Contacts of the helix formed by residues 506 - 524 (chain C) in PDB entry 5DO7
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 506 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASN* 4.5 0.2 + - - -
426C PHE* 3.9 26.9 - - + -
427C VAL* 4.4 1.1 - - - +
430C THR* 3.9 26.8 - - + +
479C THR* 3.3 18.8 - - + +
482C PHE* 3.5 29.8 - - + -
502C PHE* 3.5 37.2 + - + +
503C SER 4.1 0.4 + - - -
504C ALA 3.3 0.4 - - - -
505C ALA* 1.3 80.1 - - - +
507C LEU* 1.3 62.2 + - - +
508C ALA 3.4 0.7 - - - -
509C PRO* 3.7 4.5 - - - -
510C HIS* 3.7 15.9 + - - +
571C CYS* 4.5 4.7 - - - -
575C LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU* 5.2 1.6 - - + +
475C SER* 3.9 4.7 - - - -
476C VAL* 3.6 44.2 - - + +
479C THR* 3.3 24.8 - - + +
503C SER 3.7 13.2 + - - +
504C ALA* 3.5 1.7 + - - -
505C ALA 3.4 0.8 - - - -
506C LEU* 1.3 77.7 - - - +
508C ALA* 1.3 69.3 + - - +
509C PRO 3.5 0.2 - - - -
510C HIS* 3.5 2.6 + - + +
511C LEU* 3.2 38.4 + - + +
628C TYR* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C ALA 3.7 2.7 + - - +
507C LEU* 1.3 75.7 - - - +
509C PRO* 1.3 74.9 - - + +
511C LEU* 2.8 9.9 + - - +
512C ILE* 2.8 27.1 + - + +
627C LEU* 3.7 34.8 - - + +
628C TYR* 3.8 29.6 + - + -
631C ILE* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C VAL* 4.8 4.3 - - + +
430C THR* 3.3 25.8 - - - +
431C PRO* 3.6 19.3 - - + +
505C ALA 2.9 29.2 - - - +
506C LEU* 3.7 8.1 - - + -
508C ALA* 1.3 86.2 - - + +
510C HIS* 1.3 52.6 + - - +
512C ILE* 2.8 32.4 + - + +
513C GLY 2.8 16.1 + - - -
567C PHE* 4.6 9.9 - - + -
571C CYS* 4.1 19.3 - - + -
627C LEU* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG 4.2 10.8 + - - -
392C GLN* 4.3 2.7 - - - -
393C ASN* 3.1 30.7 + - + +
430C THR 2.6 17.4 + - - +
431C PRO* 4.5 0.7 - - - -
433C THR* 2.6 38.0 + - - -
434C GLY* 3.6 13.7 - - - +
437C ASN* 3.4 17.0 + - - -
475C SER* 2.9 36.1 + - - -
478C ALA* 4.5 2.2 - - + -
479C THR* 4.7 2.9 - - - +
506C LEU 3.7 17.4 + - - +
507C LEU* 3.5 6.7 + - - +
508C ALA 3.3 0.4 - - - -
509C PRO* 1.3 74.6 - - - +
511C LEU* 1.3 57.9 + - - +
513C GLY 4.4 0.9 - - - -
514C GLU* 3.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C VAL* 4.1 12.8 - - + -
472C LEU* 4.4 22.7 - - + -
475C SER* 4.0 21.3 - - - -
507C LEU* 3.2 38.7 + - + +
508C ALA* 2.8 11.1 + - - +
510C HIS* 1.3 72.1 - - - +
512C ILE* 1.3 68.0 + - - +
513C GLY 3.1 1.3 - - - -
514C GLU* 2.8 15.2 + - - +
515C PHE* 2.8 44.8 + - + -
628C TYR* 5.1 0.9 - - + -
631C ILE* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ALA 2.8 20.3 + - - +
509C PRO* 2.8 9.8 + - + +
511C LEU* 1.3 74.7 - - - +
513C GLY* 1.3 58.0 + - - +
515C PHE* 4.7 0.7 - - - +
516C LEU* 2.8 41.3 + - + +
567C PHE* 3.6 61.9 - - + -
627C LEU* 4.0 19.1 - - + +
630C PHE* 4.1 5.2 - - + -
631C ILE* 3.3 22.4 - - + -
634C LEU* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 513 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C PRO* 3.5 29.5 - - - +
434C GLY* 4.2 0.7 - - - -
435C MET 3.9 4.3 - - - -
509C PRO 2.8 11.8 + - - -
512C ILE* 1.3 76.6 - - - +
514C GLU* 1.3 58.8 + - - +
516C LEU* 3.9 4.4 - - - +
517C THR* 2.4 38.8 + - - -
534C VAL* 5.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG* 2.8 17.1 + - - -
434C GLY* 3.1 28.0 - - - +
437C ASN* 2.9 32.4 + - - +
438C ALA* 3.2 6.4 + - + +
467C TYR* 2.3 44.0 + - + -
471C VAL* 3.8 16.3 - - + +
510C HIS 3.8 7.2 - - - +
511C LEU* 2.8 20.1 + - - +
513C GLY* 1.3 72.5 - - - +
515C PHE* 1.3 63.5 + - + +
517C THR* 3.4 2.6 - - - -
518C LEU* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C MET* 5.2 0.2 - - - +
468C ALA* 3.4 47.1 - - + -
471C VAL* 3.6 18.8 - - + -
472C LEU* 4.9 8.3 - - + -
511C LEU* 2.8 51.7 + - + +
512C ILE 4.4 0.7 - - - +
514C GLU* 1.3 74.3 - - + +
516C LEU* 1.3 62.6 + - - +
518C LEU* 3.1 11.6 - - + +
519C VAL* 2.8 32.2 + - - +
631C ILE* 4.1 31.4 - - + -
634C LEU* 3.9 18.2 - - + -
635C VAL* 4.5 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PHE* 4.9 13.5 - - + -
512C ILE* 2.8 28.7 + - + +
513C GLY* 3.9 3.1 - - - +
515C PHE* 1.3 70.0 - - - +
517C THR* 1.3 66.9 + - - +
519C VAL* 2.8 18.0 + - + +
520C LEU* 2.8 40.3 + - + +
534C VAL* 4.1 16.8 - - + -
537C LEU* 3.7 31.0 - - + -
538C SER* 6.2 1.3 - - - -
567C PHE* 6.1 4.3 - - + -
634C LEU* 3.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C MET* 3.0 34.3 - - + +
438C ALA* 3.7 12.8 - - + -
439C VAL* 3.9 5.4 - - + +
513C GLY 2.4 27.8 + - - -
514C GLU 3.4 3.8 - - - -
516C LEU* 1.3 71.9 - - - +
518C LEU* 1.3 56.9 + - - +
520C LEU* 3.4 3.3 + - - +
521C LEU* 2.8 51.9 + - + +
530C VAL* 3.7 15.0 - - + +
534C VAL* 3.5 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA* 4.7 2.4 - - + +
442C PHE* 3.6 37.7 - - + -
464C MET* 3.3 45.5 - - + +
467C TYR* 3.5 30.1 - - + -
468C ALA* 3.8 15.9 - - + -
514C GLU 2.8 13.0 + - - +
515C PHE* 3.1 18.2 - - + +
517C THR* 1.3 72.5 - - - +
519C VAL* 1.3 70.6 + - - +
521C LEU* 2.7 18.1 + - - +
522C GLY 3.2 6.4 + - - -
635C VAL* 5.4 0.2 - - + -
642C PHE* 4.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PHE* 5.0 2.7 - - + -
464C MET* 4.8 1.6 - - + -
515C PHE 2.8 17.2 + - - +
516C LEU* 2.8 14.6 + - + +
518C LEU* 1.3 74.7 - - - +
520C LEU* 1.3 73.4 + - + +
522C GLY* 2.8 14.7 + - - -
523C ILE* 3.5 12.4 + - + +
634C LEU* 3.0 33.7 - - + +
637C LEU* 3.8 27.6 - - + -
638C GLY* 3.6 18.2 - - - +
641C VAL* 3.9 20.0 - - + +
642C PHE* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A ILE* 4.3 35.4 - - + -
565A PHE* 4.9 3.6 - - + -
516C LEU* 2.8 38.3 + - + +
517C THR* 3.7 8.1 - - - +
519C VAL* 1.3 85.9 - - + +
521C LEU* 1.3 57.0 + - - +
523C ILE* 2.8 10.4 + - + +
524C VAL* 2.8 30.6 + - + +
530C VAL* 3.8 13.9 - - + -
533C VAL* 3.6 31.6 - - + -
534C VAL* 3.9 12.6 - - + -
537C LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA* 4.5 4.3 - - + -
439C VAL* 3.8 19.3 - - - +
442C PHE* 4.5 21.5 - - + -
443C PRO* 5.0 4.3 - - + -
446C ARG* 3.3 46.5 + - - +
517C THR* 2.8 40.5 + - + +
518C LEU* 2.7 17.2 + - - +
520C LEU* 1.3 70.8 - - - +
522C GLY* 1.3 55.0 + - - -
524C VAL 3.2 13.8 - - - +
525C GLN* 5.3 0.2 - - - +
527C PRO* 3.9 30.3 - - + -
530C VAL* 3.9 13.0 - - + -
642C PHE* 4.5 1.3 - - - -
645C ARG* 4.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU 3.2 3.6 + - - -
519C VAL 2.8 10.9 + - - -
521C LEU* 1.3 78.5 - - - +
523C ILE* 1.3 61.7 + - - +
524C VAL 4.4 0.2 - - - -
525C GLN* 4.7 2.3 - - - +
641C VAL* 3.8 9.4 - - - -
642C PHE* 3.5 28.4 - - - -
645C ARG* 3.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LYS* 4.2 24.9 + - + +
561A ILE* 4.4 28.5 - - + -
564A TYR* 3.4 48.7 - - + +
565A PHE* 5.1 2.5 - - + -
519C VAL* 4.1 15.9 - - + +
520C LEU* 2.8 11.1 + - + +
522C GLY* 1.3 79.1 - - - +
524C VAL* 1.3 64.1 + - + +
525C GLN* 3.8 12.3 - - - +
641C VAL* 3.4 37.0 - - + -
645C ARG* 5.6 0.4 - - - -
648C LEU* 5.3 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ILE* 3.9 21.5 - - + +
560A LYS* 6.2 0.9 - - + +
561A ILE* 3.7 35.4 - - + -
446C ARG* 3.7 2.6 + - - -
520C LEU* 2.8 15.1 + - + +
521C LEU* 3.2 22.7 - - - +
523C ILE* 1.3 78.1 - - + +
525C GLN* 1.3 62.3 + - - +
526C ASN* 3.7 11.6 + - + +
529C ILE* 3.9 21.8 - - + -
530C VAL* 3.7 23.6 - - + +
533C VAL* 6.3 0.2 - - + -
----------------------------------------------------------
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