Contacts of the helix formed by residues 421 - 440 (chain A) in PDB entry 6FEQ
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 THR 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LYS* 5.2 1.6 - - - +
419A ASP* 3.2 21.0 + - - +
420A SER* 1.3 86.0 - - - +
422A GLY* 1.3 62.7 + - - +
423A ILE 3.3 1.8 - - - -
424A GLN* 3.5 11.2 + - - +
425A ASN* 2.9 31.6 + - - +
557B ASN* 3.4 31.9 - - - +
559B THR* 5.4 0.9 - - - +
560B THR* 3.9 17.1 - - + +
616B LYS* 4.6 13.7 - - + -
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Residues in contact with GLY 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 5.9 0.9 - - - -
417A LYS 3.3 24.0 - - - -
419A ASP* 3.0 12.6 + - - -
421A THR* 1.3 77.4 + - - +
423A ILE* 1.3 60.1 + - - +
425A ASN* 3.3 6.0 + - - +
426A ARG* 3.0 36.6 + - - +
591A PHE* 3.9 10.8 - - - -
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Residues in contact with ILE 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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420A SER* 4.2 10.9 + - - +
421A THR 3.3 0.2 - - - -
422A GLY* 1.3 75.2 - - - +
424A GLN* 1.3 63.0 + - - +
427A ALA* 3.2 25.6 + - - +
586A PHE* 4.6 8.8 - - + -
591A PHE* 3.8 36.1 - - + -
607A THR* 3.7 39.7 - - + +
609A THR 5.3 0.2 - - - +
613A TYR* 3.7 38.8 - - + -
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Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A SER 4.9 1.3 + - - +
421A THR* 3.5 13.3 + - - +
422A GLY 3.3 0.4 - - - -
423A ILE* 1.3 80.5 - - - +
425A ASN* 1.3 60.6 + - - +
427A ALA* 4.1 1.2 - - - +
428A GLY* 3.2 10.0 + - - -
553B GLY 2.8 29.1 + - - -
554B LEU* 3.8 18.0 + - + +
555B LEU 2.9 19.8 - - - +
556B VAL 3.8 5.5 + - - -
557B ASN* 3.6 27.7 + - + +
613B TYR* 5.0 1.8 + - - -
616B LYS* 5.2 2.9 - - - +
617B GLN* 3.1 30.8 + - - +
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Residues in contact with ASN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 3.8 8.0 - - + +
416A LEU* 3.9 25.2 - - + +
417A LYS 5.7 2.3 + - - -
421A THR* 2.9 23.9 + - - +
422A GLY* 3.3 8.5 + - - +
423A ILE 3.3 0.6 - - - -
424A GLN* 1.3 76.3 - - - +
426A ARG* 1.3 60.3 + - - +
428A GLY* 3.0 15.2 + - - -
429A VAL* 3.1 16.7 + - - +
555B LEU 4.1 2.2 - - - -
556B VAL* 3.4 17.8 - - - +
557B ASN* 3.1 31.2 - - - +
560B THR* 3.7 16.1 + - - -
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.8 37.8 + - + +
417A LYS 4.7 0.4 + - - -
418A ASN* 2.7 28.6 + - - +
422A GLY* 3.0 16.9 + - - +
425A ASN* 1.3 74.1 - - - +
427A ALA* 1.3 61.1 - - - +
428A GLY 3.2 1.2 + - - -
429A VAL* 3.3 8.8 - - - +
430A LEU* 3.3 31.7 + - + +
498A GLY 4.1 17.6 + - - -
499A LEU* 4.2 10.3 - - + +
585A GLU* 2.5 43.4 + - - +
586A PHE* 3.8 13.2 - - + -
589A GLN* 3.5 15.7 - - - +
591A PHE* 3.4 32.1 - - - -
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Residues in contact with ALA 427 (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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423A ILE* 3.2 18.4 + - + +
424A GLN* 4.1 1.6 - - - +
426A ARG* 1.3 76.0 - - - +
428A GLY* 1.3 64.2 + - - +
430A LEU* 4.3 5.4 - - - -
431A PHE* 3.5 17.7 + - - +
554A LEU* 4.1 15.9 - - + +
578A PHE* 3.7 5.6 - - - -
582A GLN* 4.1 12.6 - - - +
586A PHE* 4.0 11.3 - - + -
613A TYR* 3.7 23.6 - - + +
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Residues in contact with GLY 428 (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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413A TYR* 4.4 5.4 - - - -
424A GLN 3.2 6.6 + - - -
425A ASN 3.0 5.4 + - - -
427A ALA* 1.3 77.8 - - - +
429A VAL* 1.3 64.0 + - - +
431A PHE* 3.0 15.4 + - - +
432A PHE* 3.0 11.8 + - - +
554A LEU* 4.9 2.2 - - - -
554B LEU 5.2 0.4 - - - -
555B LEU* 3.4 39.5 - - - +
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Residues in contact with VAL 429 (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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409A ILE* 3.7 28.7 - - + -
413A TYR* 4.0 21.2 - - + -
416A LEU* 4.9 2.9 - - + -
425A ASN 3.1 10.3 + - - +
426A ARG* 3.3 16.6 - - - +
428A GLY* 1.3 73.0 - - - +
430A LEU* 1.3 67.1 + - + +
432A PHE* 2.9 9.1 + - + +
433A LEU* 2.8 42.9 + - + +
493A VAL* 5.6 0.2 - - + -
497A LEU* 3.7 30.3 - - + -
499A LEU* 5.6 2.5 - - + -
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Residues in contact with LEU 430 (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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426A ARG* 3.3 21.0 + - + +
427A ALA* 4.8 0.2 - - - -
428A GLY 3.3 0.6 - - - -
429A VAL* 1.3 83.0 - - + +
431A PHE* 1.3 58.8 + - - +
433A LEU* 3.9 13.2 - - + +
434A THR* 3.2 31.9 + - - +
499A LEU* 4.8 12.6 - - + -
509A MET* 4.6 9.4 - - + -
578A PHE* 3.6 15.5 - - + -
581A LEU* 3.8 52.7 - - + +
582A GLN* 4.5 3.1 - - + +
585A GLU* 4.2 22.7 - - + +
586A PHE* 4.6 7.6 - - + -
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Residues in contact with PHE 431 (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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427A ALA 3.5 12.7 + - - +
428A GLY 3.0 9.6 + - - +
430A LEU* 1.3 78.4 - - - +
432A PHE* 1.3 60.8 + - - +
434A THR* 3.3 9.8 + - - -
435A THR* 2.7 37.9 + - + +
549A MET* 3.6 33.2 - - + -
552A SER* 3.1 31.4 - - - -
554A LEU* 3.6 33.2 - - + -
555A LEU* 5.2 9.6 - - + -
574A PRO* 6.0 0.2 - - + -
578A PHE* 3.5 20.7 - + + -
1002A D6T 5.9 3.6 - + - -
431B PHE* 5.8 6.1 - + - -
549B MET* 5.9 3.4 - - + -
555B LEU* 3.8 17.0 - - + -
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Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 4.2 21.3 - - + -
409A ILE* 3.6 37.9 - - + -
413A TYR* 5.3 3.6 - - - +
428A GLY 3.0 10.5 + - - +
429A VAL* 2.9 12.4 + - + +
431A PHE* 1.3 81.6 - - - +
433A LEU* 1.3 64.7 + - + +
435A THR* 3.4 3.3 + - - -
436A ASN* 3.1 40.8 + - - +
489A PHE* 5.7 0.7 - + - -
1002A D6T 3.9 31.9 - + - -
546B VAL* 4.5 10.3 - - + -
549B MET* 4.7 3.8 - - + -
550B ILE* 4.2 23.8 - - + -
555B LEU* 4.4 21.3 - - + -
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 5.2 3.8 - - + -
429A VAL* 2.8 36.8 + - + +
430A LEU* 3.7 10.7 + - + +
431A PHE 3.4 0.2 - - - -
432A PHE* 1.3 85.7 - - + +
434A THR* 1.3 63.6 + - - +
436A ASN* 3.6 3.9 + - - +
437A GLN* 3.3 26.3 + - - +
489A PHE* 3.6 40.6 - - + -
493A VAL* 4.2 16.2 - - + -
497A LEU* 5.9 0.7 - - + -
499A LEU* 6.1 0.2 - - + -
509A MET* 3.7 29.4 - - + -
513A LEU* 4.4 13.0 - - + +
581A LEU* 4.8 4.5 - - + -
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Residues in contact with THR 434 (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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430A LEU 3.2 20.1 + - - +
431A PHE* 3.3 10.2 + - - -
433A LEU* 1.3 75.0 - - - +
435A THR* 1.3 74.9 + - - +
437A GLN* 3.1 22.5 + - - +
438A CYS* 3.4 12.8 + - - -
512A THR* 6.2 0.2 - - + -
513A LEU* 5.5 1.3 - - + -
516A VAL* 4.8 12.5 - - + +
574A PRO* 4.6 8.0 + - - +
577A GLY* 3.9 6.7 - - - -
578A PHE* 3.6 34.8 - - - +
581A LEU* 3.7 19.7 - - + -
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Residues in contact with THR 435 (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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431A PHE* 2.7 53.7 + - + +
432A PHE* 3.4 7.8 + - - -
434A THR* 1.3 82.9 + - - +
436A ASN* 1.3 64.5 + - - +
438A CYS* 3.3 8.0 + - - +
439A PHE* 3.1 42.2 + - + +
549A MET* 4.6 10.3 - - + -
574A PRO* 4.8 13.7 - - + -
1002A D6T 3.9 16.5 - - - -
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Residues in contact with ASN 436 (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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405A LEU* 3.2 19.4 - - - +
432A PHE* 3.1 27.1 + - + +
433A LEU* 3.8 7.9 - - - +
434A THR 3.2 0.4 - - - -
435A THR* 1.3 76.9 + - - +
437A GLN* 1.3 57.7 + - - +
440A SER* 2.7 39.3 + - - -
489A PHE* 3.2 29.6 - - + -
1002A D6T 3.0 40.2 + - + -
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Residues in contact with GLN 437 (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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433A LEU 3.3 17.0 - - - +
434A THR 3.1 8.9 + - - +
436A ASN* 1.3 81.7 - - - +
438A CYS* 1.3 54.8 + - - +
440A SER* 3.5 6.7 + - - -
441A SER* 2.6 32.9 + - - -
482A ARG* 5.9 0.8 - - - +
485A PRO* 5.1 6.5 - - - +
486A SER* 3.2 27.8 + - - +
489A PHE* 3.3 32.9 - - - -
513A LEU* 4.2 10.5 - - + +
516A VAL* 4.2 26.5 - - + +
517A ALA* 3.6 21.2 - - - +
520A ALA* 4.3 2.5 - - - +
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Residues in contact with CYS 438 (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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434A THR 3.8 12.8 - - - -
435A THR* 3.3 8.6 + - - +
437A GLN* 1.3 77.8 - - - +
439A PHE* 1.3 65.7 + - + +
441A SER* 2.9 21.5 + - - -
442A VAL 3.8 0.7 + - - -
516A VAL* 4.6 9.9 - - - -
520A ALA* 3.8 19.7 - - - -
545A PHE* 3.2 36.3 - - + -
573A ILE* 4.6 3.1 - - - -
574A PRO* 3.6 35.9 - - + -
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Residues in contact with PHE 439 (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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435A THR* 3.1 37.3 + - + +
438A CYS* 1.3 81.0 - - + +
440A SER* 1.3 58.5 + - - +
441A SER 3.2 0.2 - - - -
442A VAL* 3.3 26.2 + - + +
443A SER 5.1 0.2 + - - -
542A THR* 4.9 11.9 - - + -
545A PHE* 3.5 43.5 - + + -
546A VAL* 4.4 17.3 - - + -
549A MET* 4.5 12.1 - - + -
574A PRO* 6.5 0.7 - - + -
1002A D6T 3.3 75.7 - + + +
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Residues in contact with SER 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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398A GLN* 4.9 2.9 + - - -
436A ASN* 2.7 29.7 + - - -
437A GLN* 3.5 11.4 + - - -
439A PHE* 1.3 75.2 - - - +
441A SER* 1.3 57.4 + - - +
442A VAL 3.2 3.6 - - - -
443A SER* 3.2 21.9 + - - -
482A ARG* 4.4 4.7 + - - -
489A PHE* 6.1 0.3 - - - -
1002A D6T 3.8 23.0 - - - -
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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