Contacts of the helix formed by residues 499 - 526 (chain D) in PDB entry 1NKP
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 MET 499 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D ASN* 1.3 67.4 + - - +
501D VAL* 3.2 7.7 + - - +
502D LYS* 3.3 40.7 + - + +
503D ARG* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 500 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D MET* 1.3 79.2 - - - +
501D VAL* 1.3 65.4 + - + +
503D ARG* 2.7 41.4 + - - +
504D ARG* 3.0 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D MET 3.2 5.1 - - - +
500D ASN* 1.3 76.7 - - + +
502D LYS* 1.3 72.2 + - + +
504D ARG* 3.1 8.8 + - - +
505D THR* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 502 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D MET* 3.3 41.9 + - + +
501D VAL* 1.3 82.5 - - + +
503D ARG* 1.3 53.4 + - - +
505D THR* 3.2 8.0 + - - -
506D HIS* 2.8 36.9 + - - +
803J A 5.1 1.8 - - - -
804J G 3.3 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 503 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D MET 2.9 18.1 + - - +
500D ASN* 2.7 37.2 + - - +
502D LYS* 1.3 76.9 - - - +
504D ARG* 1.3 69.6 + - - +
506D HIS* 3.3 7.1 + - - +
507D ASN* 3.0 42.0 + - - +
611H G 5.0 0.4 - - - -
612H T 2.7 56.8 + - + +
613H G 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 504 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D ASN* 3.0 29.7 + - - +
501D VAL* 3.1 9.8 + - - +
503D ARG* 1.3 83.4 - - - +
505D THR* 1.3 67.4 + - - +
507D ASN* 3.2 9.7 + - + +
508D VAL* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D VAL* 2.9 22.0 + - - +
502D LYS* 3.5 10.7 - - - -
504D ARG* 1.3 77.5 - - - +
506D HIS* 1.3 62.4 + - - +
508D VAL* 3.4 5.4 + - + +
509D LEU* 3.0 43.4 + - + +
805J T 5.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D LYS 2.8 17.2 + - - +
503D ARG* 3.5 9.3 - - - +
505D THR* 1.3 77.5 - - - +
507D ASN* 1.3 63.3 + - - +
509D LEU* 4.0 8.4 - - + +
510D GLU* 3.0 26.1 + - + +
612H T 3.6 25.1 + + + +
613H G 2.9 51.5 + + - -
614H C 4.0 5.5 + - - -
806J A 5.9 2.9 - - - -
807J G 3.8 13.1 + - - -
808J C 4.7 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D ARG* 3.0 26.5 + - - +
504D ARG* 3.2 7.8 + - - +
506D HIS* 1.3 78.6 + - - +
508D VAL* 1.3 59.6 + - + +
510D GLU* 3.8 1.7 - - - +
511D ARG* 2.9 29.4 + - - +
514D ARG* 4.7 1.4 + - - -
611H G 3.4 40.6 + - - +
612H T 2.7 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 508 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D ARG* 3.1 25.9 + - + +
505D THR* 3.8 5.8 - - - +
507D ASN* 1.3 75.7 - - + +
509D LEU* 1.3 68.3 + - + +
511D ARG* 3.2 24.2 + - - +
512D GLN* 3.0 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D THR* 3.0 37.1 + - + +
506D HIS* 4.0 8.5 - - + +
508D VAL* 1.3 78.7 - - + +
510D GLU* 1.3 59.2 + - - +
512D GLN* 3.2 21.1 + - + +
513D ARG* 2.8 28.5 + - - +
805J T 5.4 9.4 - - + +
806J A 4.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D HIS* 3.0 23.8 + - + +
507D ASN 3.8 2.0 - - - +
509D LEU* 1.3 78.1 - - - +
511D ARG* 1.3 61.6 + - - +
513D ARG* 2.9 42.5 + - - +
514D ARG* 3.0 56.4 + - - +
612H T 3.2 25.8 - - + +
807J G 4.4 3.8 - - - +
808J C 3.1 23.9 + - - -
809J A 3.5 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D ASN 2.9 18.9 + - - +
508D VAL* 3.6 25.1 - - - +
510D GLU* 1.3 78.1 - - - +
512D GLN* 1.3 66.2 + - + +
514D ARG* 3.4 17.7 + - - +
515D ASN* 3.0 37.7 + - - +
610H C 3.4 35.6 + - - +
611H G 4.5 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508D VAL* 3.0 30.1 + - + +
509D LEU* 3.2 27.7 + - + +
511D ARG* 1.3 81.9 - - + +
513D ARG* 1.3 64.5 + - - +
515D ASN* 3.2 8.1 + - - +
516D GLU* 2.9 24.9 + - - +
519D ARG* 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 513 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D LEU 2.8 14.0 + - - +
510D GLU* 2.9 42.5 + - - +
512D GLN* 1.3 76.5 - - - +
514D ARG* 1.3 69.8 + - - +
516D GLU* 3.2 10.1 + - - +
517D LEU* 3.0 45.2 + - + +
739E ARG* 4.6 6.1 - - - +
807J G 3.7 28.7 - - - +
808J C 3.2 46.7 + - - +
809J A 5.0 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 514 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D ASN 4.7 1.0 + - - -
510D GLU* 3.0 42.3 + - - +
511D ARG* 3.7 25.6 - - - +
512D GLN 3.3 0.2 - - - -
513D ARG* 1.3 82.8 - - - +
515D ASN* 1.3 59.8 + - - +
517D LEU* 3.2 11.7 + - + +
518D LYS* 2.9 27.4 + - - +
609H A 4.2 8.5 - - + -
610H C 2.8 84.1 + - - +
611H G 3.1 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 515 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511D ARG* 3.0 39.5 + - - +
512D GLN* 3.2 7.8 + - - +
514D ARG* 1.3 76.8 - - - +
516D GLU* 1.3 64.7 + - - +
518D LYS* 3.3 23.3 + - - +
519D ARG* 3.1 34.3 + - - +
609H A 5.8 2.0 - - - -
610H C 4.6 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512D GLN 2.9 16.6 + - - +
513D ARG* 3.2 8.8 + - - +
515D ASN* 1.3 74.0 - - - +
517D LEU* 1.3 61.5 + - - +
519D ARG* 3.2 33.4 + - - +
520D SER* 3.0 34.4 + - - +
740E ALA* 4.0 20.3 - - + +
744E ASP* 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D ARG* 3.0 40.8 + - + +
514D ARG* 3.2 12.8 + - + +
516D GLU* 1.3 73.6 - - - +
518D LYS* 1.3 61.3 + - - +
520D SER* 3.2 4.6 + - - -
521D PHE* 2.9 52.2 + - + -
739E ARG* 4.0 22.9 - - + +
740E ALA* 3.6 39.7 - - + +
743E LEU* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 518 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D ARG 2.9 12.8 + - - +
515D ASN* 3.4 27.1 - - - +
517D LEU* 1.3 78.8 - - - +
519D ARG* 1.3 61.3 + - + +
521D PHE* 3.3 8.3 + - - +
522D PHE* 2.8 66.4 + - + -
539D LYS* 5.7 5.4 - - - +
609H A 3.2 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 519 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512D GLN 4.8 2.0 + - - -
515D ASN* 3.1 15.6 + - - +
516D GLU* 3.2 43.9 + - - +
518D LYS* 1.3 77.7 - - + +
520D SER* 1.3 63.0 + - - +
522D PHE* 3.3 13.8 + - + +
523D ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 520 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D GLU* 3.0 18.4 + - - +
517D LEU* 3.2 11.0 + - - -
519D ARG* 1.3 73.9 - - - +
521D PHE* 1.3 65.0 - - - +
523D ALA* 3.3 6.7 + - - +
524D LEU* 3.1 22.9 + - - +
740E ALA* 4.5 8.7 + - - +
743E LEU* 3.7 21.5 - - - +
744E ASP* 3.1 31.3 + - - +
747E THR* 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 521 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D LEU* 2.9 43.1 + - + -
518D LYS* 3.3 10.5 + - - +
520D SER* 1.3 75.2 - - - +
522D PHE* 1.3 65.0 + - + +
524D LEU* 3.3 5.5 + - - +
525D ARG* 2.9 30.5 + - - +
539D LYS* 3.5 59.2 - - + +
542D ILE* 4.1 26.7 - - + +
543D LEU* 4.0 9.4 - - + -
718E ILE* 5.7 1.1 - - + -
722E PHE* 3.8 25.6 - + - -
743E LEU* 3.7 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 522 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518D LYS* 2.8 62.3 + - + -
519D ARG* 3.4 15.0 - - + +
520D SER 3.2 0.2 - - - -
521D PHE* 1.3 84.6 - - + +
523D ALA* 1.3 62.5 + - - +
525D ARG* 3.3 37.5 + - - +
526D ASP* 3.0 31.2 + - - +
542D ILE* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 523 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519D ARG 3.0 12.9 + - - +
520D SER* 3.3 10.7 + - - +
522D PHE* 1.3 76.4 - - - +
524D LEU* 1.3 63.1 + - - +
526D ASP* 3.5 9.8 + - - +
527D GLN* 3.4 22.9 - - - +
744E ASP* 5.6 2.5 - - - +
747E THR* 3.7 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 524 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520D SER 3.1 12.2 + - - +
521D PHE* 3.6 7.4 - - - +
523D ALA* 1.3 75.1 - - - +
525D ARG* 1.3 66.4 + - - +
527D GLN* 3.0 13.6 + - + +
528D ILE* 3.4 13.9 - - + +
542D ILE* 3.9 18.8 - - + +
543D LEU* 4.8 1.1 - - + -
546D ALA* 3.9 19.7 - - + -
725E LEU* 4.0 10.8 - - + -
743E LEU* 3.6 31.9 - - + +
746E ALA* 4.1 2.9 - - + -
747E THR* 3.2 30.7 + - - +
750E ILE* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D PHE 2.9 16.3 + - - +
522D PHE* 3.6 45.2 - - - +
524D LEU* 1.3 78.4 - - - +
526D ASP* 1.3 82.2 + - - +
527D GLN 3.1 1.2 + - - -
528D ILE* 3.1 26.5 + - - +
531D LEU* 3.7 27.0 - - + +
534D ASN* 5.1 2.2 - - - +
537D ALA* 4.1 20.3 + - + +
542D ILE* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D PHE 3.0 23.6 + - - +
523D ALA* 3.8 8.1 - - - +
524D LEU 3.2 0.4 - - - -
525D ARG* 1.3 100.4 + - - +
527D GLN* 1.3 68.6 + - - +
528D ILE 3.4 1.8 + - - -
532D GLU* 4.9 8.4 - - - +
----------------------------------------------------------
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