Contacts of the helix formed by residues 442 - 455 (chain B) in PDB entry 1TH1
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 GLY 442 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 4.1 2.0 - - - +
439B CYS 3.5 6.8 + - - -
440B GLN 3.4 4.9 + - - -
441B VAL* 1.3 79.8 - - - +
443B GLY* 1.3 62.5 + - - +
444B ILE* 3.3 3.7 + - - -
445B GLU* 3.4 10.8 + - - +
446B ALA* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 3.8 15.3 - - - -
409B LEU* 5.9 0.2 - - - -
438B VAL* 2.9 33.3 + - - -
439B CYS 4.3 1.8 + - - -
441B VAL 3.5 1.2 - - - -
442B GLY* 1.3 76.9 - - - +
444B ILE* 1.3 58.2 + - - +
446B ALA* 3.5 1.4 + - - +
447B LEU* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B CYS* 4.4 13.0 - - + +
442B GLY 3.3 1.2 - - - -
443B GLY* 1.3 73.7 - - - +
445B GLU* 1.3 59.4 + - - +
447B LEU* 3.4 1.7 + - - +
448B VAL* 2.9 36.8 + - + +
468B LEU* 4.0 13.5 - - + -
471B LEU* 3.9 30.3 - - + -
472B THR* 4.9 1.3 - - - +
480B MET* 5.2 5.8 - - + -
481B ALA* 3.8 32.5 - - + +
484B ALA* 3.7 30.1 - - + +
485B VAL* 3.8 27.6 - - + +
488B HIS* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B GLY* 3.4 11.6 + - - +
444B ILE* 1.3 76.7 - - - +
446B ALA* 1.3 58.4 + - - +
448B VAL* 3.2 3.3 + - - +
449B ARG* 2.9 63.5 + - + +
488B HIS* 3.3 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 3.8 20.4 - - + +
409B LEU* 3.8 24.4 - - + +
410B GLY 5.8 0.2 - - - +
442B GLY 3.3 14.5 + - - +
443B GLY 3.7 3.4 - - - +
445B GLU* 1.3 79.3 - - - +
447B LEU* 1.3 56.3 + - - +
449B ARG* 3.4 10.0 + - - +
450B THR* 2.9 31.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
409B LEU* 3.9 27.1 - - + -
421B ALA* 5.0 4.0 - - + -
424B LEU* 4.7 9.6 - - + -
438B VAL* 4.7 6.1 - - + -
443B GLY* 2.9 23.0 + - - +
444B ILE 3.9 0.2 - - - +
446B ALA* 1.3 74.5 - - - +
448B VAL* 1.3 63.4 + - - +
449B ARG 3.4 0.2 - - - -
450B THR* 3.5 5.8 + - - +
451B VAL* 3.2 27.4 + - - +
464B ALA* 4.1 20.8 - - + +
467B ALA* 3.9 25.6 - - + -
468B LEU* 3.9 20.6 - - + -
471B LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 2.9 33.7 + - + +
445B GLU 3.6 4.0 - - - +
447B LEU* 1.3 74.3 - - - +
449B ARG* 1.3 63.4 + - + +
450B THR 3.2 0.2 - - - -
451B VAL* 3.2 9.7 + - - +
452B LEU* 3.0 36.2 + - + +
468B LEU* 4.3 14.6 - - + -
485B VAL* 4.4 21.5 - - + +
488B HIS* 3.6 30.3 - - + +
490B GLY* 3.8 19.1 - - - +
493B VAL* 5.2 1.3 - - + +
494B VAL* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 2.9 47.8 + - + +
446B ALA* 3.6 8.7 - - - +
447B LEU 3.4 0.2 - - - -
448B VAL* 1.3 78.3 - - + +
450B THR* 1.3 51.1 - - - +
452B LEU* 3.3 15.2 + - + +
453B ARG* 2.8 50.9 + - + +
488B HIS* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 3.7 28.6 + - + +
417B VAL* 3.7 25.4 - - + +
421B ALA* 4.7 2.5 - - + -
446B ALA 2.9 19.0 + - - -
447B LEU* 3.5 12.8 - - + -
448B VAL 3.2 0.2 - - - -
449B ARG* 1.3 77.2 - - - +
451B VAL* 1.3 56.4 + - - +
453B ARG* 3.3 8.1 + - - +
454B ALA* 3.0 31.6 + - - +
460B ILE* 3.8 18.5 - - + +
464B ALA* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU 3.2 15.3 - - - +
448B VAL* 3.2 8.3 + - - +
450B THR* 1.3 75.1 - - - +
452B LEU* 1.3 61.0 + - - +
454B ALA* 3.8 5.6 - - - +
455B GLY* 3.5 18.2 + - - +
461B THR* 4.3 9.3 + - + +
464B ALA* 3.8 20.9 - - + -
465B ILE* 3.8 22.2 - - + -
468B LEU* 4.3 9.0 - - + -
493B VAL* 4.0 25.9 - - + +
497B LEU* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 3.0 37.4 + - + +
449B ARG* 3.5 15.3 - - + +
451B VAL* 1.3 80.1 - - - +
453B ARG* 1.3 62.1 + - + +
454B ALA 3.5 0.2 + - - -
455B GLY* 4.0 6.6 + - - -
488B HIS 4.5 4.7 - - - +
489B TYR* 4.2 13.5 - - + +
493B VAL* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU 2.8 28.7 + - - -
410B GLY* 4.5 4.6 - - - -
411B SER 2.8 25.7 + - - -
412B ASP* 4.3 10.5 + - - +
414B ILE* 4.4 22.0 - - + +
417B VAL* 3.5 20.3 - - - +
449B ARG* 2.8 33.9 + - + +
450B THR* 3.9 6.4 + - - +
452B LEU* 1.3 73.6 - - + +
454B ALA* 1.3 61.0 + - - +
455B GLY 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE* 5.6 1.3 - - - +
450B THR 3.0 17.7 + - - +
451B VAL* 3.8 3.4 - - - +
452B LEU 3.3 0.4 - - - -
453B ARG* 1.3 79.3 - - - +
455B GLY* 1.3 63.7 + - - +
456B ASP* 3.5 2.6 + - - +
457B ARG* 3.5 21.1 + - - +
460B ILE* 3.9 33.0 - - + -
461B THR* 3.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B VAL 3.5 10.7 + - - +
452B LEU 4.0 5.4 + - - -
453B ARG 3.7 1.6 - - - -
454B ALA* 1.3 77.1 - - - +
456B ASP* 1.3 59.4 + - - -
457B ARG 3.2 4.1 + - - -
461B THR* 3.5 13.2 + - - -
493B VAL* 6.4 1.1 - - - -
497B LEU* 4.3 14.6 - - - +
----------------------------------------------------------
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