Contacts of the helix formed by residues 57 - 78 (chain A) in PDB entry 1TF5
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 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.8 5.4 - - - -
55A GLY 4.2 6.5 - - - +
56A ALA* 1.3 77.3 - - - +
58A THR* 1.3 64.5 + - - +
59A ASP* 3.3 10.8 + - - +
60A ASP* 2.7 50.1 + - - +
61A LEU* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.0 15.4 - - + +
57A THR* 1.3 72.5 - - - +
59A ASP* 1.3 64.6 + - - +
61A LEU* 3.2 2.1 + - - +
62A LEU* 2.8 31.9 + - - +
93A HIS* 3.2 25.6 + - - +
116A LEU* 3.6 39.1 - - + +
117A ASN* 4.8 7.6 + - - +
120A THR* 4.8 12.1 - - + +
366A LYS* 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.3 15.8 + - - -
57A THR* 3.2 10.1 + - - +
58A THR* 1.3 82.5 + - - +
60A ASP* 1.3 62.3 + - - +
62A LEU* 3.5 18.3 + - - +
63A VAL* 4.9 2.4 + - - +
93A HIS* 2.9 30.3 - - - -
94A ASP* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 5.0 2.6 + - - +
55A GLY 4.6 0.5 - - - +
56A ALA* 3.6 9.2 - - + -
57A THR* 2.7 52.6 + - - +
59A ASP* 1.3 81.1 - - - +
61A LEU* 1.3 67.6 - - + +
62A LEU 3.7 0.3 + - - -
63A VAL* 4.8 5.4 + - - +
64A GLU* 4.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.5 32.8 - - + +
51A ARG* 3.3 44.9 - - - +
52A LEU* 3.4 39.0 - - + -
56A ALA* 4.2 12.8 - - + -
57A THR 3.1 11.0 + - - +
58A THR* 3.5 3.6 - - - +
60A ASP* 1.3 78.1 - - + +
62A LEU* 1.3 55.2 + - - +
63A VAL 3.4 2.0 - - - -
64A GLU* 3.3 8.0 + - - +
65A ALA* 2.7 36.3 + - + +
116A LEU* 4.4 8.3 - - + -
119A LEU* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 5.3 5.2 - - - +
22A ILE* 3.5 32.8 - - + -
26A ILE* 4.3 0.2 - - + -
58A THR 2.8 18.6 + - - +
59A ASP* 3.7 12.3 - - - +
60A ASP 3.4 2.2 - - - -
61A LEU* 1.3 71.9 - - - +
63A VAL* 1.3 61.4 + - + +
66A PHE* 2.8 70.3 + - + +
90A VAL* 4.1 13.5 - - + -
93A HIS* 3.6 33.7 - - + +
116A LEU* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.3 24.2 - - + -
25A ASP* 4.0 19.1 - - + +
26A ILE* 3.5 36.4 - - + +
29A ILE* 3.8 17.0 - - + -
59A ASP 5.7 2.0 - - - +
60A ASP 4.8 5.1 + - - +
61A LEU 3.4 0.6 - - - -
62A LEU* 1.3 76.8 - - + +
64A GLU* 1.3 60.7 + - + +
67A ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 13.5 - - + -
33A TYR* 3.6 23.2 + - - +
44A LYS* 5.4 5.2 + - - +
48A PHE* 3.9 16.4 - - + -
51A ARG* 2.9 44.6 + - - -
60A ASP 4.9 4.3 - - - +
61A LEU* 3.3 7.1 + - - +
63A VAL* 1.3 75.5 - - + +
65A ALA* 1.3 61.0 + - - +
67A ALA* 3.1 2.3 + - - +
68A VAL* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.8 18.1 - - + -
61A LEU* 2.7 24.2 + - + +
62A LEU 3.6 2.0 - - - +
64A GLU* 1.3 73.1 - - - +
66A PHE* 1.3 60.5 + - + +
68A VAL* 3.2 4.0 + - - +
69A VAL* 3.0 32.3 + - - +
115A TYR* 4.2 16.4 - - + -
116A LEU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.5 31.4 - - + -
62A LEU* 2.8 53.3 + - + +
65A ALA* 1.3 71.5 - - + +
67A ALA* 1.3 62.0 + - - +
69A VAL* 3.3 0.6 + - - -
70A ARG* 2.8 31.2 + - - +
86A LEU* 3.9 12.3 - - + +
89A GLY* 3.7 20.9 - - - -
90A VAL* 3.6 21.3 - - + -
93A HIS* 4.5 0.7 - - + -
112A LEU* 3.6 53.2 - - + +
113A PRO* 4.0 5.8 - - + -
116A LEU* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.8 18.3 - - + +
29A ILE* 3.9 14.8 - - + +
30A ARG* 5.6 1.8 - - - -
33A TYR* 3.8 27.8 - - + -
63A VAL 3.0 19.0 + - - +
64A GLU 3.1 5.1 + - - +
66A PHE* 1.3 75.6 - - - +
68A VAL* 1.3 62.6 + - - +
70A ARG* 3.4 5.2 + - - +
71A GLU* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.6 24.7 - - + -
41A LEU* 3.9 23.4 - - + +
44A LYS* 4.1 8.3 - - + -
48A PHE* 3.4 24.7 - - + -
64A GLU 2.8 19.2 + - - +
65A ALA 3.4 7.6 - - - +
67A ALA* 1.3 77.8 - - - +
69A VAL* 1.3 57.0 + - - +
71A GLU* 3.3 3.9 + - - +
72A ALA* 2.9 26.5 + - - +
115A TYR* 4.5 6.3 - - - +
148A LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 3.0 15.7 + - - +
66A PHE 3.8 5.4 - - - +
68A VAL* 1.3 73.1 - - - +
70A ARG* 1.3 58.0 + - - +
72A ALA* 3.1 6.5 + - - +
73A SER* 2.8 37.2 + - - -
81A PRO* 5.8 1.3 - - + -
111A THR* 3.4 32.5 - - - +
112A LEU* 3.8 18.4 - - + +
115A TYR* 3.6 36.6 - - + -
144A ILE* 4.5 11.2 - - + -
145A PHE* 5.9 0.4 - - + -
148A LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.2 8.6 + - - +
27A ASP* 3.1 49.1 + - - +
30A ARG* 4.9 4.6 - - - +
66A PHE 2.8 16.9 + - - +
67A ALA* 3.5 7.0 - - - +
69A VAL* 1.3 77.9 - - - +
71A GLU* 1.3 61.8 + - - +
73A SER* 3.3 3.6 + - - -
74A ARG 3.3 15.2 + - - -
80A PHE* 3.1 50.0 - - + -
81A PRO* 3.0 55.1 + - + +
83A LYS* 4.3 21.0 - - - +
86A LEU* 3.7 25.8 - - + +
112A LEU* 4.4 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG 4.5 3.5 - - - +
33A TYR* 3.5 34.3 - - + +
34A GLU* 3.5 21.6 + - - +
41A LEU* 3.7 17.9 - - + -
67A ALA 3.1 16.3 + - - +
68A VAL 3.6 4.3 - - - +
70A ARG* 1.3 74.5 - - - +
72A ALA* 1.3 65.4 + - - +
74A ARG* 3.0 48.0 + - - +
75A ARG* 3.0 33.5 + - - +
80A PHE* 4.0 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.1 9.4 - - + +
68A VAL 2.9 17.9 + - - +
69A VAL* 3.6 4.3 - - - +
71A GLU* 1.3 75.9 - - - +
73A SER* 1.3 56.9 + - - +
75A ARG* 3.3 2.7 + - - +
76A VAL* 2.9 35.9 + - - +
144A ILE* 4.5 8.1 - - + -
147A PHE* 4.0 13.0 - - + -
148A LEU* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 2.8 20.7 + - - -
70A ARG 3.5 5.4 - - - -
71A GLU 3.1 0.2 - - - -
72A ALA* 1.3 72.4 - - - +
74A ARG* 1.3 59.2 + - - +
77A THR* 2.7 47.0 + - - -
78A GLY 3.2 0.2 + - - -
79A MET 2.7 19.4 + - - -
81A PRO* 4.0 9.0 - - - -
108A LEU* 3.3 29.0 - - - +
144A ILE* 4.1 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 5.7 1.0 - - - +
34A GLU* 4.1 22.0 + - - +
70A ARG 3.3 1.6 + - - -
71A GLU* 3.0 34.8 + - - +
73A SER* 1.3 76.1 - - - +
75A ARG* 1.3 62.6 + - - +
78A GLY* 2.8 32.8 + - - +
79A MET 3.1 13.9 + - - +
80A PHE* 3.1 67.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR 2.9 26.1 + - - -
34A GLU 4.0 6.2 + - - -
36A LEU* 2.8 30.9 + - - +
37A SER* 3.8 0.6 - - - +
38A ASP* 2.8 47.8 + - - +
41A LEU* 3.5 24.3 - - - +
71A GLU* 3.0 28.5 + - - +
72A ALA* 3.8 5.6 - - - +
74A ARG* 1.3 83.5 - - + +
76A VAL* 1.3 64.6 + - + +
78A GLY 4.7 0.2 + - - -
147A PHE* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 2.9 18.8 + - - +
75A ARG* 1.3 79.7 - - - +
77A THR* 1.3 61.6 + - + +
143A LYS* 3.7 39.7 - - + +
144A ILE* 4.1 16.8 - - + -
147A PHE* 3.7 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 2.7 28.7 + - - +
76A VAL* 1.3 85.3 - - + +
78A GLY* 1.3 57.3 + - - +
79A MET* 3.2 43.0 + - + +
140A GLN 4.9 7.9 - - - +
141A MET* 5.0 4.5 - - + -
143A LYS* 6.5 0.4 - - + -
144A ILE* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 3.2 0.4 + - - -
74A ARG* 2.8 29.7 + - - +
75A ARG 4.6 0.4 - - - -
76A VAL 3.8 0.2 - - - -
77A THR* 1.3 77.7 - - - +
79A MET* 1.3 61.1 + - - +
80A PHE* 3.8 1.9 + - - +
----------------------------------------------------------
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