Contacts of the helix formed by residues 382 - 393 (chain B) in PDB entry 6T2C
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 382 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 4.0 20.3 - - + -
387A GLN* 2.8 36.5 + - + +
388A TYR 4.9 4.6 + - - -
390A SER* 5.1 8.7 + - - +
391A GLU* 6.0 2.2 - - - +
381B PHE* 1.3 78.8 - - - +
383B GLU* 1.3 65.6 + - - +
384B ASP* 3.1 8.8 + - - +
385B THR* 2.7 38.7 + - - -
386B LYS* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASN* 1.3 79.1 - - - +
384B ASP* 1.3 62.1 + - + +
386B LYS* 3.7 6.4 - - - +
387B LYS* 3.0 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 5.6 0.2 - - - +
382B ASN* 3.1 5.8 + - - +
383B GLU* 1.3 82.6 - - + +
385B THR* 1.3 59.5 + - - +
387B LYS* 3.2 11.8 + - - +
388B LYS* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLN* 3.5 16.1 + - - +
40B MET* 4.6 8.1 - - + -
355B TYR* 3.3 35.7 - - + +
381B PHE* 4.4 10.8 - - + -
382B ASN* 2.7 30.0 + - - -
384B ASP* 1.3 75.4 + - - +
386B LYS* 1.3 57.9 + - - +
388B LYS* 3.2 13.6 + - - +
389B ILE* 2.9 36.2 + - + +
7V A 4.7 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.6 44.3 + - + +
379B ARG* 5.5 1.6 - - - +
381B PHE* 4.1 12.6 - - + +
382B ASN 3.2 21.6 + - - +
383B GLU* 3.4 7.1 + - - +
384B ASP 3.3 0.4 - - - -
385B THR* 1.3 76.8 - - - +
387B LYS* 1.3 59.5 + - - +
389B ILE* 3.9 6.8 - - - +
390B GLU* 2.9 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 3.0 35.8 + - + +
384B ASP* 3.2 15.0 + - - +
386B LYS* 1.3 77.6 - - - +
388B LYS* 1.3 57.4 + - + +
390B GLU* 3.4 13.6 + - - +
391B LYS* 2.9 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY* 2.9 40.2 + - - +
40B MET* 4.3 12.6 - - + -
41B ASP* 2.9 35.8 + - - +
44B ILE* 3.5 25.1 - - + +
384B ASP* 2.9 36.0 + - - +
385B THR* 3.2 22.9 + - - +
387B LYS* 1.3 77.3 - - + +
389B ILE* 1.3 57.4 + - - +
391B LYS* 3.3 2.3 + - + -
392B ILE* 3.0 32.4 + - - +
6V U 5.7 2.2 + - - -
7V A 5.1 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 4.1 19.5 - - + -
355B TYR* 5.3 0.2 - - + -
373B LEU* 3.8 24.5 - - + +
378B LEU* 4.0 8.7 - - + -
381B PHE* 3.6 46.9 - - + -
385B THR* 2.9 23.0 + - + +
386B LYS* 4.0 3.6 - - - +
387B LYS 3.3 0.2 - - - -
388B LYS* 1.3 75.3 - - - +
390B GLU* 1.3 57.3 + - - +
392B ILE* 3.7 9.5 - - + +
393B ARG* 2.9 59.2 + - + +
396B MET* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.7 20.4 - - + +
386B LYS* 2.9 41.0 + - - +
387B LYS* 3.8 16.5 - - - +
389B ILE* 1.3 78.7 - - - +
391B LYS* 1.3 60.5 + - + +
393B ARG* 3.9 14.8 + - - +
394B HIS* 4.9 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 4.2 32.7 - - + +
387B LYS* 2.9 43.8 + - - +
388B LYS* 3.3 5.1 + - + +
390B GLU* 1.3 78.8 - - + +
392B ILE* 1.3 58.3 + - - +
394B HIS* 3.2 27.9 - - - -
395B LEU* 4.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.7 41.7 - - + -
43B VAL* 4.1 25.6 - - + -
44B ILE* 4.5 8.3 - - + -
351B LEU* 4.1 9.0 - - + -
388B LYS 3.0 19.8 + - - +
389B ILE* 3.7 8.1 - - + +
391B LYS* 1.3 75.3 - - - +
393B ARG* 1.3 66.0 + - - +
394B HIS 3.2 2.9 - - - -
395B LEU* 3.2 23.6 + - + +
396B MET* 3.8 21.4 - - + +
401B ALA* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU 2.6 26.8 + - - -
374B SER* 2.9 32.2 + - - +
375B ASP* 4.3 1.6 - - - +
376B ILE* 3.9 14.8 + - - +
378B LEU* 3.5 26.4 - - - +
389B ILE* 2.9 32.7 + - - +
390B GLU* 4.0 12.1 - - - +
391B LYS 3.5 1.2 - - - -
392B ILE* 1.3 79.3 - - - +
394B HIS* 1.3 57.5 + - - +
395B LEU 3.2 4.4 + - - -
396B MET* 3.6 22.2 + - - +
----------------------------------------------------------
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