Contacts of the helix formed by residues 436 - 449 (chain B) in PDB entry 5KJH
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 ASN 436 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TRP* 5.1 5.3 - - - +
202B ILE* 4.8 1.3 - - - +
390B ILE* 3.6 28.2 - - - +
391B GLU* 3.8 14.2 + - - +
393B CYS* 3.4 14.9 - - - -
434B VAL* 3.4 21.6 + - + +
435B ARG* 1.4 70.4 - - - +
437B ALA* 1.4 60.7 + - - +
438B SER* 3.2 8.1 - - - -
439B MET* 3.5 34.6 + - + +
440B PHE 3.4 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B CYS* 4.2 6.7 - - - +
397B ASN* 3.9 16.8 - - + +
398B LEU* 3.5 21.2 - - + +
401B PHE* 3.8 26.5 - - + -
435B ARG* 3.1 13.3 - - + +
436B ASN* 1.4 75.9 + - - +
438B SER* 1.3 51.7 + - - +
440B PHE 3.4 1.0 + - - -
441B THR* 2.6 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PHE* 3.6 36.0 - - - -
435B ARG 3.5 15.2 + - - -
436B ASN* 4.0 1.0 - - - -
437B ALA* 1.3 76.0 - - - +
439B MET* 1.3 75.4 + - - +
441B THR* 3.4 2.3 + - - -
442B GLU* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TRP* 3.3 38.4 - - + +
198B THR* 3.7 19.1 - - - +
199B VAL* 3.8 22.8 - - + +
202B ILE* 3.8 12.6 - - + +
436B ASN* 3.5 32.3 + - + +
437B ALA 3.4 0.6 - - - -
438B SER* 1.3 85.3 + - - +
440B PHE* 1.3 60.1 + - - +
442B GLU* 3.5 2.4 + - - +
443B ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.7 24.4 - - + +
206B LEU* 4.0 13.7 - - + -
381B LEU* 3.9 14.1 - - + -
384B TRP* 5.8 1.1 - - + -
385B LEU* 3.7 21.5 - - + -
388B LEU* 3.7 26.2 - - + -
390B ILE* 4.5 3.1 - - + -
393B CYS* 3.6 28.9 - - - -
398B LEU* 3.7 31.4 - - + -
436B ASN 3.4 2.4 + - - -
437B ALA 3.4 5.4 + - - +
439B MET* 1.3 76.6 - - - +
441B THR* 1.4 57.6 + - - +
443B ALA* 3.4 1.7 + - - +
444B TRP* 2.9 53.0 + + + +
459B LEU* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.7 13.2 + - - +
401B PHE* 3.7 28.1 - - + -
437B ALA 2.6 23.0 + - - -
438B SER 3.7 4.9 - - - -
439B MET 3.3 0.2 - - - -
440B PHE* 1.4 75.3 - - - +
442B GLU* 1.3 56.5 + - + +
444B TRP* 3.5 1.6 + - - +
445B ASP* 3.0 45.1 + - - +
459B LEU* 3.9 22.5 - - + +
460B ARG 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.4 29.3 - - + +
401B PHE* 5.4 2.4 - - - -
438B SER* 3.0 31.5 + - - +
439B MET* 3.8 4.4 - - - +
440B PHE 3.4 0.2 - - - -
441B THR* 1.3 73.9 - - + +
443B ALA* 1.4 54.1 + - - +
445B ASP* 3.2 7.6 + - - +
446B ARG* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.6 15.3 - - - +
202B ILE* 3.6 14.4 - - + -
203B ALA* 3.5 31.9 - - - +
206B LEU* 4.2 3.4 - - + -
439B MET 3.0 18.4 + - - +
440B PHE 3.6 4.5 - - - +
442B GLU* 1.4 74.8 - - - +
444B TRP* 1.4 60.5 + - - +
446B ARG* 3.2 4.3 + - - +
447B VAL* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.8 15.8 - - + +
377B LEU* 3.9 17.5 - - + -
381B LEU* 4.0 20.6 - - + -
384B TRP* 3.6 39.5 - + - -
440B PHE* 2.9 43.3 + + + +
441B THR* 3.6 5.8 - - - +
443B ALA* 1.4 71.8 - - - +
445B ASP* 1.4 55.7 + - - +
447B VAL 3.3 0.3 + - - -
448B PHE* 2.8 59.6 + + - +
457B VAL 3.6 14.7 + - - -
458B ALA 4.0 0.8 - - - -
459B LEU* 3.4 47.9 - - + +
462B ILE* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B THR* 3.0 28.0 + - - +
442B GLU* 3.7 7.0 - - - +
444B TRP* 1.4 72.8 - - - +
446B ARG* 1.3 61.4 + - - +
449B ASN* 2.9 47.9 + - + +
458B ALA* 3.5 22.8 - - - +
459B LEU* 3.4 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.5 26.3 - - - +
200B ASP* 2.9 43.9 + - - +
203B ALA* 4.1 13.6 - - + +
442B GLU 2.9 11.9 + - - +
443B ALA* 3.2 11.0 + - - +
445B ASP* 1.3 77.9 - - - +
447B VAL* 1.3 61.0 + - + +
450B ASP* 3.7 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA* 3.4 35.2 - - + +
206B LEU* 4.4 3.4 - - + -
207B SER* 3.7 24.0 - - - +
210B ALA* 4.8 2.7 - - + -
443B ALA 3.0 17.0 + - - +
444B TRP 4.0 2.0 - - - +
446B ARG* 1.3 81.5 - - + +
448B PHE* 1.3 91.2 + - + +
450B ASP* 4.6 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.3 11.9 - - + -
210B ALA* 3.6 32.1 - - + -
213B VAL* 5.6 0.4 - - + -
373B TYR* 3.8 18.7 - - + -
377B LEU* 3.5 34.8 - - + -
384B TRP* 3.6 16.8 - + - -
444B TRP* 2.8 61.9 + + - +
447B VAL* 1.3 91.2 - - + +
449B ASN* 1.3 56.7 + - - +
450B ASP* 3.6 2.9 + - - -
455B ARG 4.6 0.5 - - - +
456B ARG* 3.3 9.7 - - - +
457B VAL* 2.8 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ASP* 2.9 34.9 + - - +
448B PHE* 1.3 77.2 - - - +
450B ASP* 1.4 60.0 + - - +
451B GLN* 3.8 5.9 + - - +
456B ARG* 3.1 36.0 + - - +
457B VAL 3.5 18.0 + - - +
458B ALA* 3.5 28.9 + - - +
----------------------------------------------------------
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