 79.8 + - - +
437A ARG* 1.3 64.1 + - - +
439A SER* 3.2 15.1 + - - -
440A PHE* 2.9 40.6 + - + -
471A ASN 5.2 0.6 + - - -
472A LYS* 3.5 34.5 - - + +
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A MET* 4.2 13.5 - - + -
429A ASP 3.8 4.4 + - - -
430A SER* 3.2 26.5 + - - +
432A TYR* 3.0 44.7 + - + +
433A PRO 3.1 11.2 + - - +
434A TRP* 3.1 42.5 + - + +
436A GLN* 1.3 75.8 - - - +
438A VAL* 1.3 62.4 + - - +
440A PHE* 3.3 13.8 + - - +
441A ALA* 3.2 19.9 + - - +
542A ILE* 3.1 49.5 + - + +
543A ILE 3.5 14.5 + - - -
545A ARG* 3.8 14.3 - - - +
572A PRO* 4.9 1.2 - - - +
579A PHE* 4.3 2.0 - - + -
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TRP 2.9 19.7 + - - +
435A SER 3.8 4.0 - - - +
437A ARG* 1.3 75.4 - - - +
439A SER* 1.3 59.2 + - - +
441A ALA* 3.1 2.9 + - - +
442A LYS* 2.8 27.3 + - - +
576A PRO* 4.3 3.1 - - + -
579A PHE* 3.9 23.3 - - + -
604A LEU* 3.3 34.3 - - + +
607A LEU* 3.8 28.0 - - + -
608A ARG* 3.7 16.8 - - + +
611A LEU* 4.0 13.0 - - + -
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Residues in contact with SER 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER 2.9 16.6 + - - -
436A GLN* 3.2 24.0 + - - -
438A VAL* 1.3 75.5 - - - +
440A PHE* 1.3 61.7 + - - +
442A LYS* 3.2 4.6 + - - +
443A ASP* 2.9 38.4 + - - +
472A LYS 5.0 0.3 + - - -
473A ASN* 4.6 6.9 + - - -
608A ARG* 3.9 23.5 - - - +
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Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 3.7 23.1 - - + -
424A ILE* 4.1 10.8 - - + -
428A MET* 3.9 22.9 - - + -
432A TYR* 3.4 30.7 - + - -
436A GLN* 2.9 29.8 + - + -
437A ARG* 3.4 13.9 - - - +
439A SER* 1.3 76.3 - - - +
441A ALA* 1.3 61.9 + - - +
443A ASP* 3.3 2.4 + - - +
444A ILE* 3.1 30.3 + - + +
468A VAL* 4.1 15.9 - - + -
472A LYS* 3.3 23.6 - - + -
474A VAL* 3.4 25.2 - - + +
542A ILE* 4.3 12.8 - - + -
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG 3.2 8.6 + - - +
438A VAL 3.1 9.1 + - - +
440A PHE* 1.3 78.5 - - - +
442A LYS* 1.3 63.4 + - - +
444A ILE* 3.4 2.6 + - - -
445A ALA* 3.0 19.4 + - - +
535A PHE* 3.5 17.5 - - + -
539A LEU* 3.5 30.7 - - + -
542A ILE* 4.7 5.8 - - + -
579A PHE* 4.2 4.5 - - + -
604A LEU* 3.7 18.2 - - + -
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GOL 4.7 7.3 - - - -
395A ASN* 5.1 1.6 + - - -
438A VAL 2.8 16.5 + - - +
439A SER* 3.6 8.5 - - - +
441A ALA* 1.3 76.9 - - - +
443A ASP* 1.3 68.7 + - - +
445A ALA* 3.2 4.7 + - - +
446A SER* 2.8 32.7 + - - -
601A GLU* 2.9 38.5 + - + +
604A LEU* 3.9 17.6 - - + +
605A GLU* 3.6 49.6 - - - +
608A ARG* 5.3 2.2 - - - +
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Residues in contact with ASP 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN* 3.2 37.1 + - - +
439A SER* 2.9 26.6 + - - +
440A PHE 3.6 4.5 - - - +
442A LYS* 1.3 87.6 + - - +
444A ILE* 1.3 62.2 + - - +
446A SER* 3.2 2.7 + - - -
447A GLY 3.1 18.4 + - - -
472A LYS 4.3 0.5 - - - +
473A ASN* 3.2 22.4 - - - +
474A VAL* 3.0 33.0 + - + +
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Residues in contact with ILE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 3.8 24.2 - - + -
440A PHE 3.1 19.8 + - - +
441A ALA* 3.8 7.0 - - - +
443A ASP* 1.3 75.6 - - - +
445A ALA* 1.3 57.8 + - - +
446A SER 3.3 0.2 + - - -
447A GLY* 3.3 1.9 + - - -
448A MET* 2.9 39.1 + - + +
461A LEU* 4.1 24.7 - - + -
466A CYS* 3.7 19.5 - - - -
474A VAL* 3.7 20.2 - - + -
476A VAL* 4.1 10.2 - - + +
535A PHE* 3.7 22.7 - - + -
538A VAL* 4.2 12.1 - - + -
542A ILE* 5.0 0.9 - - + -
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ALA 3.0 13.9 + - - +
442A LYS 3.5 7.9 - - - +
444A ILE* 1.3 77.5 - - - +
446A SER* 1.3 52.8 + - - +
449A ALA* 2.7 37.0 + - - +
535A PHE* 4.1 3.5 - - + -
597A PHE* 3.7 18.5 - - + +
600A LEU* 4.1 14.6 - - + -
601A GLU* 3.9 25.8 - - - +
604A LEU* 4.1 6.1 - - + -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A HIS* 3.2 21.0 + - - -
395A ASN* 3.3 16.3 + - - -
442A LYS* 2.8 19.7 + - - -
443A ASP* 3.5 5.2 - - - -
444A ILE 3.2 0.2 - - - -
445A ALA* 1.3 77.6 - - - +
447A GLY* 1.3 62.4 + - - +
449A ALA* 3.7 2.4 - - - +
450A TYR* 3.0 23.7 + - - +
601A GLU* 2.7 36.5 + - - +
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A HIS* 4.0 3.8 - - - -
395A ASN* 3.7 29.0 - - - +
396A VAL* 3.7 17.0 - - - +
443A ASP 3.1 9.7 + - - -
444A ILE 3.8 2.2 - - - -
446A SER* 1.3 76.2 - - - +
448A MET* 1.3 59.6 + - - +
450A TYR* 3.3 4.5 + - - +
451A LEU* 3.0 23.6 + - - +
476A VAL* 4.6 2.7 - - - -
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Residues in contact with MET 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 2.9 25.3 + - + +
447A GLY* 1.3 74.4 - - - +
449A ALA* 1.3 65.1 + - - +
451A LEU* 3.2 16.3 + - + +
452A HIS* 2.9 36.9 + - - +
458A HIS* 3.8 12.8 - - + -
461A LEU* 4.0 20.2 - - + -
476A VAL* 4.1 26.2 - - + +
531A ASP* 3.3 40.6 - - + +
597A PHE* 3.5 31.4 - - + -
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ALA 2.7 22.7 + - - +
446A SER 3.7 4.3 - - - +
448A MET* 1.3 73.2 - - - +
450A TYR* 1.3 57.7 + - - +
452A HIS* 3.9 4.4 - - - +
453A SER* 2.9 30.1 + - - -
597A PHE* 3.5 10.8 - - - +
598A VAL* 3.6 41.4 - - + +
601A GLU* 4.1 9.4 - - - +
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Residues in contact with TYR 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A CYS 4.0 4.9 + - - -
391A LEU* 3.6 25.5 - - + -
392A GLU* 2.9 40.8 + - - +
393A HIS* 3.4 46.0 - + + -
396A VAL* 3.9 11.4 - - + -
446A SER 3.0 8.2 + - - +
447A GLY 3.4 7.0 - - - +
448A MET 3.2 0.2 - - - -
449A ALA* 1.3 77.1 - - - +
451A LEU* 1.3 65.2 + - - +
453A SER* 2.6 27.8 + - - -
454A MET* 3.2 34.7 + - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A VAL* 4.8 0.2 - - + -
391A LEU* 3.9 25.4 - - + -
396A VAL* 5.4 2.0 - - + -
447A GLY 3.0 14.2 + - - +
448A MET* 3.2 21.5 + - + +
450A TYR* 1.3 80.7 - - + +
452A HIS* 1.3 57.1 + - + +
454A MET* 3.0 20.3 + - - +
456A ILE* 3.1 62.2 + - + +
458A HIS* 3.7 33.9 - - + +
479A PHE* 4.0 20.6 - - + -
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Residues in contact with HIS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A MET* 2.9 23.2 + - + +
449A ALA* 4.0 5.8 - - - +
451A LEU* 1.3 74.6 - - - +
453A SER* 1.3 56.7 + - - +
455A ASN* 3.0 23.7 + - - +
456A ILE 3.2 22.0 - - - +
485A MET* 4.2 6.3 - - + +
528A GLU* 3.2 52.2 + - + +
531A ASP* 2.8 25.0 + - - +
532A VAL* 4.8 2.4 - - + +
597A PHE* 3.4 33.5 + + - +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ALA 2.9 15.3 + - - -
450A TYR* 2.6 27.0 + - - -
452A HIS* 1.3 76.2 - - - +
454A MET* 1.3 76.3 + - - +
455A ASN* 3.2 9.9 + - - -
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Residues in contact with MET 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A CYS 5.4 4.0 - - - +
391A LEU* 4.3 7.2 - - + -
450A TYR* 3.4 48.2 - - + +
451A LEU* 3.0 9.2 + - - +
453A SER* 1.3 99.5 - - - +
455A ASN* 1.3 69.3 + - - +
456A ILE* 3.3 23.3 + - + +
484A LEU* 4.0 6.2 - - - +
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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