Contacts of the helix formed by residues 521 - 547 (chain C) in PDB entry 4DAJ
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 521 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C SER 5.5 1.8 - - - +
519C CYS 3.4 9.2 - - - +
520C ILE* 1.3 86.7 - - - +
522C LYS* 1.3 65.8 + - - +
523C THR* 3.1 16.2 + - - +
524C TYR* 3.2 47.4 + - + -
525C TRP* 3.3 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C ILE 4.1 0.4 + - - -
521C PRO* 1.3 72.2 - - - +
523C THR* 1.3 62.2 + - - +
525C TRP* 3.4 11.5 + - - +
526C ASN* 2.6 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C PRO* 4.4 9.5 - - - +
522C LYS* 1.3 81.9 - - - +
524C TYR* 1.3 83.6 + - + +
526C ASN* 3.1 6.1 + - - +
527C LEU* 2.9 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C MET* 3.5 22.9 - - - +
519C CYS 5.0 2.9 - - - -
520C ILE* 4.1 8.7 - - + -
521C PRO* 3.2 38.3 + - + +
523C THR* 1.3 95.7 - - + +
525C TRP* 1.3 62.9 + - - +
527C LEU* 3.4 7.1 + - + +
528C GLY* 2.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 525 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C THR* 6.1 2.5 - - + -
506C TYR* 4.0 31.2 - + + -
509C MET* 3.5 47.3 - - + +
510C VAL* 4.2 14.8 - - + -
513C ASN* 3.6 35.9 - - + -
520C ILE* 3.1 32.4 + - + +
521C PRO 3.3 23.6 + - - -
522C LYS* 3.6 10.1 - - - +
523C THR 3.2 0.4 - - - -
524C TYR* 1.3 75.9 - - - +
526C ASN* 1.3 67.6 + - - +
528C GLY* 3.0 4.7 + - - -
529C TYR* 2.9 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 526 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 3.5 26.0 - - + -
127C TYR* 5.7 4.9 - - - -
128C ILE* 5.8 4.6 - - - +
522C LYS* 2.6 39.2 + - - +
523C THR* 3.6 5.2 + - - +
525C TRP* 1.3 80.1 - - - +
527C LEU* 1.3 58.2 + - - +
529C TYR* 3.0 12.2 - - - +
530C TRP* 2.9 34.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 527 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C THR* 2.9 19.2 + - + +
524C TYR* 3.7 9.0 - - + +
526C ASN* 1.3 73.6 - - - +
528C GLY* 1.3 66.6 + - - +
530C TRP* 2.8 21.5 + - - +
531C LEU* 2.9 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 528 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C PRO* 5.6 1.1 - - - -
506C TYR* 3.9 21.7 - - - +
509C MET* 4.4 5.6 - - - -
524C TYR 2.9 14.8 + - - -
525C TRP 3.5 3.6 - - - -
527C LEU* 1.3 74.3 - - - +
529C TYR* 1.3 61.9 + - - +
531C LEU* 3.2 16.9 + - - +
532C CYS* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 529 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 4.2 29.2 - + + -
143C TRP* 5.2 4.7 - + - -
144C LEU* 4.9 6.9 - - - +
147C ASP* 4.0 5.2 + - - -
148C TYR* 3.7 20.6 + - - -
506C TYR* 3.8 27.6 - + - -
525C TRP* 2.9 11.2 + - + +
526C ASN* 3.0 15.9 - - - +
528C GLY* 1.3 76.1 - - - +
530C TRP* 1.3 57.0 + - - +
532C CYS* 3.2 9.7 + - - +
533C TYR* 3.0 67.0 + + - -
2000C 0HK 3.7 41.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 530 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.8 22.4 - - - -
77C LEU* 4.5 12.3 - - + -
121C MET* 3.6 31.9 - - + -
124C PHE* 3.4 28.1 - + - -
125C THR* 3.1 30.7 - - + -
526C ASN* 2.9 26.9 + - + +
527C LEU* 2.8 13.2 + - - +
529C TYR* 1.3 77.2 - - - +
531C LEU* 1.3 55.9 + - + +
533C TYR* 3.0 42.5 + + + +
534C ILE* 2.8 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C ILE 5.7 0.2 - - - +
502C THR* 3.1 25.3 - - - +
505C PRO* 4.3 23.8 - - + -
527C LEU* 2.9 20.5 + - + +
528C GLY* 3.2 12.1 + - - +
530C TRP* 1.3 69.9 - - + +
532C CYS* 1.3 60.2 + - - +
533C TYR 2.9 4.3 - - - -
534C ILE* 2.9 54.3 + - + +
535C ASN 2.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 532 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.8 3.5 - - - +
503C TRP* 3.1 64.1 + - + +
506C TYR* 3.8 20.4 - - - -
528C GLY 3.0 17.9 + - - +
529C TYR 3.4 9.2 - - - +
531C LEU* 1.3 75.7 - - - +
533C TYR* 1.3 63.5 + - - +
535C ASN* 3.7 4.4 - - - +
536C SER* 4.3 5.9 + - - -
2000C 0HK 3.6 28.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 5.3 0.4 - - + -
81C THR* 5.8 0.2 - - - +
116C ILE* 3.6 30.1 - - + -
120C SER* 3.6 13.7 + - - -
121C MET* 3.9 32.4 - - + +
124C PHE* 4.2 18.7 - + - +
143C TRP* 4.6 0.3 - - - -
147C ASP* 2.7 24.6 + - - -
529C TYR* 3.0 36.7 + + - -
530C TRP* 3.0 48.2 + + + +
531C LEU 2.9 0.8 - - - -
532C CYS* 1.3 78.3 - - - +
534C ILE* 1.3 54.9 + - + +
535C ASN 3.0 4.7 - - - -
536C SER* 3.0 10.2 + - - -
537C THR* 3.0 26.0 + - - -
2000C 0HK 4.0 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.6 26.7 - - + -
502C THR* 3.9 18.6 - - + -
530C TRP* 2.8 25.4 + - + +
531C LEU* 2.9 44.7 + - + +
533C TYR* 1.3 68.5 - - - +
535C ASN* 1.3 60.0 + - - +
537C THR* 3.6 11.9 - - - -
538C VAL* 2.9 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C SER* 5.3 3.3 + - - -
498C ALA* 3.5 3.1 - - - +
499C PHE* 2.9 46.2 - - - +
502C THR* 2.9 22.9 + - - +
503C TRP* 3.5 28.9 + - + +
531C LEU 2.9 5.5 + - - -
532C CYS 3.7 2.7 - - - +
534C ILE* 1.3 78.3 - - - +
536C SER* 1.3 66.4 + - - +
538C VAL* 3.0 6.7 + - - +
539C ASN* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C THR* 4.0 7.4 - - - +
113C ASP* 2.7 43.2 + - - +
116C ILE* 4.0 26.9 - - - +
154C SER* 5.0 3.6 + - - -
503C TRP* 5.7 2.1 + - - -
532C CYS 4.5 2.8 + - - -
533C TYR 3.0 9.6 + - - -
535C ASN* 1.3 82.7 + - - +
537C THR* 1.3 65.0 + - - +
539C ASN* 3.9 5.4 - - - +
540C PRO* 3.4 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.5 36.8 - - + +
80C VAL* 4.2 17.6 - - + +
81C THR* 2.7 31.8 + - - +
121C MET* 4.5 3.3 - - - +
533C TYR 3.0 14.1 + - - -
534C ILE* 3.6 16.9 - - - -
536C SER* 1.3 78.7 - - - +
538C VAL* 1.3 61.3 + - + +
540C PRO* 3.3 16.8 - - - +
541C VAL* 4.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ALA* 4.5 11.7 - - + -
502C THR* 5.4 4.9 - - + -
534C ILE* 2.9 34.8 + - + +
535C ASN* 3.0 5.4 + - - +
537C THR* 1.3 79.6 - - + +
539C ASN* 1.3 66.7 + - - +
540C PRO 3.4 0.2 - - - -
541C VAL* 3.0 16.0 + - + +
542C CYS* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 5.1 7.5 - - - +
113C ASP* 3.2 32.8 + - - +
154C SER* 5.0 5.1 + - - -
158C LEU* 6.0 0.6 - - - +
495C ILE* 3.5 33.2 - - + +
498C ALA* 4.9 1.6 - - - +
535C ASN* 3.0 35.9 + - - +
536C SER* 3.9 3.9 - - - +
538C VAL* 1.3 75.0 - - - +
540C PRO* 1.3 71.5 - - + +
542C CYS* 2.9 11.9 + - - +
543C TYR* 2.9 33.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C THR* 4.7 3.1 - - - +
84C GLY* 4.1 21.5 - - - +
85C ASN* 3.1 31.9 - - - +
88C VAL* 4.2 7.4 - - + +
536C SER 3.4 8.1 - - - +
537C THR* 3.3 18.4 - - - +
538C VAL 3.5 0.4 - - - -
539C ASN* 1.3 94.5 - - + +
541C VAL* 1.3 57.8 + - + +
543C TYR* 2.9 37.8 - - + +
544C ALA* 3.0 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 5.7 8.1 - - + -
537C THR 4.3 11.4 - - - +
538C VAL* 3.0 17.8 + - + +
540C PRO* 1.3 74.8 - - + +
542C CYS* 1.3 66.9 + - - +
544C ALA* 3.2 9.8 + - + +
545C LEU* 2.9 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C THR* 5.4 0.4 - - - -
494C ALA* 4.2 16.8 - - + -
495C ILE* 3.2 27.1 - - + -
498C ALA* 4.1 15.9 - - - -
538C VAL* 2.9 46.3 + - - -
539C ASN* 3.1 7.0 - - - +
541C VAL* 1.3 72.0 - - - +
543C TYR* 1.3 70.0 + - - +
545C LEU* 2.8 19.7 + - - +
546C CYS* 2.9 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 3.8 36.3 - - + -
106C LEU* 2.7 62.8 + - + -
109C LEU* 3.1 22.6 - - + +
110C ALA* 4.4 5.4 - - + -
113C ASP* 5.0 0.4 + - - -
491C THR* 4.4 12.1 + - + -
495C ILE* 3.9 21.5 - - + -
539C ASN* 2.9 17.8 + - + +
540C PRO* 2.9 16.4 - - + +
542C CYS* 1.3 78.0 - - - +
544C ALA* 1.3 64.0 + - - +
545C LEU 3.0 0.3 + - - -
546C CYS* 3.2 8.1 + - - +
547C ASN* 3.2 17.5 + - - +
550C PHE* 4.5 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C PRO 3.0 8.4 + - - +
541C VAL* 3.2 13.0 + - + +
543C TYR* 1.3 79.5 - - - +
545C LEU* 1.3 60.8 + - - +
547C ASN 3.9 9.9 - - - +
548C LYS* 4.8 0.7 + - - -
550C PHE* 4.6 13.2 - - + +
551C ARG* 4.1 21.3 - - + +
554C PHE* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ALA* 5.6 8.3 - - + -
541C VAL* 2.9 13.9 + - + +
542C CYS* 2.8 15.0 + - - +
544C ALA* 1.3 79.6 - - - +
546C CYS* 1.3 65.6 + - - +
547C ASN 5.0 0.5 - - - -
548C LYS* 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C GLN* 5.2 1.4 - - + +
491C THR* 3.1 51.4 - - + +
493C SER* 6.2 1.1 - - - -
494C ALA* 3.6 23.6 - - - -
542C CYS 2.9 11.0 + - - +
543C TYR 4.3 0.7 - - - +
545C LEU* 1.3 84.2 - - - +
547C ASN* 1.3 64.6 + - - +
548C LYS 4.0 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 547 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 4.4 12.7 + - - +
106C LEU* 5.6 2.6 - - - +
490C GLN* 2.9 43.4 + - - +
491C THR* 3.4 5.6 + - - +
543C TYR 3.2 10.9 + - - +
544C ALA 3.9 4.4 - - - +
546C CYS* 1.3 83.5 - - - +
548C LYS* 1.3 63.3 + - - +
549C THR* 2.9 16.3 + - - +
550C PHE* 3.0 21.3 + - + +
551C ARG 3.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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