Contacts of the helix formed by residues 56 - 70 (chain A) in PDB entry 1TD2
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 PRO 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.9 5.8 - - + +
55A MET* 1.3 87.8 - - + +
57A PRO* 1.3 67.1 - - + +
58A SER* 4.2 11.0 - - - +
59A HIS* 2.7 47.9 + - + +
60A LEU* 3.5 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.9 0.7 - - + -
55A MET 3.5 4.0 - - - +
56A PRO* 1.3 82.0 - - + +
58A SER* 1.3 63.5 + - - +
60A LEU* 3.0 22.5 + - + +
61A THR 3.5 0.5 + - - -
86A SER* 3.9 15.7 - - - +
88A GLU* 3.8 31.4 - - + +
89A GLN* 4.0 14.6 - - + +
92A HIS* 3.4 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 4.2 11.4 - - - +
57A PRO* 1.3 78.8 - - - +
59A HIS* 1.3 57.6 + - - +
61A THR* 3.1 5.4 + - - -
62A GLU* 2.9 34.7 + - - +
92A HIS* 3.7 16.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET* 3.8 20.6 - - + +
56A PRO* 2.7 39.9 + - + +
58A SER* 1.3 76.2 + - - +
60A LEU* 1.3 66.8 + - + -
62A GLU* 3.3 14.0 + - - +
63A ILE* 3.0 60.2 + - + +
40B GLN* 2.7 42.0 + - + +
52B GLY* 4.0 7.8 - - - -
53B CYS* 3.8 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.2 17.9 - - + -
36A LEU* 3.6 31.6 - - + +
37A ASN 4.2 12.1 - - - +
38A THR* 4.3 4.3 - - + -
55A MET* 4.4 5.6 - - + -
56A PRO 4.2 5.4 - - - +
57A PRO* 3.0 10.3 + - + +
59A HIS* 1.3 89.2 - - + +
61A THR* 1.3 63.5 + - - +
63A ILE* 3.5 2.8 + - - +
64A VAL* 3.4 25.5 + - - +
89A GLN* 3.7 46.7 - - + +
92A HIS* 4.8 3.1 - - + -
93A ILE* 4.4 4.7 - - + -
96A ILE* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 3.5 0.4 + - - -
58A SER* 3.1 9.6 + - - -
60A LEU* 1.3 77.4 - - - +
62A GLU* 1.3 66.2 + - - +
64A VAL* 3.1 5.2 + - + +
65A GLN* 3.0 31.5 + - + +
92A HIS* 2.8 40.9 + - - +
95A GLY 6.4 1.3 - - - -
96A ILE* 4.5 9.8 - - + +
99A GLN* 5.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 2.9 19.4 + - - +
59A HIS* 3.3 21.3 + - - +
61A THR* 1.3 77.1 - - - +
63A ILE* 1.3 60.4 + - - +
65A GLN* 3.2 12.4 + - + +
66A GLY 2.9 12.1 + - - -
51B THR* 2.7 28.6 + - + +
52B GLY* 3.1 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.8 16.8 - - + -
59A HIS* 3.0 53.5 + - + +
60A LEU 3.6 5.6 - - - +
61A THR 3.2 0.2 - - - -
62A GLU* 1.3 77.1 - - - +
64A VAL* 1.3 63.5 + - - +
66A GLY 3.0 9.4 + - - -
67A ILE* 3.1 16.4 + - + +
13B VAL* 3.7 30.1 - - + -
40B GLN* 3.6 19.1 - - + +
41B PHE 3.9 2.5 - - - +
42B SER* 3.3 23.3 - - - +
51B THR* 3.4 3.6 - - - -
52B GLY* 3.7 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.1 8.5 - - + -
36A LEU* 3.9 12.6 - - + -
60A LEU 3.4 13.6 + - - +
61A THR* 3.1 7.4 + - - +
63A ILE* 1.3 75.9 - - + +
65A GLN* 1.3 64.8 + - - +
67A ILE* 3.0 11.5 + - + +
68A ALA* 2.9 22.0 + - - +
73A LEU* 3.9 27.3 - - + +
96A ILE* 3.8 39.5 - - + -
99A GLN* 3.8 20.4 - - + +
100A VAL* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.0 26.3 + - + +
62A GLU* 3.4 14.4 - - + +
64A VAL* 1.3 75.3 - - - +
66A GLY* 1.3 58.1 + - - +
68A ALA* 3.3 6.8 + - - +
69A ALA* 2.9 29.1 + - - +
99A GLN* 3.2 24.2 + - - +
51B THR* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU 2.9 10.9 + - - -
63A ILE 3.0 6.6 + - - -
65A GLN* 1.3 78.2 - - - +
67A ILE* 1.3 60.6 + - - +
69A ALA* 3.2 22.1 + - - +
70A ILE* 3.3 10.4 + - - +
42B SER* 3.6 12.3 - - - -
43B ASN* 4.0 5.2 - - - +
50B TRP* 5.4 1.1 - - - -
51B THR* 3.4 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.6 7.6 - - + -
34A TRP* 4.3 24.0 - - + -
63A ILE* 3.4 24.9 - - + +
64A VAL* 3.0 15.1 + - + +
66A GLY* 1.3 75.1 - - - +
68A ALA* 1.3 61.8 + - - +
70A ILE* 3.3 13.3 - - - +
72A LYS* 3.0 44.2 + - + -
73A LEU* 3.9 17.3 - - + +
13B VAL* 4.4 10.5 - - + -
14B TYR* 4.0 23.3 - - + -
42B SER* 4.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL 2.9 6.9 + - - +
65A GLN* 3.4 12.3 - - - +
67A ILE* 1.3 76.5 - - - +
69A ALA* 1.3 55.6 + - - +
71A ASP* 2.7 31.9 + - - +
73A LEU* 4.1 18.0 - - + +
99A GLN* 3.4 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN 2.9 13.4 + - - +
66A GLY* 3.2 15.0 - - - +
68A ALA* 1.3 76.7 - - - +
70A ILE* 1.3 59.2 + - - +
71A ASP* 3.2 9.4 + - - +
49B LYS* 3.5 35.9 + - + +
51B THR* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 3.6 9.6 - - - +
67A ILE* 3.3 15.9 - - - +
69A ALA* 1.3 76.6 - - - +
71A ASP* 1.3 75.9 + - - +
72A LYS* 3.5 26.6 + - + +
14B TYR* 4.0 12.6 - - + -
43B ASN* 3.7 33.4 - - + +
47B TYR* 3.5 48.4 - - + +
49B LYS* 4.0 20.2 - - + +
----------------------------------------------------------
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