Contacts of the helix formed by residues 509 - 523 (chain M) in PDB entry 4K4I
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 SER 509 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420M ARG* 3.6 26.4 - - - +
507M THR 3.7 0.4 + - - -
508M GLY* 1.3 76.6 + - - -
510M ALA* 1.3 59.6 + - - +
511M HIS* 3.3 10.3 + - - +
512M PHE* 3.0 10.3 + - - +
513M ASN* 2.9 25.5 + - - +
573M ARG 3.0 13.1 + - - -
574M ASP* 2.8 26.2 + - - -
601M 1RY 3.4 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509M SER* 1.3 72.8 - - - +
511M HIS* 1.3 59.4 + - + +
513M ASN* 3.3 4.0 + - - +
514M ARG* 3.0 49.4 + - - +
601M 1RY 2.8 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 511 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M LEU* 4.7 3.3 - - + +
280M ALA* 4.0 35.6 + - + +
281M LYS* 4.3 19.5 + - + +
284M ASN* 3.3 27.6 + - - +
509M SER* 3.1 13.2 + - - +
510M ALA* 1.3 75.8 - - + +
512M PHE* 1.3 64.0 + - - +
514M ARG* 3.2 31.0 + - - +
515M SER* 2.8 30.0 + - - +
574M ASP 4.1 6.1 - - - +
575M TRP* 4.7 6.1 - - + -
601M 1RY 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 512 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504M LEU* 4.5 3.6 - - + -
508M GLY 3.8 12.8 - - - -
509M SER* 3.0 11.3 + - - +
511M HIS* 1.3 80.4 - - - +
513M ASN* 1.3 61.3 + - - +
515M SER* 3.3 5.8 + - - -
516M MET* 3.0 59.3 + - + +
560M PHE* 3.9 20.4 - + - -
568M ARG* 3.9 8.7 - - - -
572M GLU 4.5 0.4 - - - -
573M ARG* 3.2 59.5 - - + +
574M ASP 4.3 0.6 + - - -
575M TRP* 3.9 17.7 - - - +
576M LEU* 3.2 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 513 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504M LEU* 3.6 12.5 - - - +
505M TYR* 3.0 35.7 + - + +
508M GLY* 3.5 12.2 - - - +
509M SER 2.9 15.3 + - - +
510M ALA 3.6 4.3 - - - +
512M PHE* 1.3 80.3 - - - +
514M ARG* 1.3 60.5 + - - +
516M MET* 3.0 7.4 + - - +
517M ARG* 2.8 42.0 + - + +
527M LEU* 6.0 1.8 - - + -
601M 1RY 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 514 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M LEU* 3.9 37.3 - - - +
281M LYS* 6.0 9.0 - - - +
510M ALA* 3.0 32.8 + - - +
511M HIS* 3.2 39.6 + - - +
513M ASN* 1.3 75.8 - - - +
515M SER* 1.3 58.7 + - - +
517M ARG* 3.3 17.0 + - - +
518M ALA* 3.0 27.9 + - - +
601M 1RY 3.8 27.7 + - - -
4N C 4.5 6.5 - - - +
5N G 3.4 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 515 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M LYS* 4.4 15.2 + - - -
511M HIS* 2.8 19.0 + - - +
512M PHE* 3.7 5.1 - - - -
513M ASN 3.2 0.2 - - - -
514M ARG* 1.3 75.8 - - - +
516M MET* 1.3 58.2 + - - +
518M ALA* 3.4 7.7 + - - +
519M LEU* 3.0 28.1 + - - +
575M TRP* 6.0 0.2 - - - +
576M LEU* 3.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 516 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504M LEU* 3.7 34.8 - - + -
512M PHE* 3.0 47.0 + - + +
513M ASN* 3.0 6.7 + - - +
515M SER* 1.3 75.4 - - - +
517M ARG* 1.3 65.4 + - - +
519M LEU* 3.3 6.2 + - - +
520M ALA* 2.9 23.2 + - - +
527M LEU* 3.6 20.0 - - + -
559M VAL* 4.8 0.7 - - + -
560M PHE* 3.9 14.6 - - + -
563M LEU* 4.4 17.7 - - + +
565M LEU* 3.8 25.6 - - - -
576M LEU* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 517 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M TYR* 4.0 8.1 - - - -
513M ASN* 2.8 30.3 + - + +
514M ARG* 3.5 20.8 - - - +
516M MET* 1.3 72.1 - - - +
518M ALA* 1.3 53.9 + - - +
520M ALA* 3.3 8.3 + - - +
521M LYS* 2.8 34.1 + - - +
525M MET 4.9 0.2 - - - +
526M SER* 5.7 0.3 - - - -
527M LEU* 3.5 34.4 + - + +
601M 1RY 3.0 42.4 + - - -
5N G 3.0 83.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 518 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514M ARG 3.0 16.6 + - - +
515M SER* 3.7 8.3 - - - +
516M MET 3.2 0.2 - - - -
517M ARG* 1.3 74.0 - - - +
519M LEU* 1.3 66.3 + - - +
521M LYS* 3.2 10.2 + - - +
522M THR* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515M SER 3.0 16.2 + - - +
516M MET* 3.6 5.6 - - - +
518M ALA* 1.3 74.4 - - - +
520M ALA* 1.3 66.1 + - - +
522M THR* 2.8 31.3 + - + +
523M LYS* 3.3 24.6 + - - +
563M LEU* 3.9 29.4 - - + +
565M LEU* 3.6 35.4 - - + -
576M LEU* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516M MET 2.9 13.9 + - - +
517M ARG* 3.4 9.9 - - - +
519M LEU* 1.3 78.4 - - - +
521M LYS* 1.3 63.9 + - - +
523M LYS* 3.0 9.0 + - - +
525M MET* 2.8 42.1 + - + +
526M SER* 4.3 0.9 - - - -
527M LEU* 4.2 18.4 - - + +
532M LEU* 4.5 0.2 - - + -
563M LEU* 3.5 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 521 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517M ARG 2.8 19.8 + - - +
518M ALA* 3.5 10.3 - - - +
519M LEU 3.1 0.6 - - - -
520M ALA* 1.3 74.1 - - - +
522M THR* 1.3 62.1 + - + +
524M GLY* 3.2 12.5 + - - -
525M MET 3.6 9.6 - - - +
3N G 3.4 14.8 + - - -
4N C 2.7 34.6 + - - +
5N G 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 522 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518M ALA* 3.2 15.2 + - + +
519M LEU* 2.8 27.3 + - + +
521M LYS* 1.3 77.1 - - + +
523M LYS* 1.3 67.8 + - - +
524M GLY 3.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 523 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519M LEU* 3.6 28.3 - - - +
520M ALA* 3.0 8.0 + - - +
522M THR* 1.3 84.1 - - - +
524M GLY* 1.3 61.9 + - - +
525M MET* 3.3 22.2 - - + +
562M LEU 5.0 3.6 - - - +
563M LEU* 3.0 37.4 + - + +
564M GLY* 4.2 8.9 + - - -
----------------------------------------------------------
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