Contacts of the helix formed by residues 66 - 84 (chain A) in PDB entry 3T2E
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.5 37.3 - - + +
63A GLY 3.6 18.8 + - - +
64A GLU 3.1 1.7 + - - +
65A ASP* 1.3 75.7 - - - +
67A LYS* 1.3 62.0 + - - +
68A ASP* 2.9 38.4 - - - +
69A ILE* 3.0 18.3 + - + +
70A HIS* 3.0 35.1 + - - -
104A GLY 4.6 0.4 - - - -
115A GLU* 5.1 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.7 4.2 + - - +
66A ASN* 1.3 76.4 + - - +
68A ASP* 1.3 68.4 + - - +
70A HIS* 4.5 0.2 - - - -
71A GLY* 2.8 26.0 + - - -
102A PHE* 3.4 7.3 - - + -
103A SER 5.4 1.1 - - - -
104A GLY* 3.2 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.6 9.3 - - + +
62A LYS* 3.8 23.5 - - + -
66A ASN* 2.9 18.3 - - - +
67A LYS* 1.3 85.7 - - - +
69A ILE* 1.3 60.1 + - - +
71A GLY* 3.8 0.6 - - - -
72A LEU* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 4.3 8.7 - - - +
8A ILE* 4.3 4.3 - - + -
41A VAL* 3.9 15.9 - - + +
42A ILE* 3.7 22.4 - - + -
58A MET* 3.8 24.3 - - + +
60A HIS* 3.6 53.4 - - + +
62A LYS* 4.0 7.4 - - + -
66A ASN* 3.0 26.1 - - + +
68A ASP* 1.3 74.4 - - - +
70A HIS* 1.3 70.5 + - + +
72A LEU* 3.2 6.6 + - + +
73A ALA* 3.0 22.5 + - - +
115A GLU* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 17.5 - - + -
65A ASP* 3.7 15.8 - - - -
66A ASN 3.0 25.8 + - - +
69A ILE* 1.3 79.7 - - + +
71A GLY* 1.4 57.2 + - - +
73A ALA* 3.2 3.8 + - - +
74A TRP* 2.9 27.2 + - - +
102A PHE* 3.6 17.9 - - + -
104A GLY 4.3 1.8 - - - +
105A ASN* 3.4 21.2 + - - -
106A ILE* 3.1 35.0 + - + +
107A ARG* 4.0 12.1 - - + -
113A VAL* 4.1 4.4 - - + +
115A GLU* 3.1 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS 2.8 24.6 + - - -
68A ASP* 3.8 1.3 - - - -
70A HIS* 1.4 71.9 - - - +
72A LEU* 1.3 58.2 + - - +
74A TRP* 3.7 3.4 - - - +
75A GLU* 2.9 32.6 + - - +
102A PHE* 3.4 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 4.2 16.6 - - + +
33A LEU* 3.8 20.9 - - + -
36A ALA* 3.6 34.5 - - + -
41A VAL* 4.1 11.0 - - + -
42A ILE* 3.8 24.5 - - + -
58A MET* 4.0 7.0 - - - -
68A ASP 2.9 19.3 + - - +
69A ILE* 3.4 7.0 - - + +
71A GLY* 1.3 75.7 - - - +
73A ALA* 1.3 57.8 + - - +
75A GLU* 3.4 5.8 + - - +
76A THR* 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.6 45.5 - - + -
56A LEU* 4.0 19.1 - - + -
58A MET* 4.3 4.9 - - + +
69A ILE 3.0 7.3 + - - +
70A HIS 3.6 7.0 - - - +
71A GLY 3.2 0.2 - - - -
72A LEU* 1.3 76.2 - - - +
74A TRP* 1.3 65.2 + - - +
76A THR* 3.1 1.9 + - - -
77A PHE* 2.9 31.2 + - + -
106A ILE* 4.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS 2.9 17.1 + - - +
71A GLY* 3.3 5.3 + - - +
73A ALA* 1.3 75.6 - - - +
75A GLU* 1.3 61.1 + - + +
77A PHE* 3.3 4.9 + - - +
78A LYS* 2.8 46.1 + - + +
97A LEU* 3.8 42.3 - - + +
98A LEU 4.1 4.0 - - - -
99A LYS 3.4 28.0 - - - -
100A ASP 4.6 10.8 + - - -
102A PHE* 3.8 39.8 - + + +
106A ILE* 3.7 30.2 - - + +
109A MET* 3.8 41.3 - - + -
111A PRO* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 2.7 26.6 + - - +
71A GLY 2.9 18.0 + - - +
72A LEU* 3.8 7.3 - - - +
74A TRP* 1.3 81.4 - - + +
76A THR* 1.3 57.3 + - - +
78A LYS* 3.2 6.5 + - + +
79A GLU* 2.9 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.8 1.0 - - + -
29A ALA* 3.8 38.1 - - + +
32A LYS* 3.3 30.9 - - + +
33A LEU* 4.0 10.1 - - + +
56A LEU* 3.9 19.1 - - + -
72A LEU* 2.8 22.3 + - - +
73A ALA 3.5 4.7 - - - -
75A GLU* 1.3 77.5 - - - +
77A PHE* 1.3 59.0 + - + +
79A GLU* 3.8 2.5 - - - +
80A VAL* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.6 26.7 - - + -
9A LYS 4.0 2.7 - - - -
10A ALA* 3.5 40.8 - - + -
12A VAL* 4.0 22.2 - - + +
29A ALA* 6.1 0.7 - - + -
54A ILE* 3.5 36.8 - - + -
56A LEU* 3.6 25.4 - - + -
73A ALA* 2.9 25.4 + - + +
74A TRP* 3.8 5.4 - - - +
76A THR* 1.3 77.1 - - + +
78A LYS* 1.4 62.9 + - - +
80A VAL* 3.8 7.3 - - + +
81A THR* 2.8 28.6 + - - -
97A LEU* 3.8 14.1 - - + -
106A ILE* 4.9 6.3 - - + -
111A PRO* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 2.8 40.0 + - + +
75A GLU* 3.7 8.3 - - + +
77A PHE* 1.4 73.7 - - - +
79A GLU* 1.3 58.8 + - + +
81A THR* 3.2 7.7 + - + -
82A ASP* 2.8 59.0 + - - +
86A LYS* 5.7 1.6 - - - +
97A LEU* 3.7 21.7 - - + +
99A LYS 5.6 2.9 - - - -
100A ASP* 5.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.6 45.2 + - + +
32A LYS* 2.9 34.7 + - - +
75A GLU* 2.9 33.0 + - + +
76A THR 3.8 1.6 - - - +
78A LYS* 1.3 72.9 - - + +
80A VAL* 1.3 62.5 + - - +
82A ASP* 4.4 4.3 - - - +
83A GLN* 2.8 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.6 11.7 - - + -
25A MET* 3.6 60.6 - - + +
28A TYR* 3.8 22.9 - - + -
29A ALA* 4.2 11.0 - - + +
54A ILE* 4.8 3.6 - - + -
76A THR* 2.9 24.7 + - + +
77A PHE* 3.8 9.0 - - + +
79A GLU* 1.3 77.9 - - - +
81A THR* 1.3 56.7 + - - +
84A ILE* 3.0 13.1 + - + +
85A ALA 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.3 22.2 - - - +
77A PHE 2.8 18.5 + - - -
78A LYS* 3.3 14.4 - - + -
79A GLU 3.2 0.2 - - - -
80A VAL* 1.3 78.0 - - - +
82A ASP* 1.4 70.0 + - - +
85A ALA* 3.9 9.0 - - + -
86A LYS* 2.8 48.3 + - + +
94A GLY* 3.6 28.5 - - - +
97A LEU* 3.8 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.8 49.5 + - - +
79A GLU* 4.2 4.7 - - - +
81A THR* 1.4 83.5 - - - +
83A GLN* 1.3 68.5 + - + +
86A LYS* 3.6 39.2 + - + +
87A ARG* 4.4 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.0 31.8 - - + +
79A GLU* 2.8 26.9 + - + +
82A ASP* 1.3 81.7 - - + +
84A ILE* 1.3 71.8 + - + +
87A ARG* 3.5 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 4.8 1.8 - - + -
24A LYS* 4.2 32.8 - - + +
25A MET* 3.5 33.2 - - + +
28A TYR* 4.3 20.6 - - + -
80A VAL* 3.0 13.8 + - - +
82A ASP 3.5 0.4 - - - -
83A GLN* 1.3 97.8 - - + +
85A ALA* 1.3 63.0 + - - +
86A LYS 3.4 1.1 - - - -
87A ARG* 3.3 4.3 + - - +
88A PHE* 2.9 55.0 + - + +
90A LEU* 4.7 2.9 - - + -
----------------------------------------------------------
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