Contacts of the helix formed by residues 432 - 446 (chain E) in PDB entry 1K9A
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 THR 432 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E GLU* 3.6 18.0 + - - +
365E THR* 6.1 0.2 - - - -
366E LYS* 4.2 8.9 + - - +
369E VAL* 5.0 1.1 - - - -
431E PRO* 1.3 77.1 - - - +
433E PHE* 1.3 59.0 + - - +
434E LEU* 2.9 19.1 - - + +
435E GLN* 2.9 47.7 + - + +
436E LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E CYS* 3.6 15.0 - - - +
302E MET* 3.3 53.2 - - + -
303E GLU* 3.7 20.2 - - + +
306E GLU* 3.1 26.7 + - - +
365E THR* 3.8 17.0 - - + -
368E ASP* 3.8 18.4 - - + -
369E VAL* 3.7 30.4 - - + +
372E PHE* 3.8 15.9 - + + -
432E THR* 1.3 73.7 - - - +
434E LEU* 1.3 56.5 + - - +
436E LEU* 3.1 26.8 + - + +
437E ARG* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E GLU* 3.3 31.3 - - + +
306E GLU* 4.3 1.4 + - - -
432E THR* 2.9 10.5 - - + +
433E PHE* 1.3 78.8 - - - +
435E GLN* 1.3 73.6 + - + +
437E ARG* 2.9 32.4 + - - +
438E GLU* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E LYS* 5.3 0.5 + - - -
430E ARG 4.9 0.2 - - - +
431E PRO* 3.6 13.7 - - + +
432E THR* 2.9 48.9 + - + +
434E LEU* 1.3 86.6 - - + +
436E LEU* 1.3 56.4 + - - +
438E GLU* 3.9 6.2 - - - +
439E GLN* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E CYS* 3.7 10.1 - - - -
369E VAL* 4.1 17.5 - - + -
372E PHE* 3.7 20.2 - - + -
418E VAL* 3.5 31.6 - - + -
422E CYS* 3.8 7.0 - - - -
431E PRO* 3.7 20.9 - - + -
432E THR 2.9 15.7 + - - +
433E PHE* 3.3 37.2 - - + +
434E LEU 3.0 0.2 - - - -
435E GLN* 1.3 75.7 - - - +
437E ARG* 1.3 66.4 + - - +
439E GLN* 3.3 8.1 + - - +
440E LEU* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E LEU* 4.5 8.7 - - + -
299E CYS* 3.6 14.3 - - + -
300E GLU* 4.0 29.8 - - + +
303E GLU* 2.7 40.0 + - - +
433E PHE 2.8 13.1 + - - +
434E LEU* 2.9 27.8 + - - +
436E LEU* 1.3 76.7 - - - +
438E GLU* 1.3 68.4 + - - +
440E LEU* 3.4 6.4 + - - +
441E GLU* 2.8 77.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E LEU* 3.0 36.4 + - + +
435E GLN* 4.0 5.4 - - - +
437E ARG* 1.3 85.5 + - - +
439E GLN* 1.3 67.3 + - - +
440E LEU 3.1 0.9 - - - -
441E GLU* 3.6 19.3 - - - +
442E HIS* 2.6 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E ASP 5.4 0.2 - - - -
418E VAL* 3.6 37.1 - - + +
421E ASN* 4.3 17.7 + - - +
431E PRO* 3.8 25.1 - - - +
435E GLN* 2.9 27.8 + - - +
436E LEU* 3.7 8.7 - - - +
438E GLU* 1.3 78.6 - - - +
440E LEU* 1.3 58.7 + - - +
442E HIS* 3.1 9.0 + - - +
443E ILE* 2.9 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 4.1 18.5 - - + +
295E SER* 4.2 31.6 - - - +
296E LEU* 3.6 20.8 - - + +
299E CYS* 4.3 7.9 - - - -
372E PHE* 4.2 17.3 - - + -
376E LEU* 4.7 7.4 - - + -
415E VAL* 5.5 3.8 - - + -
418E VAL* 4.0 30.1 - - + -
436E LEU 3.0 21.8 + - - +
437E ARG 3.5 4.3 - - - +
439E GLN* 1.3 76.2 - - - +
441E GLU* 1.3 60.8 + - - +
443E ILE* 3.3 15.7 + - + +
444E ARG* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E LEU* 4.1 10.5 - - + -
437E ARG* 2.8 65.6 + - + +
438E GLU* 3.0 16.7 + - - +
440E LEU* 1.3 70.9 - - - +
442E HIS* 1.3 54.7 + - - +
444E ARG* 2.7 30.0 + - - +
445E THR* 2.4 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 442 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E GLU 2.6 16.6 + - - +
439E GLN* 3.1 13.9 - - - +
441E GLU* 1.3 70.4 - - - +
443E ILE* 1.3 66.4 + - + +
444E ARG 3.0 0.9 + - - -
445E THR* 3.2 16.9 + - - -
446E HIS* 3.2 46.0 + + - +
448E LEU* 4.4 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 443 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 4.5 7.6 - - + -
414E ALA* 3.5 43.3 - - + +
415E VAL* 3.8 14.4 - - + +
418E VAL* 4.2 13.5 - - + -
439E GLN* 2.9 17.2 + - + +
440E LEU* 3.4 17.3 - - + +
442E HIS* 1.3 79.0 - - + +
444E ARG* 1.3 52.9 + - - +
446E HIS 2.4 19.8 - - - +
448E LEU* 3.2 33.3 + - + -
449E HIS* 3.5 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 3.5 21.1 - - + -
293E LYS* 2.9 38.9 - - - +
296E LEU* 3.3 25.2 - - + +
440E LEU 3.2 4.7 + - - +
441E GLU* 2.7 38.9 + - - +
443E ILE* 1.3 72.4 - - - +
445E THR* 1.3 63.6 + - - +
446E HIS 2.8 14.1 + - - +
447E GLU* 3.8 2.4 + - - -
449E HIS* 4.3 8.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E GLU* 2.4 37.9 + - - +
442E HIS* 3.6 7.5 - - - -
444E ARG* 1.3 68.0 - - - +
446E HIS* 1.3 81.5 + - + +
447E GLU 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 446 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442E HIS* 3.2 40.1 + + - +
443E ILE 2.4 32.2 - - - +
444E ARG 3.0 4.9 - - - +
445E THR* 1.3 94.3 - - + +
447E GLU* 1.3 61.6 + - - +
448E LEU* 3.9 11.4 - - + +
----------------------------------------------------------
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