Contacts of the helix formed by residues 510 - 536 (chain B) in PDB entry 5NC5
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 LYS 510 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B GLY 4.0 17.5 - - - +
509B LYS* 1.3 80.6 - - - +
511B GLY* 1.3 72.7 + - - +
512B PHE 3.5 0.5 + - - -
513B PHE* 3.7 3.6 + - - +
514B GLY 3.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LYS* 1.3 81.2 - - - +
512B PHE* 1.3 64.3 + - - -
513B PHE 3.2 0.5 + - - -
514B GLY* 3.9 0.2 - - - -
515B TRP* 3.2 18.9 + - - +
518B ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.9 24.7 - - + -
510B LYS 3.5 0.4 + - - -
511B GLY* 1.3 70.8 - - - -
513B PHE* 1.3 76.7 + + + +
515B TRP* 3.2 32.3 + + + +
516B PHE* 2.7 45.5 + + + +
16H PRO* 6.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B TYR* 3.8 39.7 - + - -
357B LEU* 4.5 13.5 - - + -
360B GLN* 3.4 50.9 - - + +
509B LYS* 4.1 11.9 - - + -
510B LYS 3.7 4.1 + - - +
511B GLY 3.2 1.0 + - - -
512B PHE* 1.3 100.0 - + + +
514B GLY* 1.3 62.3 + - - +
516B PHE* 3.5 3.0 - - + +
517B ASN* 2.7 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLY 3.7 15.5 - - - -
507B GLU 4.1 0.4 - - - +
509B LYS* 3.4 27.0 - - - +
510B LYS 3.6 5.3 + - - -
511B GLY 3.4 4.0 + - - -
513B PHE* 1.3 78.8 - - - +
515B TRP* 1.3 60.6 + - - +
517B ASN* 3.2 0.7 + - - +
518B ARG* 2.9 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B GLY 3.2 12.4 + - - +
512B PHE* 3.2 36.5 + + + +
513B PHE 3.2 0.4 - - - -
514B GLY* 1.3 75.5 - - - +
516B PHE* 1.3 84.1 + + - +
518B ARG* 3.5 26.1 - - - +
519B MET* 2.8 73.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.8 52.9 - - + -
358B PHE* 4.2 22.2 - + - -
360B GLN* 4.3 1.1 - - - +
512B PHE* 2.7 42.5 + + + +
513B PHE* 3.5 8.3 - - + +
515B TRP* 1.3 89.1 - + + +
517B ASN* 1.3 68.3 + - - +
519B MET* 3.4 13.9 + - + +
520B PHE* 2.8 39.5 + + + +
19H MET* 4.1 26.2 - - + -
23H LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PHE 4.6 3.5 - - - +
360B GLN* 3.0 35.7 + - - -
505B HIS 3.8 13.6 - - - +
506B GLY* 2.8 41.8 + - - +
507B GLU* 4.1 2.2 - - - +
509B LYS* 4.1 1.2 - - - +
513B PHE 2.7 24.5 + - - +
514B GLY 3.6 1.1 - - - +
516B PHE* 1.3 75.7 - - - +
518B ARG* 1.3 61.5 + - - +
520B PHE* 3.2 4.0 + - - +
521B GLU* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B GLU* 3.3 52.6 + - + +
509B LYS 4.2 5.7 + - - -
511B GLY 5.5 0.4 + - - -
514B GLY* 2.9 26.6 + - - +
515B TRP* 3.5 34.1 - - - +
517B ASN* 1.3 75.2 - - - +
519B MET* 1.3 64.3 + - - +
521B GLU* 3.9 1.4 - - - +
522B LYS* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B TRP* 2.8 60.7 + - + +
516B PHE* 3.7 16.6 - - + +
518B ARG* 1.3 78.0 - - - +
520B PHE* 1.3 64.9 + - - +
522B LYS* 3.5 13.7 + - - +
523B SER* 3.0 36.8 + - - +
19H MET* 6.0 0.2 - - + -
20H ALA* 6.3 1.1 - - - -
23H LEU* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PHE* 4.2 21.8 - + - -
516B PHE* 2.8 33.7 + + + +
517B ASN* 3.2 5.1 + - - +
519B MET* 1.3 76.7 - - - +
521B GLU* 1.3 65.7 + - + +
523B SER* 3.2 5.1 + - - +
524B THR* 2.8 53.4 + - + -
972B LEU* 3.9 14.8 - - + -
973B ARG* 4.2 32.5 - - + -
976B LEU* 3.8 23.8 - - + -
23H LEU* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B HIS* 3.7 33.8 + - + +
507B GLU* 3.7 39.0 - - + +
517B ASN 2.9 16.7 + - - +
518B ARG 3.9 0.4 - - - +
520B PHE* 1.3 79.8 - - + +
522B LYS* 1.3 63.8 + - - +
524B THR* 3.3 9.2 + - - -
525B HIS* 3.2 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B GLU* 6.1 0.4 - - - +
518B ARG* 3.0 27.8 + - + +
519B MET* 3.7 12.3 - - - +
521B GLU* 1.3 76.7 - - - +
523B SER* 1.3 62.4 + - - +
525B HIS* 3.0 21.7 + - - +
526B HIS* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B MET* 3.0 28.1 + - - +
520B PHE* 3.2 11.9 + - - -
522B LYS* 1.3 76.8 - - - +
524B THR* 1.3 61.4 + - - +
526B HIS* 3.5 8.8 + - - +
527B TYR* 3.1 22.7 + - - +
972B LEU* 5.3 1.7 - - - +
23H LEU* 4.5 21.5 - - - +
26H ILE* 6.1 1.5 - - - +
27H TYR* 6.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B PHE* 2.8 42.5 + - + -
521B GLU* 3.6 9.2 - - - -
522B LYS 3.2 0.2 - - - -
523B SER* 1.3 75.6 - - - +
525B HIS* 1.4 53.9 + - - +
527B TYR* 3.4 4.4 + - + +
528B THR* 2.7 36.6 + - - +
969B ARG* 4.2 31.9 - - + +
972B LEU* 3.8 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B GLU* 3.2 34.3 + - + -
522B LYS* 3.0 14.2 + - + +
524B THR* 1.4 71.2 - - - +
526B HIS* 1.3 68.2 + - - +
528B THR* 3.0 8.8 + - - -
529B ASP* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS 3.1 8.9 + - - +
523B SER* 3.7 11.0 - - - +
524B THR 3.4 0.2 - - - -
525B HIS* 1.3 79.7 - - - +
527B TYR* 1.3 65.2 + - - +
529B ASP* 3.3 8.1 + - + +
530B SER* 2.8 23.3 + - - -
26H ILE 5.1 0.4 + - - -
27H TYR* 3.2 55.7 + + + -
30H GLY* 4.0 4.7 - - - -
31H GLU* 3.3 30.1 + - - -
34H ASN* 3.7 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B SER 3.1 14.0 + - - +
524B THR* 3.7 9.6 - - + +
525B HIS 3.3 0.2 - - - -
526B HIS* 1.3 80.8 + - - +
528B THR* 1.3 62.3 + - + +
530B SER* 3.0 8.6 + - - -
531B VAL* 2.8 43.1 + - + +
968B VAL* 2.9 52.2 + - + +
969B ARG* 5.0 0.4 - - - -
972B LEU* 3.8 26.4 - - + -
1019B ILE* 2.9 51.0 + - + +
1020B PHE* 3.7 21.8 - + + -
26H ILE* 5.2 12.6 - - + +
30H GLY* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B THR* 2.7 20.4 + - - +
525B HIS* 3.0 18.4 + - - -
527B TYR* 1.3 83.2 - - + +
529B ASP* 1.3 55.8 + - - +
531B VAL* 3.2 6.6 + - - +
532B GLY* 2.7 31.9 + - - -
965B LEU* 3.8 24.4 - - + +
968B VAL* 4.3 6.5 - - + -
969B ARG* 4.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B HIS* 2.8 38.4 + - - +
526B HIS* 3.6 6.3 - - - +
528B THR* 1.3 72.2 + - - +
530B SER* 1.3 64.2 + - - +
532B GLY* 3.2 2.9 + - - -
533B GLY* 3.0 18.7 + - - -
536B ARG* 5.0 2.9 + - - -
34H ASN* 4.5 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B HIS* 2.8 15.8 + - - -
527B TYR* 3.3 9.0 - - - -
529B ASP* 1.3 78.7 - - - +
531B VAL* 1.3 56.6 + - - +
533B GLY* 3.2 3.1 + - - -
534B ILE* 2.9 30.2 + - - +
1020B PHE* 4.2 7.4 - - - -
30H GLY* 2.9 39.7 + - - -
33H PHE* 4.0 8.5 - - - +
34H ASN* 3.5 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 2.8 55.5 + - + +
528B THR* 3.5 8.3 - - - +
530B SER* 1.3 71.6 - - - +
532B GLY* 1.3 61.8 + - - +
534B ILE* 3.2 9.4 + - + +
535B LEU* 2.9 35.1 + - + +
964B THR* 5.2 0.2 - - + -
965B LEU* 3.4 21.5 - - + -
968B VAL* 4.4 5.4 - - + -
1019B ILE 4.2 4.7 - - - +
1020B PHE* 4.0 13.9 - - + +
1023B PRO* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B THR 2.7 18.2 + - - -
529B ASP* 3.2 4.7 + - - -
531B VAL* 1.3 73.5 - - - +
533B GLY* 1.3 61.2 + - - +
535B LEU* 3.3 7.1 + - - +
536B ARG* 3.2 33.1 + - - +
961B ILE* 5.8 1.2 - - - +
965B LEU* 4.0 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASP 3.0 12.9 + - - -
530B SER* 3.2 3.3 + - - -
532B GLY* 1.3 71.7 - - - +
534B ILE* 1.3 66.7 + - - +
536B ARG* 3.1 35.9 + - - +
537B SER* 3.2 13.6 + - - -
541B TYR* 5.5 0.4 - - - -
33H PHE 5.8 0.9 - - - -
34H ASN* 5.2 5.6 - - - -
37H SER* 5.1 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B SER 2.9 19.6 + - - +
531B VAL* 3.5 9.6 - - + +
533B GLY* 1.3 75.4 - - - +
535B LEU* 1.3 62.0 + - + +
537B SER 3.2 22.5 + - - +
538B THR* 3.8 2.6 + - - +
541B TYR* 3.5 43.8 - - + +
1020B PHE* 3.7 39.5 - - + +
1024B VAL* 3.5 30.3 - - + -
33H PHE* 3.9 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B VAL* 2.9 35.9 + - + +
532B GLY* 3.7 5.8 - - - +
533B GLY 3.2 0.4 - - - -
534B ILE* 1.3 77.3 - - + +
536B ARG* 1.3 61.1 + - - +
537B SER 3.2 1.1 + - - -
538B THR* 3.5 17.8 - - + +
961B ILE* 4.1 31.6 - - + +
964B THR* 3.9 17.9 - - + -
965B LEU* 4.0 12.6 - - + -
1023B PRO* 3.3 33.0 - - + +
1024B VAL* 4.0 9.4 - - + +
1027B VAL* 3.5 19.7 - - + -
1031B ARG* 4.0 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASP 5.0 2.6 + - - -
532B GLY* 3.2 11.4 + - - +
533B GLY* 3.1 43.4 + - - +
535B LEU* 1.3 76.8 - - - +
537B SER* 1.3 57.0 + - - +
538B THR* 4.1 0.7 - - - -
1031B ARG* 5.9 2.0 - - - +
----------------------------------------------------------
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