Contacts of the helix formed by residues 37 - 56 (chain A) in PDB entry 1T6S
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 THR 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.2 1.3 - - - -
35A LYS 4.3 6.3 - - - +
36A PHE* 1.3 75.7 - - - +
38A PRO* 1.3 74.7 - - - +
39A SER* 3.7 6.2 + - - -
40A GLU* 2.9 38.1 + - - +
41A LEU* 2.9 21.7 + - - +
416A NO3 4.1 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.3 18.6 - - + -
36A PHE 4.4 1.8 - - - +
37A THR* 1.3 86.3 - - - +
39A SER* 1.3 62.0 + - - +
41A LEU* 4.0 2.6 - - + +
42A GLN* 3.4 21.7 + - - +
68A TYR* 4.8 2.3 + - - -
421A NO3 3.8 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.1 6.0 + - - -
38A PRO* 1.3 81.1 - - - +
40A GLU* 1.3 64.9 + - - +
42A GLN* 3.4 6.2 + - - +
43A GLU* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 5.8 1.9 + - - +
8A LEU* 5.3 0.9 - - - +
34A HIS* 2.8 34.5 + - - -
35A LYS 3.9 3.5 - - - +
36A PHE* 3.5 14.9 - - + -
37A THR* 2.9 35.6 + - - +
39A SER* 1.3 77.6 - - - +
41A LEU* 1.3 61.5 + - - +
43A GLU* 3.3 13.5 + - - +
44A ALA* 3.1 20.9 + - + +
416A NO3 3.4 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 30.3 - - + -
25A LEU* 3.8 35.0 - - + -
28A LEU* 4.0 13.9 - - + -
36A PHE* 3.7 22.2 - - + -
37A THR 2.9 16.1 + - - +
38A PRO* 4.0 4.5 - - + +
40A GLU* 1.3 78.4 - - - +
42A GLN* 1.3 62.2 + - - +
44A ALA* 3.2 1.6 + - - +
45A VAL* 3.0 33.6 + - + +
68A TYR* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO 3.4 16.0 + - - +
39A SER* 3.8 5.8 - - - +
40A GLU 3.4 0.6 - - - -
41A LEU* 1.3 79.9 - - - +
43A GLU* 1.3 53.2 - - - +
45A VAL* 3.3 6.2 + - - +
46A ASP* 2.8 68.5 + - - +
63A ALA* 3.9 8.0 - - - +
68A TYR* 2.7 32.9 + - - +
407A NO3 3.2 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.3 12.4 + - - +
39A SER* 3.1 20.6 + - - +
40A GLU* 3.4 16.1 - - - +
42A GLN* 1.3 74.7 - - - +
44A ALA* 1.3 63.2 + - - +
46A ASP* 3.5 12.6 + - + +
47A GLU* 3.2 21.1 + - - +
50A ARG* 4.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.1 12.3 - - - +
9A LEU* 3.4 27.8 - - + +
12A LEU* 3.6 19.3 - - + -
36A PHE* 4.4 6.7 - - + -
40A GLU* 3.1 12.4 + - + +
41A LEU 3.2 8.5 + - - +
43A GLU* 1.3 73.8 - - - +
45A VAL* 1.3 66.1 + - - +
47A GLU* 3.3 4.9 + - - +
48A LEU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.5 1.6 - - + -
16A ILE* 4.5 13.7 - - + -
41A LEU* 3.0 30.7 + - + +
42A GLN* 3.5 11.4 - - - +
44A ALA* 1.3 77.3 - - + +
46A ASP* 1.3 62.3 + - - +
48A LEU* 3.2 11.9 + - + +
49A ASN* 3.0 26.6 + - - +
61A ILE* 3.6 23.6 - - + -
68A TYR* 3.7 23.3 - - + -
407A NO3 3.5 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.8 52.1 + - - +
43A GLU* 3.6 12.3 - - - +
44A ALA 3.3 0.2 - - - -
45A VAL* 1.3 76.8 - - - +
47A GLU* 1.3 57.8 + - - +
49A ASN* 3.2 9.4 + - - +
50A ARG* 2.8 53.9 + - - +
407A NO3 4.0 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.0 32.8 + - - -
6A GLN* 4.0 12.5 + - - +
9A LEU* 3.3 24.2 - - + +
43A GLU 3.2 10.9 + - - +
44A ALA 3.6 8.5 - - - +
45A VAL 3.3 0.2 - - - -
46A ASP* 1.3 76.4 - - - +
48A LEU* 1.3 65.6 + - - +
50A ARG* 3.0 20.8 + - + +
51A ASP* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 44.9 - - + +
10A ARG* 5.6 0.7 - - - -
12A LEU* 4.5 8.3 - - + -
13A GLU* 4.0 22.4 - - + +
16A ILE* 5.3 1.6 - - + -
44A ALA 3.2 14.6 + - - +
45A VAL* 3.6 10.3 - - + +
47A GLU* 1.3 78.1 - - - +
49A ASN* 1.3 64.6 + - - +
51A ASP* 2.9 21.8 + - + +
52A TYR* 2.9 40.1 + - + +
61A ILE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.0 26.4 + - - +
46A ASP* 3.6 11.4 + - - +
48A LEU* 1.3 75.5 - - - +
50A ARG* 1.3 62.7 + - - +
52A TYR* 3.3 12.2 + - - +
53A GLU* 3.0 23.2 + - - +
60A ARG* 3.4 22.1 + - - +
61A ILE* 2.7 50.0 + - - +
407A NO3 4.1 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 4.6 7.5 + - - +
46A ASP* 2.8 39.9 + - - +
47A GLU* 3.0 23.1 + - + +
49A ASN* 1.3 77.9 - - - +
51A ASP* 1.3 58.0 + - - +
53A GLU* 3.3 8.2 + - + +
54A ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.0 2.1 - - - +
47A GLU* 3.0 30.8 + - - +
48A LEU* 2.9 17.6 + - + +
50A ARG* 1.3 74.3 - - - +
52A TYR* 1.3 64.7 + - + +
54A ALA* 3.6 8.1 - - - +
55A THR* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 2.7 33.0 + - - +
48A LEU* 2.9 36.4 + - + +
49A ASN* 3.4 29.4 - - - +
50A ARG 3.3 0.2 - - - -
51A ASP* 1.3 77.4 - - + +
53A GLU* 1.3 65.4 + - - +
55A THR* 5.2 0.2 - - - -
56A GLY* 3.1 4.3 + - - -
57A ARG* 2.9 48.9 + - + +
59A PHE* 3.8 32.3 - + - +
60A ARG* 3.8 7.2 - - - +
61A ILE* 3.8 9.0 - - + +
70A PHE* 3.3 36.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN 3.0 13.2 + - - +
50A ARG* 3.5 11.4 - - + +
52A TYR* 1.3 78.3 - - - +
54A ALA* 1.3 64.3 + - - +
56A GLY* 3.5 8.5 + - - -
60A ARG* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG 2.9 17.3 + - - +
51A ASP* 3.6 11.7 - - - +
52A TYR 3.3 0.2 - - - -
53A GLU* 1.3 80.5 - - - +
55A THR* 1.3 63.7 + - + +
56A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 2.8 27.4 + - + +
52A TYR* 4.0 0.5 - - - -
54A ALA* 1.3 79.6 - - + +
56A GLY* 1.3 61.5 + - - +
57A ARG* 3.5 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR 3.1 5.6 + - - -
53A GLU 3.5 7.0 + - - -
54A ALA 3.3 4.0 + - - -
55A THR* 1.3 79.7 - - - +
57A ARG* 1.3 73.9 + - - +
58A THR* 3.9 6.8 + - - +
60A ARG* 6.0 0.4 - - - -
----------------------------------------------------------
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