Contacts of the helix formed by residues 407 - 426 (chain A) in PDB entry 4FYT
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 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 4.8 0.9 - - - +
401A ILE* 4.1 11.4 - - + -
404A TRP* 3.0 35.1 + - + +
405A ASN 3.3 2.8 + - - -
406A ASP* 1.3 76.5 - - - +
408A TRP* 1.3 56.0 + - - +
410A ASN* 2.8 29.5 + - + +
411A GLU* 3.0 29.9 + - + +
471A LEU* 3.5 30.7 - - + +
472A PHE* 3.6 50.0 - - + -
476A SER* 4.2 10.5 - - - +
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Residues in contact with TRP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 2.9 28.7 + - - -
407A LEU* 1.3 77.1 - - - +
409A LEU* 1.3 79.3 + - + +
412A GLY* 2.7 26.5 + - - +
413A PHE* 3.2 11.3 + + - -
455A LEU* 3.5 54.2 + - + +
456A SER* 4.0 7.3 - - - -
476A SER* 3.5 31.8 + - - +
480A GLY* 4.3 11.4 - - - -
483A VAL* 5.2 4.5 - - + -
484A LEU* 3.9 26.0 - - + -
514A TYR* 4.0 7.2 - - + +
517A LEU* 3.8 11.9 - - + -
518A TRP* 3.6 27.4 - + - -
544A THR* 3.9 19.0 - - + +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 4.0 9.4 - - - +
401A ILE* 3.8 9.2 - - + -
406A ASP* 2.9 22.8 + - + +
408A TRP* 1.3 111.6 - - + +
410A ASN* 1.3 60.7 + - - +
413A PHE* 3.3 28.6 - - + +
503A TYR* 4.3 15.4 + - - +
512A THR* 3.9 18.2 - - - +
513A ILE* 3.6 35.2 - - - +
514A TYR* 3.6 7.9 - - - +
517A LEU* 4.1 17.7 - - + -
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 4.7 5.5 - - - +
278A TYR* 3.0 30.3 + - - -
355A GLU* 4.5 6.5 + - - -
392A HIS* 3.2 21.1 + - + -
395A PHE 3.6 8.1 - - - +
396A GLY* 3.3 21.8 + - - -
399A VAL 4.4 0.3 - - - +
400A THR* 4.3 0.3 - - - -
401A ILE* 3.4 37.4 + - - +
407A LEU* 2.8 11.8 + - + +
409A LEU* 1.3 81.0 - - - +
411A GLU* 1.3 65.0 + - + +
412A GLY 3.5 0.2 - - - -
413A PHE* 3.6 1.2 + - - +
414A ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 4.4 1.2 + - - +
355A GLU* 4.3 1.6 - - - +
388A HIS* 3.2 0.2 + - - -
392A HIS* 3.4 8.5 + - - -
407A LEU* 3.0 34.8 + - + +
410A ASN* 1.3 77.3 - - + +
412A GLY* 1.3 59.8 + - - +
414A ALA* 4.1 0.2 - - - +
415A SER* 2.7 37.6 + - - -
472A PHE* 3.9 6.0 - - + -
476A SER 3.8 7.2 - - - +
477A TYR* 3.2 40.5 + - + +
1012A ZN 1.9 32.3 - - - -
1B L2O 2.9 30.0 + - - +
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Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP 2.7 19.0 + - - -
411A GLU* 1.3 70.8 - - - +
413A PHE* 1.3 61.5 + - - +
415A SER* 3.3 1.0 + - - -
416A TYR* 3.0 20.3 + - - +
476A SER 3.2 19.7 + - - -
477A TYR 3.6 9.0 - - - -
480A GLY* 3.7 11.2 - - - -
481A ALA* 3.6 11.1 - - - -
484A LEU* 3.7 7.4 - - - +
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Residues in contact with PHE 413 (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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395A PHE* 3.6 41.1 - + + -
408A TRP* 3.2 9.9 + + - -
409A LEU* 3.3 38.8 - - + +
410A ASN 3.6 0.6 + - - +
412A GLY* 1.3 73.4 - - - +
414A ALA* 1.3 61.1 + - - +
416A TYR* 3.2 1.4 + + - -
417A VAL* 2.8 43.0 + - + +
484A LEU* 3.6 30.5 - - + -
496A PHE* 4.2 6.1 - + - -
500A LEU* 3.5 36.1 - - + -
503A TYR* 5.5 3.4 - + - -
517A LEU* 3.7 33.2 - - + -
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Residues in contact with ALA 414 (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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388A HIS* 3.4 34.3 + - + +
391A ALA* 3.9 13.5 - - + -
392A HIS* 3.4 35.7 - - + +
395A PHE* 5.0 0.6 - - - +
410A ASN 3.0 8.6 + - - +
411A GLU 4.1 0.4 - - - +
412A GLY 3.4 0.2 - - - -
413A PHE* 1.3 75.4 - - - +
415A SER* 1.3 57.6 + - - +
418A GLU* 2.9 34.0 + - - +
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Residues in contact with SER 415 (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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388A HIS* 3.6 4.8 - - - -
411A GLU 2.7 22.3 + - - -
412A GLY 3.7 1.3 - - - -
413A PHE 3.1 0.2 - - - -
414A ALA* 1.3 78.3 - - - +
416A TYR* 1.3 55.9 - - - +
418A GLU* 3.3 14.3 + - - +
419A TYR* 3.1 28.8 - - - -
439A ASP* 4.5 6.4 - - - +
477A TYR* 3.3 45.0 + - - +
481A ALA* 3.7 7.8 - - - +
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Residues in contact with TYR 416 (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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332A TYR* 5.0 0.7 - - - -
412A GLY 3.0 15.9 + - - +
413A PHE* 3.8 1.8 - + - +
415A SER* 1.3 76.6 - - - +
417A VAL* 1.3 77.9 + - + +
418A GLU 3.2 1.8 - - - -
419A TYR* 3.1 24.2 + - - +
420A LEU* 3.9 33.2 + - + +
435A MET* 4.0 21.3 - - + -
481A ALA* 3.7 18.1 - - - +
484A LEU* 4.1 15.7 - - + -
485A ARG* 3.7 32.8 - - + -
488A SER* 3.2 14.6 + - - -
493A GLU* 2.8 23.0 + - - -
496A PHE* 3.9 18.6 - + - -
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Residues in contact with VAL 417 (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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328A PHE* 3.4 31.5 - - + -
332A TYR* 3.3 31.6 - - + +
391A ALA* 3.7 15.5 - - + -
395A PHE* 4.2 15.9 - - + -
413A PHE* 2.8 33.0 + - + +
416A TYR* 1.3 83.4 - - + +
418A GLU* 1.3 66.2 + - - +
420A LEU* 3.0 18.0 + - + +
421A GLY 3.1 8.8 + - - -
496A PHE* 6.3 0.2 - - + -
500A LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 418 (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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384A THR* 3.7 24.7 - - - +
387A ALA* 3.3 15.6 - - - +
388A HIS* 2.8 48.7 + - - +
391A ALA* 4.6 0.8 - - - +
414A ALA 2.9 13.9 + - - +
415A SER* 3.3 23.5 + - - +
417A VAL* 1.3 76.7 - - - +
419A TYR* 1.3 79.8 + - + +
422A ALA* 2.9 32.2 + - - +
2B VAL* 5.3 1.4 - - - +
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Residues in contact with TYR 419 (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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380A GLU* 5.7 2.2 - - - -
384A THR* 5.6 7.6 - - + -
415A SER 3.1 28.7 - - - -
416A TYR 3.1 9.5 + - - +
417A VAL 3.1 0.6 - - - -
418A GLU* 1.3 92.3 + - + +
420A LEU* 1.3 61.6 + - + +
422A ALA* 4.1 3.8 - - - +
423A ASP* 2.8 33.4 + - - +
431A LEU* 3.5 35.3 - - + +
432A LYS* 4.1 10.8 - - + +
434A LEU* 4.5 6.7 - - + -
435A MET* 3.3 40.5 - - + -
438A ASN* 3.5 23.0 + - - +
439A ASP* 2.7 28.1 + - - -
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Residues in contact with LEU 420 (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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327A PHE* 3.6 20.7 - - + -
328A PHE* 4.6 1.3 - - + -
331A HIS* 4.0 10.5 - - + +
332A TYR* 3.5 25.1 - - + +
416A TYR* 3.9 40.6 - - + +
417A VAL* 3.0 10.8 + - - +
419A TYR* 1.3 82.1 - - + +
421A GLY* 1.3 56.3 - - - +
423A ASP* 3.8 6.1 - - - +
424A TYR* 3.0 27.4 + - - +
432A LYS* 4.3 23.6 - - + +
435A MET* 5.3 1.1 - - + -
493A GLU* 3.7 22.0 - - + +
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Residues in contact with GLY 421 (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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324A ILE* 3.6 20.5 - - - +
327A PHE* 4.0 8.1 - - - -
328A PHE* 3.5 27.5 - - - -
387A ALA* 4.2 1.1 - - - -
417A VAL 3.1 10.5 + - - -
418A GLU 3.9 0.9 - - - -
420A LEU* 1.3 74.5 - - - +
422A ALA* 1.3 64.4 + - - +
424A TYR* 3.2 5.4 + - - +
425A ALA 3.1 17.0 + - - -
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Residues in contact with ALA 422 (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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383A VAL* 4.2 23.1 - - + +
384A THR* 3.9 17.7 - - + -
387A ALA* 3.7 2.9 - - - +
418A GLU 2.9 18.8 + - - +
419A TYR* 4.1 3.4 - - - +
421A GLY* 1.3 75.5 - - - +
423A ASP* 1.3 52.3 + - - +
425A ALA* 3.2 2.9 + - - +
426A GLU* 2.8 38.6 + - - +
431A LEU* 3.5 23.1 - - + -
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Residues in contact with ASP 423 (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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419A TYR 2.8 20.1 + - - +
420A LEU* 3.8 4.8 - - - +
422A ALA* 1.3 73.1 - - - +
424A TYR* 1.3 67.9 + - - +
426A GLU 4.2 6.4 - - - +
427A PRO* 3.0 41.4 - - - +
430A ASN* 4.8 5.0 - - - +
431A LEU* 4.5 16.1 + - + +
432A LYS* 3.9 32.4 + - + +
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Residues in contact with TYR 424 (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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323A PRO* 3.5 37.4 + - + +
324A ILE* 4.6 1.8 - - - -
326A ASN* 5.4 5.6 + - - -
327A PHE* 3.5 46.2 - + + -
420A LEU 3.0 14.4 + - - +
421A GLY 3.2 10.5 + - - +
423A ASP* 1.3 82.4 + - - +
425A ALA* 1.3 65.3 + - - +
427A PRO* 3.6 9.9 - - - +
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Residues in contact with ALA 425 (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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320A VAL* 4.0 17.9 - - + +
323A PRO* 5.8 2.7 - - + -
324A ILE* 4.0 14.1 - - + +
383A VAL* 4.0 21.1 - - + -
421A GLY 3.1 11.4 + - - +
422A ALA 3.2 6.5 + - - +
424A TYR* 1.3 82.4 - - + +
426A GLU* 1.3 68.3 + - - +
427A PRO* 3.5 6.0 - - - +
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Residues in contact with GLU 426 (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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316A TYR* 2.7 38.7 + - - +
320A VAL* 4.7 2.1 - - - +
379A LYS* 4.5 2.4 + - - -
383A VAL* 4.5 3.4 - - + -
422A ALA 2.8 18.0 + - - +
423A ASP* 3.3 8.2 - - - +
425A ALA* 1.3 85.9 - - + +
427A PRO* 1.3 65.5 - - - +
428A THR* 3.2 6.1 + - - -
429A TRP* 3.2 65.0 + - + +
430A ASN 4.5 1.6 + - - -
431A LEU* 5.0 2.3 + - + +
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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