Contacts of the helix formed by residues 35 - 47 (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 GLY 35 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLY 4.0 0.6 + - - -
34B THR* 1.3 72.9 - - - +
36B THR* 1.3 58.0 + - - +
37B GLY 3.4 2.2 - - - -
38B TYR* 3.5 10.3 + - - +
39B THR* 2.9 35.7 + - - -
226B THR* 5.6 3.1 - - - -
227B MET* 5.4 3.3 - - - -
228B THR* 3.4 24.3 + - - -
240B ALA* 5.1 0.2 - - - +
351B LEU 4.5 2.0 - - - -
352B GLY* 5.3 3.9 - - - -
353B ARG* 4.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.3 4.2 - - - -
35B GLY* 1.3 75.8 - - - +
37B GLY* 1.3 60.9 + - - +
39B THR* 3.4 0.9 + - - -
40B MET* 2.9 39.8 + - + +
351B LEU* 2.8 26.9 + - + +
353B ARG 3.6 4.2 + - - -
354B GLY 3.3 34.4 + - - +
355B TYR* 3.7 22.9 - - + +
373B LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.9 2.4 + - - -
35B GLY* 3.4 0.4 - - - -
36B THR* 1.3 78.3 - - - +
38B TYR* 1.3 58.6 + - - +
40B MET* 4.1 1.1 - - - -
41B ASP* 3.0 21.2 + - - +
355B TYR* 3.6 16.7 + - - -
388B LYS* 2.9 32.8 + - - -
7V A 3.8 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 5.0 5.7 - - - -
34B THR 4.3 9.0 - - - -
35B GLY* 3.5 11.8 + - - +
36B THR 3.3 0.2 - - - -
37B GLY* 1.3 78.8 - - - +
39B THR* 1.3 58.0 + - - +
41B ASP* 3.3 11.0 + - + +
42B THR* 2.9 30.0 + - - -
45B ARG* 5.3 0.5 + - - -
228B THR* 4.1 24.7 - - + +
237B LYS* 5.9 1.8 - - + -
238B ARG* 3.3 55.7 + - + +
239B ARG* 4.4 3.6 - - - -
240B ALA* 4.0 21.5 + - + +
6V U 3.2 38.9 + - + +
7V A 4.2 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 2.9 18.8 + - - -
36B THR* 4.0 4.0 - - - -
38B TYR* 1.3 73.6 - - - +
40B MET* 1.3 61.0 + - - +
42B THR* 3.2 8.3 + - + -
43B VAL* 3.0 29.6 + - + +
226B THR* 2.9 46.4 + - + +
227B MET 5.2 0.3 + - - -
240B ALA* 3.9 10.7 - - + +
349B ALA* 4.7 7.4 - - + -
350B ARG 4.2 0.9 - - - +
351B LEU* 3.9 23.8 - - + -
408B MET* 5.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B THR* 2.9 28.2 + - + +
37B GLY* 4.1 4.0 - - - +
39B THR* 1.3 75.9 - - - +
41B ASP* 1.3 58.4 + - - +
43B VAL* 3.9 0.9 - - - +
44B ILE* 3.0 38.5 + - + +
351B LEU* 4.2 19.3 - - + -
355B TYR* 3.7 25.6 - - + +
373B LEU* 4.5 6.3 - - + -
385B THR* 4.6 2.0 - - + -
388B LYS* 4.3 19.3 - - + +
389B ILE* 4.1 24.0 - - + -
392B ILE* 3.7 44.6 - - + -
396B MET* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.0 14.5 + - - +
38B TYR* 3.5 12.3 - - + +
39B THR 3.2 0.2 - - - -
40B MET* 1.3 77.9 - - - +
42B THR* 1.3 57.5 + - - +
44B ILE* 4.1 5.6 - - - +
45B ARG* 2.9 44.3 + - - +
384B ASP* 5.6 0.3 - - - +
388B LYS* 2.9 35.8 + - - +
6V U 5.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR 2.9 15.7 + - - -
39B THR* 3.2 12.3 + - + +
41B ASP* 1.3 76.7 - - - +
43B VAL* 1.3 56.9 + - + +
45B ARG* 3.8 18.3 + - - +
46B THR* 2.6 44.7 + - - +
240B ALA* 4.2 15.0 + - - +
311B GLU* 4.7 11.0 + - + +
403B LEU* 4.9 7.0 - - + -
408B MET* 3.9 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.0 20.9 + - + +
40B MET 3.9 3.6 - - - +
41B ASP 3.3 0.2 - - - -
42B THR* 1.3 77.4 - - + +
44B ILE* 1.3 56.6 + - - +
46B THR* 3.3 1.4 + - - -
47B HIS* 3.0 53.4 + - + +
349B ALA* 4.7 10.1 - - + -
351B LEU* 4.9 0.7 - - + -
392B ILE* 4.1 18.4 - - + -
395B LEU* 3.9 18.6 - - + -
401B ALA* 4.3 18.8 - - + -
402B SER 4.4 0.2 - - - +
403B LEU* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.0 23.5 + - + +
41B ASP* 4.1 5.4 - - - +
43B VAL* 1.3 76.8 - - + +
45B ARG* 1.3 62.8 - - - +
47B HIS* 3.5 4.5 + - - +
48B ASP* 3.2 26.9 + - + +
388B LYS* 3.5 50.9 - - + +
391B LYS* 4.2 32.5 - - + +
392B ILE* 4.5 15.5 - - + +
395B LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR 5.3 0.6 + - - -
41B ASP* 2.9 31.9 + - - +
42B THR* 4.0 17.8 + - - +
44B ILE* 1.3 77.6 - - - +
46B THR* 1.3 62.1 + - - +
48B ASP* 3.5 8.7 + - + +
49B TYR* 3.2 49.6 + - + +
239B ARG* 6.1 2.8 - - - +
308B LYS* 3.3 30.1 - - - +
311B GLU* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 2.6 28.4 + - - +
43B VAL* 3.7 4.0 - - - -
44B ILE 3.3 0.2 - - - -
45B ARG* 1.3 78.4 - - - +
47B HIS* 1.3 61.4 + - - +
48B ASP 3.2 1.3 + - - -
49B TYR* 3.5 11.5 + - - +
50B SER* 3.7 14.0 + - - -
311B GLU* 3.3 41.4 - - + +
403B LEU* 4.5 11.5 - - + +
405B PRO* 3.3 35.7 - - + +
406B GLY* 4.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.0 26.0 + - + +
44B ILE* 3.8 4.3 - - - +
46B THR* 1.3 75.3 - - - +
48B ASP* 1.3 56.7 + - - +
49B TYR 3.5 0.7 - - - -
50B SER 4.3 2.7 - - - -
51B SER* 4.0 16.5 - - - -
55B TRP* 4.4 16.9 - + + -
64B GLN 5.3 1.6 + - - -
65B GLN* 6.2 0.2 - - - -
66B LEU* 3.6 23.9 + - + +
395B LEU* 3.7 29.4 - - + +
402B SER 3.2 27.9 + - - -
403B LEU* 3.8 16.4 - - + -
404B SER 4.7 0.2 + - - -
405B PRO* 3.4 32.4 - - + +
----------------------------------------------------------
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