Contacts of the helix formed by residues 438 - 451 (chain A) in PDB entry 1TF5
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 ALA 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A THR* 3.6 1.7 + - - +
437A VAL* 1.3 83.1 - - + +
439A VAL* 1.3 60.0 + - - +
440A GLU* 3.3 24.7 - - + +
441A THR* 2.8 33.4 + - - +
442A SER* 3.2 12.0 + - - -
484A THR* 3.8 5.6 - - - -
511A GLU* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 1.3 72.5 - - - +
440A GLU* 1.3 88.6 + - + +
442A SER* 3.2 10.1 + - - -
443A GLU* 3.1 30.6 + - + +
460A ASN* 3.8 36.8 - - + +
462A LYS* 5.4 7.6 - - - +
484A THR* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 3.0 19.6 - - + +
439A VAL* 1.3 109.3 + - + +
441A THR* 1.3 61.0 + - - +
443A GLU* 3.7 7.1 + - - +
444A LEU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 3.7 36.2 - - + -
436A THR* 2.9 26.0 - - - +
437A VAL 5.1 0.2 - - - -
438A ALA* 2.8 18.3 + - - +
440A GLU* 1.3 77.2 - - - +
442A SER* 1.3 64.0 + - - +
444A LEU* 3.1 8.0 + - - +
445A ILE* 3.0 25.1 + - + +
510A THR* 4.3 6.5 - - - +
511A GLU* 4.6 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A THR* 2.8 31.6 + - - +
438A ALA 3.2 3.3 + - - -
439A VAL* 3.2 9.1 + - - -
441A THR* 1.3 78.9 - - - +
443A GLU* 1.3 52.4 + - - +
445A ILE* 3.2 5.8 + - - +
446A SER* 2.7 37.2 + - - -
458A VAL* 4.4 16.8 - - - -
459A LEU 5.2 0.2 + - - -
460A ASN* 4.4 2.5 - - - -
482A ILE* 3.6 26.3 - - - +
484A THR* 3.6 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 3.1 18.6 + - + +
440A GLU* 4.0 6.7 - - - +
442A SER* 1.3 73.5 - - - +
444A LEU* 1.3 65.8 + - - +
446A SER* 3.8 12.9 + - - -
447A LYS* 3.1 44.1 + - - +
458A VAL* 3.7 24.8 - - - +
460A ASN* 3.9 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 3.6 41.1 - - + -
440A GLU 3.2 14.3 + - - +
441A THR* 3.1 13.2 + - - +
443A GLU* 1.3 78.1 - - - +
445A ILE* 1.3 67.2 + - + +
447A LYS* 3.5 9.2 + - + +
448A LEU* 3.4 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 3.1 46.9 - - + -
418A VAL* 4.2 23.6 - - + -
419A ALA 5.3 2.0 - - - +
434A VAL* 4.7 10.1 - - + -
436A THR* 5.6 0.4 - - - +
441A THR* 3.0 21.0 + - + +
442A SER* 3.6 6.7 - - - +
444A LEU* 1.3 79.1 - - + +
446A SER* 1.3 60.2 + - - +
448A LEU* 3.0 11.0 + - + +
449A LEU* 2.9 39.1 + - + +
482A ILE* 4.0 16.4 - - + -
510A THR* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER 2.7 20.6 + - - -
443A GLU* 3.8 18.3 + - - -
444A LEU 3.4 0.2 - - - -
445A ILE* 1.3 72.8 - - - +
447A LYS* 1.3 58.5 + - - +
449A LEU* 3.1 3.5 + - - +
450A LYS* 2.8 42.9 + - - +
456A HIS* 2.6 30.9 + - - -
458A VAL* 4.0 10.3 - - - +
482A ILE* 3.8 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU* 3.1 29.5 + - - +
444A LEU* 3.7 8.7 - - + +
445A ILE 3.2 0.2 - - - -
446A SER* 1.3 74.5 - - - +
448A LEU* 1.3 61.2 + - + +
450A LYS* 3.8 13.1 - - + +
451A ASN* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 3.7 42.0 - - + +
416A LYS* 4.3 4.9 - - - +
419A ALA* 4.0 16.8 - - + -
444A LEU* 3.4 22.2 + - + +
445A ILE* 3.0 13.3 + - + +
447A LYS* 1.3 79.3 - - + +
449A LEU* 1.3 63.0 + - - +
451A ASN* 3.4 19.9 + - + +
452A LYS* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA* 4.0 32.1 - - + +
422A VAL* 4.1 20.4 - - + -
423A ALA* 5.3 0.4 - - - +
434A VAL* 5.5 0.7 - - + -
445A ILE* 2.9 21.1 + - + +
446A SER 3.1 6.7 + - - +
448A LEU* 1.3 75.2 - - - +
450A LYS* 1.3 61.3 + - - +
452A LYS* 3.1 10.7 + - + +
454A ILE* 3.0 38.9 + - + +
456A HIS* 3.7 23.6 - - + +
480A VAL* 4.0 20.2 - - + -
482A ILE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 2.8 36.7 + - - +
447A LYS* 3.8 12.3 - - + +
448A LEU 3.3 0.2 - - - -
449A LEU* 1.3 72.3 - - - +
451A ASN* 1.3 59.6 + - - +
452A LYS 3.0 4.7 - - - -
453A GLY* 3.0 19.4 + - - +
454A ILE 4.8 2.5 - - - +
456A HIS* 3.7 15.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 2.7 28.7 + - - +
448A LEU* 3.7 15.5 - - + +
449A LEU 3.3 0.4 - - - -
450A LYS* 1.3 77.5 - - - +
452A LYS* 1.3 62.0 + - + +
453A GLY 3.3 1.2 + - - -
----------------------------------------------------------
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