Contacts of the helix formed by residues 438 - 451 (chain A) in PDB entry 6TXA
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 LEU 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LYS 5.7 0.4 - - - -
393A ALA* 3.6 41.5 - - + +
396A TYR* 4.3 16.2 - - + +
397A ILE* 4.2 20.4 - - + -
429A GLU* 5.3 1.1 - - + +
430A ILE* 4.9 8.7 - - + -
433A SER* 3.4 26.0 - - - +
435A ASP* 3.2 17.3 + - + +
436A PRO 3.2 0.8 - - - -
437A LYS* 1.3 76.0 - - - +
439A LYS* 1.3 56.4 + - - -
440A ASP 3.3 2.9 - - - -
441A ALA* 3.3 7.9 + - + +
442A ARG* 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASP 3.8 1.6 + - - -
436A PRO* 3.3 18.9 + - + +
437A LYS 3.3 3.4 - - - -
438A LEU* 1.3 77.4 - - - +
440A ASP* 1.3 71.3 + - - +
442A ARG* 3.7 21.8 - - - +
443A GLU* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LYS* 3.7 31.4 - - + +
437A LYS 4.7 5.0 + - - +
438A LEU 3.3 0.8 - - - -
439A LYS* 1.3 91.0 - - - +
441A ALA* 1.3 60.8 + - - +
443A GLU* 3.6 6.6 + - - +
444A ILE* 3.5 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA* 3.2 37.2 - - - +
392A LYS* 4.2 7.8 + - + +
393A ALA* 3.7 24.2 - - + +
430A ILE* 3.8 11.4 - - + -
437A LYS 5.6 0.2 + - - -
438A LEU* 3.3 10.3 + - - +
440A ASP* 1.3 75.2 - - - +
442A ARG* 1.3 65.7 + - - +
444A ILE* 3.1 15.2 + - - +
445A LEU* 3.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 3.7 16.5 - - - +
431A LEU* 3.3 24.7 - - - +
433A SER* 2.7 51.8 + - - -
434A THR* 4.2 6.6 + - - +
435A ASP 3.3 28.9 + - - -
436A PRO* 4.5 1.8 - - - +
438A LEU 2.9 24.3 + - - +
439A LYS* 3.7 23.8 - - - +
441A ALA* 1.3 75.7 - - - +
443A GLU* 1.3 60.5 + - + +
445A LEU* 3.5 3.6 + - - +
446A LYS* 3.0 44.0 + - + +
----------------------------------------------------------
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 LYS* 3.0 40.8 + - + +
440A ASP* 3.8 7.2 - - - +
441A ALA 3.2 0.4 - - - -
442A ARG* 1.3 78.2 + - - +
444A ILE* 1.3 61.6 + - + +
446A LYS* 3.4 21.7 + - - +
447A GLN* 3.0 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MET* 3.2 45.2 - - + +
388A ASP* 4.0 20.2 - - + +
389A ALA* 3.9 24.9 - - + +
392A LYS* 4.1 16.4 - - + +
440A ASP 3.5 12.9 + - - +
441A ALA 3.1 7.9 + - - +
443A GLU* 1.3 77.2 - - + +
445A LEU* 1.3 63.4 + - + +
447A GLN* 3.1 18.5 + - - +
448A ILE* 3.2 12.4 + - + +
454A PHE* 5.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.3 9.0 - - + -
389A ALA* 3.5 20.6 - - + -
390A PHE* 5.5 1.1 - - + -
427A PHE* 3.3 63.4 - - + +
430A ILE* 3.6 24.5 - - + -
431A LEU* 3.9 19.5 - - + +
441A ALA 3.3 11.2 + - - +
442A ARG 4.0 3.8 - - - +
444A ILE* 1.3 76.1 - - + +
446A LYS* 1.3 62.5 + - - +
448A ILE* 3.2 27.2 + - + +
449A GLU* 3.3 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 4.0 16.8 - - + +
442A ARG* 3.0 34.6 + - + +
443A GLU* 3.8 24.9 - - - +
445A LEU* 1.3 76.2 - - - +
447A GLN* 1.3 68.1 + - - +
449A GLU* 3.2 20.1 + - - +
450A TYR* 3.2 45.8 + - + -
139B PRO* 5.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MET* 4.4 6.3 - - + -
443A GLU* 3.0 30.3 + - + +
444A ILE* 3.1 11.4 + - - +
446A LYS* 1.3 82.9 + - - +
448A ILE* 1.3 55.6 + - - +
450A TYR* 3.9 10.9 - - - +
451A ARG 3.1 5.0 + - - -
452A ASN* 2.7 80.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 4.4 27.0 - - + -
382A ILE* 4.3 17.7 - - + +
385A MET* 3.7 35.0 - - + -
386A ILE* 3.8 29.8 - - + -
427A PHE* 4.7 7.0 - - + -
444A ILE 3.2 9.2 + - - +
445A LEU* 3.5 19.7 - - + +
446A LYS 3.2 0.6 - - - -
447A GLN* 1.3 76.0 - - - +
449A GLU* 1.3 67.4 + - + +
451A ARG* 3.2 21.6 + - - +
453A LEU* 3.9 13.5 - - + -
142B GLN* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 5.9 2.5 - - + -
431A LEU* 3.7 34.0 - - + +
432A TYR* 5.8 0.5 - - - -
445A LEU 3.3 10.0 + - - +
446A LYS* 3.2 17.8 + - - +
448A ILE* 1.3 82.0 - - + +
450A TYR* 1.3 61.0 + - - +
451A ARG 3.3 0.2 + - - -
137B ASN* 3.8 14.3 - - - +
138B THR 4.9 0.9 - - - -
139B PRO* 3.6 47.5 - - + +
142B GLN* 3.7 37.1 - - + +
143B ARG* 4.6 3.6 + - - -
146B TYR* 4.6 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LYS* 3.2 47.9 + - + +
447A GLN* 4.3 10.8 - - - +
449A GLU* 1.3 77.1 - - + +
451A ARG* 1.3 67.9 + - - +
452A ASN* 3.7 23.6 + - - +
137B ASN* 3.8 24.4 - - - +
138B THR* 5.7 0.2 - - + -
139B PRO* 3.6 31.8 - - + +
247B SER 5.5 1.2 + - - -
248B ASN* 3.5 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 2.8 38.2 + - - +
156A VAL* 4.6 4.6 - - - +
378A VAL* 4.1 17.8 - - - +
382A ILE* 4.1 10.1 - - - +
447A GLN 3.1 5.1 + - - -
448A ILE* 3.2 17.5 + - - +
450A TYR* 1.3 81.8 - - - +
452A ASN* 1.3 61.6 + - - +
453A LEU* 3.3 29.9 + - + +
455A LYS* 5.6 4.3 + - - -
116B LYS* 4.5 16.4 - - - +
137B ASN* 3.6 35.1 + - - +
142B GLN* 5.2 5.4 + - - +
145B ARG* 4.5 8.1 - - - +
----------------------------------------------------------
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