Contacts of the helix formed by residues 430 - 451 (chain D) in PDB entry 3FZ7
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 430 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU 4.3 3.5 - - - +
15C ASP* 3.6 16.5 - - - +
16C SER* 2.5 52.0 + - - -
17C ARG* 3.4 36.0 + - - +
345D ALA* 4.5 2.4 - - - +
349D VAL* 4.0 7.4 - - - +
428D GLY* 2.9 26.3 + - - +
429D PHE* 1.3 77.6 + - - +
431D MET* 1.3 59.9 + - - +
432D ASP* 3.2 3.6 - - + +
433D PHE* 2.7 36.1 + - + -
434D ALA* 3.0 9.7 + - - +
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Residues in contact with MET 431 (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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13C LEU* 4.0 40.2 - - + -
14C LEU 5.8 3.4 - - - +
22C SER* 5.0 9.2 - - - +
24C SER* 6.5 0.9 - - - -
348D GLN* 3.4 34.5 - - + +
349D VAL* 3.7 18.4 - - + +
352D TYR* 3.4 40.6 - - + -
430D GLU* 1.3 75.6 + - - +
432D ASP* 1.3 64.6 + - - +
434D ALA* 3.1 7.0 + - - +
435D GLU* 2.9 24.5 + - + +
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Residues in contact with ASP 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE 4.1 3.5 - - - +
24C SER* 2.6 30.9 + - - -
25C THR* 2.7 35.8 + - - +
26C ILE* 3.6 30.8 - - + +
45C ILE* 5.5 0.9 - - - +
49C GLU* 4.5 5.5 - - - +
430D GLU* 3.2 3.1 - - + +
431D MET* 1.3 79.7 - - - +
433D PHE* 1.3 70.7 + - + +
435D GLU* 3.3 8.0 + - - +
436D LEU* 3.2 18.5 + - - +
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Residues in contact with PHE 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 4.2 17.3 - - - -
45C ILE 5.7 0.2 - - - -
48C ASP* 3.8 37.5 - - + -
49C GLU* 4.0 13.9 - - + -
52C LEU* 3.9 37.5 - - + -
57D ARG* 6.1 1.6 - - + -
404D TRP* 3.6 11.9 - + + -
428D GLY 3.7 14.1 - - - -
429D PHE* 3.7 21.8 - + + -
430D GLU* 2.7 34.1 + - + +
432D ASP* 1.3 78.9 - - + +
434D ALA* 1.3 57.9 + - - +
436D LEU* 3.2 9.0 + - - +
437D LEU* 3.0 23.4 + - - +
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Residues in contact with ALA 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D VAL* 3.8 24.9 - - + -
352D TYR* 5.0 2.5 - - + -
353D LEU* 4.0 14.8 - - + +
429D PHE* 3.7 16.1 - - + -
430D GLU 3.0 10.0 + - - +
431D MET* 3.1 17.5 + - - +
433D PHE* 1.3 74.4 - - - +
435D GLU* 1.3 65.8 + - - +
437D LEU* 3.3 5.3 - - - +
438D LEU* 3.0 25.2 + - - +
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Residues in contact with GLU 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 4.4 25.6 - - + -
352D TYR* 2.8 31.9 + - + +
431D MET* 2.9 15.8 + - + +
432D ASP* 3.3 11.6 + - - +
434D ALA* 1.3 74.3 - - - +
436D LEU* 1.3 57.3 + - - +
438D LEU* 3.1 23.8 + - - +
439D GLU* 3.0 37.7 + - - +
442D LYS* 5.4 5.2 + - - -
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Residues in contact with LEU 436 (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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92B GLN* 4.4 8.1 - - - +
26C ILE* 5.1 5.6 - - + +
52C LEU* 3.3 36.6 - - + -
58D GLN* 5.7 0.4 - - - +
404D TRP* 3.8 18.6 - - + -
432D ASP 3.2 8.9 + - - +
433D PHE* 3.2 10.3 + - - +
435D GLU* 1.3 75.8 - - - +
437D LEU* 1.3 65.7 + - - +
439D GLU* 3.2 24.1 + - - +
440D ASP* 2.9 41.9 + - - +
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Residues in contact with LEU 437 (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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60D LEU* 4.1 19.1 - - + -
353D LEU* 3.8 32.3 - - + -
357D ILE* 5.1 3.1 - - + -
399D LEU* 4.2 14.6 - - + -
404D TRP* 3.5 42.1 - - + +
406D VAL* 4.3 11.0 - - + -
423D ILE* 4.4 14.1 - - + -
429D PHE* 4.4 1.1 - - + -
433D PHE 3.0 12.4 + - - +
434D ALA* 3.3 11.7 - - - +
436D LEU* 1.3 74.0 - - - +
438D LEU* 1.3 52.4 + - + +
440D ASP* 3.0 3.6 + - - +
441D TYR* 2.7 42.9 + - + +
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Residues in contact with LEU 438 (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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352D TYR* 3.7 13.9 - - + +
353D LEU* 3.8 18.4 - - + -
356D GLU* 3.5 37.9 - - + +
357D ILE* 4.0 19.5 - - + +
360D LEU* 4.6 11.9 - - + -
434D ALA 3.0 11.0 + - - +
435D GLU* 3.1 32.3 + - - +
437D LEU* 1.3 80.6 - - + +
439D GLU* 1.3 61.4 + - - +
441D TYR* 3.3 6.4 + - + +
442D LYS* 3.1 42.0 + - - +
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Residues in contact with GLU 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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26C ILE* 5.0 11.6 - - - +
402D ARG* 5.2 0.6 + - - -
435D GLU* 3.0 25.9 + - - +
436D LEU* 3.2 25.0 + - + +
438D LEU* 1.3 75.8 - - - +
440D ASP* 1.3 59.7 + - - +
442D LYS* 3.6 13.0 + - + +
443D ALA* 3.1 28.2 + - - +
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Residues in contact with ASP 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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399D LEU* 4.1 5.8 - - + -
402D ARG* 3.0 46.5 + - - +
404D TRP* 2.8 33.7 + - + +
436D LEU* 2.9 32.0 + - - +
437D LEU 3.5 7.4 - - - +
439D GLU* 1.3 77.3 - - - +
441D TYR* 1.3 61.9 + - - +
443D ALA* 3.4 3.0 + - - +
444D SER* 2.9 33.1 + - - -
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Residues in contact with TYR 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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357D ILE* 3.8 28.4 - - + +
360D LEU* 3.6 24.9 - - + -
363D TYR* 2.9 37.2 + + - -
380D PHE* 3.5 17.9 - + - -
395D LEU* 3.3 27.1 - - + +
399D LEU* 4.1 21.3 - - + +
406D VAL* 6.2 0.2 - - + -
421D MET* 4.6 6.5 - - - -
423D ILE* 5.4 2.5 - - + -
437D LEU* 2.7 23.7 + - + +
438D LEU* 3.4 10.3 - - + +
439D GLU 3.2 0.2 - - - -
440D ASP* 1.3 74.4 - - - +
442D LYS* 1.3 53.9 + - - +
444D SER* 3.2 6.2 + - - -
445D LEU* 2.8 51.5 + - + +
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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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356D GLU* 5.4 7.5 + - - -
360D LEU* 3.9 35.9 - - + -
435D GLU* 5.4 5.1 + - - -
438D LEU* 3.1 34.8 + - - +
439D GLU* 3.8 10.9 - - + +
441D TYR* 1.3 74.6 - - - +
443D ALA* 1.3 57.0 + - - +
445D LEU* 3.2 11.8 + - + +
446D LYS* 3.0 29.6 + - - +
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Residues in contact with ALA 443 (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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402D ARG* 3.7 36.6 - - - +
439D GLU 3.1 18.2 + - - +
440D ASP 3.8 2.9 - - - +
441D TYR 3.2 0.2 - - - -
442D LYS* 1.3 76.4 - - - +
444D SER* 1.3 56.6 - - - +
446D LYS* 3.5 9.8 - - - +
447D TYR* 3.0 28.8 + - - +
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Residues in contact with SER 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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395D LEU* 3.8 15.7 - - - -
398D ARG* 3.4 33.2 + - - +
399D LEU* 3.8 11.0 - - - +
402D ARG* 4.8 5.7 + - - +
440D ASP 2.9 17.1 + - - -
441D TYR* 3.3 10.3 - - - -
443D ALA* 1.3 74.9 - - - +
445D LEU* 1.3 59.5 + - - +
447D TYR* 3.2 5.4 + - - +
448D LEU* 2.9 34.3 + - - +
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Residues in contact with LEU 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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360D LEU* 3.4 44.0 - - + +
363D TYR* 4.2 3.1 - - - +
390D TYR* 3.5 41.8 - - + +
395D LEU* 4.0 17.5 - - + -
441D TYR* 2.8 32.5 + - + +
442D LYS* 3.5 10.1 - - + +
444D SER* 1.3 71.9 - - - +
446D LYS* 1.3 57.1 + - - +
448D LEU* 3.2 7.1 + - + +
449D SER* 2.9 28.7 + - - -
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Residues in contact with LYS 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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442D LYS 3.0 11.7 + - - +
443D ALA* 3.5 13.0 - - - +
445D LEU* 1.3 75.6 - - - +
447D TYR* 1.3 62.7 + - - +
449D SER* 3.3 7.3 + - - -
450D ASP* 3.0 49.3 + - - +
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Residues in contact with TYR 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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397C GLU* 4.6 4.9 + - - -
457C ILE* 4.1 11.4 + - + +
458C ALA* 4.1 11.3 - - - +
459C GLN 4.8 1.7 + - - -
460C GLN* 6.5 0.4 - - + -
398D ARG* 3.6 38.1 - - - -
443D ALA 3.0 18.4 + - - +
444D SER* 3.7 7.0 - - - +
446D LYS* 1.3 77.9 - - - +
448D LEU* 1.3 58.4 + - - +
450D ASP* 3.4 3.3 + - + -
451D HIS* 2.9 78.6 + + - +
454D LEU* 3.9 9.4 - - + -
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Residues in contact with LEU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D GLY 4.6 6.3 - - - +
390D TYR* 3.8 38.4 - - + -
394D ASP* 4.2 15.9 - - + +
395D LEU* 4.0 29.8 - - + -
398D ARG* 3.9 14.4 - - + -
444D SER 2.9 22.2 + - - +
445D LEU* 3.4 9.4 - - - +
447D TYR* 1.3 76.3 - - - +
449D SER* 1.3 61.3 + - - +
451D HIS* 3.2 22.9 - - - +
452D PRO* 3.4 5.4 - - - +
454D LEU* 4.0 32.5 - - + -
455D GLN 5.5 0.4 - - - +
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Residues in contact with SER 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D GLY 5.9 0.7 - - - -
390D TYR* 5.9 0.4 - - - -
445D LEU 2.9 13.5 + - - -
446D LYS* 3.6 11.0 - - - -
448D LEU* 1.3 77.8 - - - +
450D ASP* 1.3 63.8 + - - +
451D HIS 3.5 0.2 + - - -
452D PRO* 3.7 15.3 - - - +
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Residues in contact with ASP 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D LYS* 3.0 46.0 + - - +
447D TYR* 4.5 2.8 - - - -
449D SER* 1.3 79.4 + - - +
451D HIS* 1.3 82.6 + - + +
452D PRO* 3.4 7.7 - - - +
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Residues in contact with HIS 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 3.7 42.1 + - + -
459C GLN* 5.7 4.0 + - - +
447D TYR* 2.9 66.1 + + - +
448D LEU* 3.2 7.7 + - - +
450D ASP* 1.3 96.1 + - + +
452D PRO* 1.3 58.8 - - - +
453D LYS 3.1 3.6 - - - +
454D LEU* 2.9 32.4 + - + +
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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