Contacts of the helix formed by residues 32 - 49 (chain E) in PDB entry 1V8P
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 LEU 32 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 3.9 17.9 - - + +
31E ILE* 1.3 86.1 - - - +
33E HIS* 1.3 66.7 + - - +
34E LEU* 3.7 10.8 - - + +
35E THR* 3.1 24.9 + - - +
36E ILE* 4.0 1.6 + - - +
70E VAL* 4.1 3.8 - - - +
71E LEU* 4.3 11.9 - - + +
72E GLU 4.6 6.5 - - - +
74E PRO* 4.9 0.2 - - + -
94E SER* 3.6 35.4 - - - +
95E TYR* 3.9 28.3 - - + -
98E VAL* 3.9 26.0 - - + -
37F TYR* 4.2 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 1.3 72.9 - - - +
34E LEU* 1.3 64.4 + - - +
36E ILE* 3.3 16.6 + - - +
37E TYR* 3.3 16.3 - - - -
70E VAL* 3.4 22.7 + - + +
71E LEU 3.5 23.8 + - - -
72E GLU* 5.2 1.4 - - - -
73E ASP* 3.1 26.4 + - - +
33F HIS* 3.3 55.0 - + + -
37F TYR* 4.7 0.7 - - + -
73F ASP* 2.7 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.7 6.2 - - + +
33E HIS* 1.3 78.8 - - - +
35E THR* 1.3 64.0 + - - +
37E TYR* 2.8 27.1 + - + -
38E GLU* 3.0 31.8 + - + +
91E TYR* 3.5 43.7 - - + +
94E SER* 4.6 0.2 - - - -
95E TYR* 3.7 29.2 - - + +
34F LEU* 5.2 6.1 - - + -
37F TYR* 3.5 46.4 - - + -
91F TYR* 5.0 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL 3.7 0.3 + - - -
8E ASP 4.1 4.3 - - - -
9E ALA* 4.1 21.0 - - - +
12E LEU* 4.2 14.4 - - + -
31E ILE* 3.6 27.0 - - + +
32E LEU 3.1 26.2 + - - -
34E LEU* 1.3 78.4 - - - +
36E ILE* 1.3 61.1 + - - +
38E GLU* 3.9 4.5 - - - +
39E ALA* 2.9 24.0 + - + +
65E LEU* 4.4 3.6 - - + -
95E TYR* 2.7 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ILE* 4.4 16.4 - - + -
32E LEU 4.5 1.3 - - - +
33E HIS* 3.6 13.5 - - - +
34E LEU 3.0 0.4 + - - -
35E THR* 1.3 76.1 - - - +
37E TYR* 1.3 67.4 + - + +
39E ALA* 3.7 0.7 - - - +
40E GLY* 3.0 22.0 + - - -
65E LEU* 4.3 26.0 - - + -
70E VAL* 5.0 12.3 - - + -
73F ASP* 3.3 35.4 - - + +
74F PRO 4.9 9.9 - - - +
76F LEU* 3.7 21.3 - - + +
90F PHE* 4.4 3.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E HIS 3.3 26.9 - - - -
34E LEU* 2.8 11.4 + - + +
36E ILE* 1.3 80.6 - - + +
38E GLU* 1.3 60.8 + - - +
40E GLY* 3.7 0.2 - - - -
41E ASN* 2.9 31.5 + - - +
32F LEU* 4.2 13.4 - - + +
33F HIS* 4.7 0.7 - - + -
34F LEU* 3.6 47.3 - - + -
73F ASP* 2.8 32.0 + - + -
74F PRO* 3.2 24.3 - - + +
79F VAL* 6.3 0.2 - - + -
90F PHE* 3.8 16.3 - + - -
91F TYR* 3.6 20.6 - - + -
94F SER* 3.6 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 3.5 24.2 + - + +
34E LEU* 3.0 35.7 + - + +
35E THR 3.9 3.1 - - - +
37E TYR* 1.3 75.3 - - - +
39E ALA* 1.3 62.7 + - - +
41E ASN* 3.4 2.3 + - - +
42E ALA* 3.1 22.0 + - - +
91E TYR* 3.8 17.7 - - + +
92E ASP* 5.2 3.6 - - - +
95E TYR* 2.7 34.5 + - - -
91F TYR* 3.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 4.3 7.3 - - + +
12E LEU* 4.8 6.3 - - + -
13E TYR* 3.8 21.0 - - + -
35E THR* 2.9 18.0 + - + +
36E ILE 3.7 3.8 - - - +
38E GLU* 1.3 78.1 - - - +
40E GLY* 1.3 63.4 + - - +
42E ALA* 3.1 6.4 + - - +
43E LEU* 3.1 19.4 + - - +
61E LEU* 4.1 27.1 - - + +
65E LEU* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ILE 3.0 12.6 + - - -
37E TYR 3.3 2.9 + - - -
39E ALA* 1.3 78.5 - - - +
41E ASN* 1.3 54.5 + - - +
43E LEU* 3.2 7.7 + - - +
44E TRP* 2.9 28.2 + - - +
76F LEU* 3.5 23.1 - - - +
80F LEU* 4.9 0.9 - - - +
90F PHE* 3.6 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E TYR 2.9 17.7 + - - +
38E GLU* 3.6 5.2 - - - +
40E GLY* 1.3 76.3 - - - +
42E ALA* 1.3 62.6 + - - +
44E TRP* 3.3 30.2 + - - +
45E LYS* 3.1 41.9 + - - +
89F THR* 4.5 1.6 - - - -
90F PHE* 3.6 17.8 - - + +
91F TYR* 3.6 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.7 23.1 - - + +
38E GLU 3.1 13.0 + - - +
39E ALA* 3.1 8.9 + - - +
41E ASN* 1.3 78.0 + - - +
43E LEU* 1.3 62.3 + - - +
45E LYS* 3.1 21.9 + - - +
46E GLU* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.3 16.9 + - - +
39E ALA 3.1 10.7 + - - +
40E GLY* 3.5 9.9 - - - +
42E ALA* 1.3 76.4 - - - +
44E TRP* 1.3 57.5 + - - +
46E GLU* 3.3 15.5 + - + +
47E ALA* 3.0 22.7 + - - +
51E ARG* 4.6 2.2 - - - +
54E TRP* 4.3 15.9 - - + -
57E ALA* 4.0 20.9 - - + +
58E SER* 3.5 42.2 - - - +
61E LEU* 3.8 18.8 - - + -
76F LEU* 4.4 1.6 - - + -
80F LEU* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLY 2.9 12.7 + - - +
41E ASN* 3.4 38.8 - - - +
42E ALA 3.1 0.2 - - - -
43E LEU* 1.3 75.5 - - - +
45E LYS* 1.3 79.5 + - + +
47E ALA* 3.2 1.7 + - - +
48E ARG* 2.8 69.6 + - + +
80F LEU* 4.1 18.8 - - + -
83F ALA* 3.8 22.3 + - + +
84F VAL* 4.6 9.3 - - + +
87F GLY* 5.8 0.8 - - - -
88F LEU 3.3 16.4 + - - +
89F THR* 3.5 32.3 - - + -
90F PHE* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ASN* 3.1 33.9 + - - +
42E ALA* 3.1 12.5 + - - +
44E TRP* 1.3 92.0 - - + +
46E GLU* 1.3 63.3 + - + +
48E ARG* 3.2 7.7 + - - +
49E LEU* 3.0 37.2 + - + +
45G LYS* 3.9 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 2.9 39.1 + - - -
42E ALA* 3.2 9.6 + - - +
43E LEU* 3.5 8.5 - - - +
44E TRP 3.2 0.4 - - - -
45E LYS* 1.3 78.7 - - + +
47E ALA* 1.3 61.7 + - - +
49E LEU* 3.1 15.1 + - - +
50E GLY 3.3 0.7 + - - -
51E ARG* 2.5 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU 3.0 14.0 + - - +
44E TRP* 3.2 10.1 + - + +
46E GLU* 1.3 76.5 - - - +
48E ARG* 1.3 63.8 + - - +
50E GLY* 3.2 13.0 + - - -
51E ARG* 4.2 14.1 + - - +
54E TRP* 3.7 31.4 - - + +
80F LEU* 4.8 1.1 - - + -
84F VAL* 4.3 18.6 - - + -
111G ARG* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E TRP* 2.8 54.9 + - + +
45E LYS* 3.2 13.2 + - - +
47E ALA* 1.3 76.4 - - - +
49E LEU* 1.3 65.0 + - + +
50E GLY 3.3 0.2 - - - -
87F GLY* 5.2 9.3 + - - -
87G GLY 5.8 0.6 + - - -
88G LEU* 5.7 0.6 - - - +
92G ASP* 4.6 8.7 + - - -
109G GLN 3.4 0.2 - - - +
110G ASP* 3.2 33.5 + - - +
111G ARG* 2.9 38.3 + - - +
112G GLU* 3.3 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS* 3.0 24.2 + - + +
46E GLU* 3.1 8.4 + - - +
48E ARG* 1.3 82.8 - - + +
50E GLY* 1.3 55.7 + - - -
51E ARG 3.7 0.4 - - - -
10G SER* 3.9 28.9 - - - -
109G GLN* 3.3 32.9 - - + +
110G ASP* 4.1 18.8 - - + +
111G ARG* 3.5 0.2 + - - -
----------------------------------------------------------
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