Contacts of the helix formed by residues 436 - 448 (chain B) in PDB entry 1SIW
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 436 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 3.9 3.4 - - - +
434B GLY 5.4 1.3 - - - +
435B LEU* 1.3 78.4 - - - +
437B GLU* 1.3 65.4 + - - +
438B ALA* 3.3 9.9 + - - +
439B GLN* 3.0 40.5 + - + +
440B ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR* 3.2 34.1 + - + +
425B VAL* 3.3 24.4 - - - +
427B THR* 3.5 24.1 - - + +
430B LEU* 3.9 7.1 - - + +
436B THR* 1.3 73.6 - - - +
438B ALA* 1.3 58.2 + - - +
440B ALA* 3.3 3.5 + - - +
441B GLN* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B THR* 3.2 7.5 + - - +
437B GLU* 1.3 80.6 - - - +
439B GLN* 1.3 57.6 + - + +
441B GLN* 3.2 9.0 + - - +
442B GLU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU* 4.5 17.8 + - - +
337B TRP* 4.1 25.9 + - + +
408B ARG* 5.6 0.8 - - - +
434B GLY 3.9 5.2 - - - +
435B LEU* 3.5 24.2 - - + +
436B THR* 3.0 47.6 + - + +
438B ALA* 1.3 76.6 - - + +
440B ALA* 1.3 58.5 + - - +
442B GLU* 3.3 6.2 + - - +
443B MET* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B MET* 4.1 13.5 - - + +
415B TYR* 4.0 15.5 - - + -
416B LYS* 5.1 0.9 - - - +
430B LEU* 3.7 35.2 - - + -
435B LEU* 5.2 1.3 - - + +
436B THR 3.1 9.1 + - - +
437B GLU 3.7 6.3 - - - +
439B GLN* 1.3 77.5 - - - +
441B GLN* 1.3 57.5 + - - +
443B MET* 3.5 13.3 - - - +
444B TYR* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR* 2.9 25.8 + - - -
416B LYS* 3.5 26.2 - - - +
419B GLU* 3.6 14.6 + - - +
437B GLU* 2.9 15.1 + - - +
438B ALA* 3.3 13.6 - - - +
440B ALA* 1.3 75.7 - - - +
442B GLU* 1.3 59.8 + - - +
444B TYR* 3.3 9.4 + - + +
445B ARG* 3.0 25.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
332B LYS* 3.1 30.9 + - - +
336B GLU* 4.2 9.0 - - - +
337B TRP* 3.5 25.8 + - + -
438B ALA 2.9 16.5 + - - +
439B GLN* 3.8 5.0 - - - +
441B GLN* 1.3 73.4 - - - +
443B MET* 1.3 66.5 + - - +
445B ARG* 3.1 14.9 + - - +
446B TYR* 3.0 45.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B TRP* 3.5 45.1 - - + -
339B LEU* 3.9 25.8 - - + -
408B ARG 4.0 22.2 - - - +
409B MET* 4.6 2.7 - - - -
412B MET* 3.8 21.8 - - + -
435B LEU* 3.8 26.5 - - + -
439B GLN 2.9 24.9 + - - +
440B ALA* 3.5 9.4 - - - +
441B GLN 3.3 0.2 - - - -
442B GLU* 1.3 76.1 - - - +
444B TYR* 1.3 57.8 + - - +
446B TYR* 3.3 0.5 + - - -
447B LEU* 2.8 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP 4.6 1.9 + - - -
244A TYR* 2.7 32.9 + - - -
272A TYR* 3.7 16.4 - - + -
273A LYS* 3.6 31.6 - - + +
412B MET* 3.7 9.4 - - - -
416B LYS* 3.8 34.3 - - + -
440B ALA 2.9 18.2 + - - +
441B GLN* 3.5 9.0 - - + +
443B MET* 1.3 77.8 - - - +
445B ARG* 1.3 60.3 + - + +
448B ALA* 2.9 56.6 + - + +
449B ILE* 3.4 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLN 3.0 13.3 + - - +
442B GLU* 3.1 16.9 + - - +
444B TYR* 1.3 81.9 - - - +
446B TYR* 1.3 78.1 + - + +
449B ILE* 3.5 13.3 - - + +
450B ALA* 3.0 24.6 + - - -
451B ASN* 4.6 0.4 + - - +
453B GLU* 6.0 0.6 - - - +
454B ASP* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 2.5 31.7 + + - -
327B GLN* 4.4 9.1 + - - +
329B PRO* 3.7 32.5 - - + -
332B LYS* 3.3 20.3 - - - -
333B MET* 4.5 7.2 - - + -
337B TRP* 3.9 21.8 - + + -
442B GLU* 3.0 48.9 + - + +
443B MET 4.1 1.3 - - - +
445B ARG* 1.3 102.1 + - + +
447B LEU* 1.3 52.9 + - - +
450B ALA* 3.3 14.8 - - - +
454B ASP* 3.7 43.8 + - + -
457B VAL* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.6 24.8 - - + -
12B ASN* 3.8 22.2 - - + +
15B LYS* 3.3 27.0 + - - +
269B TYR* 3.6 9.6 - - + +
333B MET* 4.4 25.6 - - + -
337B TRP* 5.3 1.3 - - + -
339B LEU* 3.9 26.7 - - + -
356B VAL* 5.5 3.1 - - + -
409B MET* 5.2 9.0 - - + -
412B MET* 4.2 20.6 - - + -
443B MET* 2.8 31.3 + - + +
446B TYR* 1.3 75.5 - - + +
448B ALA* 1.3 61.1 - - - +
450B ALA* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.9 1.6 - - - +
244A TYR* 3.4 11.9 - - - +
269A GLU* 3.1 35.0 - - - +
272A TYR* 3.8 19.3 - - + -
444B TYR* 2.9 46.1 + - + +
447B LEU* 1.3 77.8 - - - +
449B ILE* 1.3 65.8 + - - +
----------------------------------------------------------
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