Contacts of the helix formed by residues 433 - 453 (chain D) in PDB entry 7ATU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431D GLN 3.6 7.0 - - - +
432D TYR* 1.3 104.4 - - + +
434D TRP* 1.3 62.7 + - + +
435D SER* 3.4 7.9 - - - +
436D GLN* 3.8 18.8 + - + +
437D ARG* 3.4 23.7 + - - +
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Residues in contact with TRP 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D SER 5.5 4.2 + - - -
432D TYR 4.7 4.1 + - - -
433D PRO* 1.3 72.4 - - + +
435D SER* 1.3 67.0 + - - +
436D GLN 3.2 0.2 - - - -
437D ARG* 3.0 36.6 - - + +
438D VAL* 2.9 28.6 + - + +
543D ILE* 3.6 19.3 - - + -
572D PRO* 4.1 9.4 - - + -
574D ASN* 2.8 34.4 + - + +
575D CYS* 3.3 25.4 - - + -
576D PRO* 3.2 32.3 - - + +
579D PHE* 3.5 34.3 - + - -
611D LEU* 5.1 6.7 - - + -
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Residues in contact with SER 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D PRO* 4.2 7.2 - - - +
434D TRP* 1.3 77.3 - - - +
436D GLN* 1.3 64.4 + - - +
438D VAL* 3.5 9.7 - - - +
439D SER* 3.1 22.2 + - - -
608D ARG* 4.5 6.8 - - - +
611D LEU 4.5 22.8 - - - -
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Residues in contact with GLN 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D TYR* 4.3 17.5 - - + +
433D PRO* 3.8 20.2 + - + +
434D TRP 3.2 0.6 - - - -
435D SER* 1.3 81.3 - - - +
437D ARG* 1.3 59.2 + - - +
439D SER* 3.2 15.1 - - - -
440D PHE* 3.1 42.9 + - + -
472D LYS* 3.4 32.8 - - + +
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Residues in contact with ARG 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D MET* 3.6 23.5 - - + -
430D SER 5.7 2.8 + - - -
432D TYR* 3.6 30.4 + - + -
433D PRO 3.4 15.9 + - - +
434D TRP* 3.0 60.4 + - + +
436D GLN* 1.3 74.1 - - - +
438D VAL* 1.3 64.9 + - - +
440D PHE* 3.4 16.4 + - + +
441D ALA* 3.3 15.9 + - - +
542D ILE* 2.5 59.0 + - + +
543D ILE 4.3 2.4 + - - -
545D ARG* 3.7 25.3 - - - +
572D PRO* 5.6 0.6 - - - +
579D PHE* 4.7 0.7 - - - -
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Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D TRP 2.9 20.1 + - - +
435D SER* 3.5 9.0 - - - +
437D ARG* 1.3 74.1 - - - +
439D SER* 1.3 68.2 + - - +
441D ALA* 3.3 1.9 + - + +
442D LYS* 3.0 23.2 + - - +
576D PRO* 6.0 2.0 - - + -
579D PHE* 4.0 21.4 - - + -
604D LEU* 4.1 21.5 - - + +
607D LEU* 3.4 33.9 - - + +
608D ARG* 3.7 26.7 - - + +
611D LEU* 5.0 4.3 - - + -
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Residues in contact with SER 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D SER 3.1 16.0 + - - -
436D GLN* 3.2 25.5 + - - -
438D VAL* 1.3 78.0 - - - +
440D PHE* 1.3 59.6 + - - +
442D LYS* 3.1 5.6 + - - +
443D ASP* 2.6 38.2 + - - +
472D LYS 5.4 0.9 - - - -
608D ARG* 4.4 20.2 - - - +
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Residues in contact with PHE 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 4.0 21.1 - - + -
424D ILE* 4.7 7.4 - - + -
428D MET* 5.0 2.5 - - + -
432D TYR* 4.0 29.8 - + - -
436D GLN* 3.1 33.7 + - + -
437D ARG* 3.5 19.3 - - + +
438D VAL 3.2 0.4 - - - -
439D SER* 1.3 76.2 - - - +
441D ALA* 1.3 61.9 + - - +
442D LYS 3.3 0.7 + - - -
443D ASP 3.5 0.3 + - - -
444D ILE* 3.3 28.2 + - - +
468D VAL* 4.5 15.7 - - + -
472D LYS* 3.1 37.5 - - + -
474D VAL* 3.3 28.9 - - + +
542D ILE* 4.2 12.6 - - + -
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Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ARG 3.3 9.2 + - - +
438D VAL 3.3 6.1 + - - +
439D SER 3.3 0.6 - - - -
440D PHE* 1.3 79.6 - - - +
442D LYS* 1.3 61.2 + - - +
444D ILE* 4.6 4.3 - - - -
445D ALA* 3.3 18.5 + - - +
535D PHE* 3.5 6.7 - - - -
539D LEU* 3.4 32.8 - - + -
542D ILE* 4.4 2.9 - - + +
579D PHE* 4.2 11.4 - - + -
604D LEU* 3.1 25.2 - - + +
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Residues in contact with LYS 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C GLU* 4.5 12.9 + - - +
393C HIS* 6.1 1.6 - - - -
450C TYR* 4.8 4.9 - - - -
395D ASN* 5.9 1.0 - - - +
438D VAL 3.0 16.4 + - - +
439D SER* 3.1 5.8 + - - +
441D ALA* 1.3 77.2 - - - +
443D ASP* 1.3 73.0 + - - +
445D ALA* 3.8 2.2 - - - +
446D SER* 2.9 36.2 + - - -
601D GLU* 4.0 30.0 - - + +
604D LEU* 3.6 19.5 - - + +
605D GLU* 3.1 42.5 + - - +
608D ARG* 5.3 5.3 - - + +
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Residues in contact with ASP 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D ASN* 3.0 47.9 + - - +
439D SER* 2.6 29.9 + - - +
440D PHE* 3.5 1.8 + - - +
442D LYS* 1.3 85.9 + - - +
444D ILE* 1.3 65.4 + - - +
446D SER* 4.1 0.2 - - - -
447D GLY 3.0 7.4 + - - -
472D LYS 4.4 1.7 - - - +
473D ASN* 3.9 19.4 - - - +
474D VAL* 3.7 32.2 + - + -
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Residues in contact with ILE 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 4.3 15.7 - - + -
440D PHE 3.3 18.0 + - - +
441D ALA* 4.6 4.0 - - - -
442D LYS 3.3 0.4 - - - -
443D ASP* 1.3 71.1 - - - +
445D ALA* 1.3 55.5 - - - +
446D SER 2.6 4.0 + - - -
447D GLY* 2.5 29.6 + - - -
448D MET* 3.0 23.2 + - + +
461D LEU* 4.3 14.4 - - + -
466D CYS* 3.6 23.3 - - - -
474D VAL* 3.4 22.2 - - + -
476D VAL* 4.2 10.5 - - + +
535D PHE* 3.3 28.0 - - + -
538D VAL* 4.3 12.6 - - + -
539D LEU* 6.1 0.4 - - + -
542D ILE* 5.4 1.6 - - + -
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Residues in contact with ALA 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D ALA 3.3 16.6 + - - +
442D LYS* 3.8 4.9 - - - +
444D ILE* 1.3 77.3 - - - +
446D SER* 1.3 56.3 + - - +
449D ALA* 2.9 30.6 + - - +
535D PHE* 3.6 12.5 - - + -
597D PHE* 3.5 28.7 - - + +
600D LEU* 4.2 8.3 - - + +
601D GLU* 4.1 21.5 - - - -
604D LEU* 4.5 0.2 - - + -
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Residues in contact with SER 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D HIS* 3.2 19.5 + - - -
395D ASN* 3.2 23.0 + - - -
442D LYS* 2.9 26.2 + - - -
443D ASP* 4.1 0.4 - - - -
444D ILE 2.6 4.6 + - - -
445D ALA* 1.3 72.2 - - - +
447D GLY* 1.3 64.6 + - - -
449D ALA* 3.2 4.9 + - - +
450D TYR 3.1 17.3 + - - -
601D GLU* 3.1 28.6 + - - +
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Residues in contact with GLY 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D HIS* 4.2 4.5 - - - -
395D ASN* 3.7 27.8 - - - +
396D VAL* 3.8 11.2 - - - +
443D ASP 3.0 7.3 + - - -
444D ILE 2.5 12.3 + - - -
446D SER* 1.3 72.3 + - - +
448D MET* 1.3 57.9 + - - -
450D TYR* 3.3 5.0 + - - +
451D LEU* 3.0 30.6 + - - +
476D VAL* 4.9 1.6 - - - -
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Residues in contact with MET 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ILE* 3.0 24.3 + - + +
447D GLY* 1.3 74.0 - - - +
449D ALA* 1.3 65.6 + - - +
451D LEU* 3.0 15.5 + - + -
452D HIS* 2.8 36.6 + - + +
458D HIS* 3.7 19.7 - - + -
461D LEU* 4.1 12.8 - - + -
476D VAL* 4.0 26.5 - - + -
531D ASP* 3.7 29.6 - - + +
597D PHE* 3.6 37.0 - - + -
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Residues in contact with ALA 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D ALA 2.9 20.7 + - - +
446D SER 3.4 5.8 - - - +
448D MET* 1.3 74.4 - - - +
450D TYR* 1.3 62.3 + - - +
452D HIS* 3.7 3.4 + - - +
453D SER* 3.3 22.7 + - - -
597D PHE* 3.6 23.8 - - + +
598D VAL* 4.2 9.9 - - + +
601D GLU* 3.6 20.4 - - - +
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Residues in contact with TYR 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C LYS* 5.6 2.9 - - - -
605C GLU* 3.1 26.1 + - + -
609C MET* 3.6 9.9 - - - +
391D LEU* 3.9 25.6 - - + +
392D GLU 3.0 32.1 + - - -
393D HIS* 3.3 49.4 - + + +
396D VAL* 3.9 12.1 - - + -
446D SER 3.1 6.2 + - - +
447D GLY 3.5 6.5 - - - +
448D MET 3.1 0.4 - - - -
449D ALA* 1.3 75.7 - - - +
451D LEU* 1.3 67.8 + - + +
453D SER* 2.8 24.8 + - - -
454D MET* 3.5 28.7 - - + +
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D LEU* 3.6 24.2 - - + -
396D VAL* 4.3 15.3 - - + -
447D GLY 3.0 17.2 + - - +
448D MET* 3.6 29.6 - - + +
450D TYR* 1.3 78.5 - - + +
452D HIS* 1.3 53.6 + - - +
454D MET* 2.8 31.2 + - - +
456D ILE* 3.4 31.8 + - + +
458D HIS* 5.4 0.4 - - + -
476D VAL* 4.8 2.7 - - + -
701D RXN 3.3 54.5 - - + -
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Residues in contact with HIS 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D MET* 2.8 27.0 + - + +
449D ALA* 4.1 5.4 - - - +
451D LEU* 1.3 71.1 - - - +
453D SER* 1.3 57.7 + - - +
454D MET 2.9 5.2 - - - -
455D ASN* 2.9 24.1 + - - +
456D ILE 3.5 15.3 - - - -
528D GLU* 2.8 47.6 + - + +
529D LYS* 6.0 0.9 - - + +
531D ASP* 2.4 33.1 + - + +
532D VAL* 4.8 2.9 - - + -
597D PHE* 3.6 26.2 + + + +
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Residues in contact with SER 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C HIS* 3.3 34.9 + - - -
449D ALA 3.3 14.4 + - - -
450D TYR* 2.8 19.7 + - - -
451D LEU 3.2 0.4 - - - -
452D HIS* 1.3 75.3 - - - +
454D MET* 1.3 68.9 + - - +
455D ASN* 3.6 2.9 + - - -
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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
------------------------------------------------------------
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