Contacts of the helix formed by residues 36 - 59 (chain A) in PDB entry 2NUF
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 TYR 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS 3.4 6.7 + - - +
24A ALA* 3.5 26.0 - - - +
25A LEU 4.6 0.9 - - - -
26A THR 2.9 27.3 + - - -
27A HIS* 2.9 43.8 + + + -
28A VAL 5.5 0.4 - - - -
35A HIS* 1.3 72.9 - - - +
37A GLU* 1.3 73.5 + - + +
38A THR 3.4 1.3 - - - -
39A LEU* 3.2 9.6 + - - +
40A GLU* 3.0 24.6 + - + -
93A ILE* 6.1 0.2 - - + -
104A ILE* 3.4 19.0 - - + +
107A ASP* 3.5 39.1 + - + +
108A VAL* 4.0 16.8 - - + -
111A ALA* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.8 0.5 - - - +
35A HIS* 3.1 34.8 + - + +
36A TYR* 1.3 87.7 - - + +
38A THR* 1.3 64.9 + - - +
40A GLU* 3.4 11.5 + - - +
41A PHE* 3.3 16.5 + - - +
62B LYS 4.6 5.7 - - - +
63B ARG* 4.9 1.2 - - - -
64B GLU* 2.9 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.6 8.9 + - - -
35A HIS* 4.7 4.8 + - - -
36A TYR 3.4 0.4 - - - -
37A GLU* 1.3 77.7 - - - +
39A LEU* 1.3 64.0 + - - +
41A PHE* 3.1 21.2 - - - +
42A LEU* 3.3 7.8 + - - +
56B VAL* 4.5 22.2 - - + +
62B LYS* 4.4 32.1 + - + +
67B LEU* 4.5 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.5 10.1 - - + +
23A LYS* 3.6 43.3 - - + +
24A ALA* 3.7 26.9 - - + +
35A HIS 5.2 0.4 + - - +
36A TYR* 3.2 9.5 + - - +
38A THR* 1.3 75.3 - - - +
40A GLU* 1.3 54.5 + - - +
42A LEU* 3.1 4.6 + - + +
43A GLY* 2.6 33.8 + - - -
111A ALA* 3.8 14.6 - - + +
114A ALA* 3.3 17.2 - - + +
115A ALA* 4.4 8.5 - - + +
118A ILE* 3.7 29.6 - - + -
56B VAL* 6.4 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
36A TYR* 3.0 22.4 + - + +
37A GLU* 3.6 9.2 - - - +
38A THR 3.3 0.2 - - - -
39A LEU* 1.3 77.1 - - - +
41A PHE* 1.3 62.6 + - - +
43A GLY 4.3 0.2 - - - +
44A ASP* 2.9 42.4 + - - +
107A ASP* 3.2 35.1 - - + +
110A GLU* 3.4 10.7 - - + +
111A ALA* 3.8 11.2 - - + +
223A MG 2.4 25.1 - - - -
224A MG 2.3 28.7 - - - -
64B GLU* 5.0 2.4 - - - +
1C C 5.2 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 3.3 7.3 + - - +
38A THR* 3.1 17.2 + - + +
39A LEU 3.1 0.2 - - - -
40A GLU* 1.3 82.5 + - - +
42A LEU* 1.3 60.9 + - - +
44A ASP* 3.3 16.3 - - + +
45A ALA* 3.8 3.1 + - - +
224A MG 4.0 18.4 - - - -
52B VAL* 4.1 17.1 - - + +
55B LEU* 4.3 12.1 - - + -
56B VAL* 3.5 28.5 - - + -
64B GLU* 6.3 2.9 - - + -
67B LEU* 3.9 53.6 - - + -
68B SER* 4.5 11.2 - - - -
71B LYS* 4.0 26.7 - - + -
1C C 5.1 5.4 - - - -
2C A 4.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR 3.3 7.4 + - - +
39A LEU* 3.1 8.4 + - + +
41A PHE* 1.3 77.8 - - - +
43A GLY* 1.3 68.1 + - - +
45A ALA* 3.1 12.0 + - - +
46A LEU* 3.2 12.4 + - + +
114A ALA* 3.8 13.2 - - + -
117A TYR* 4.2 12.6 - - + -
118A ILE* 3.9 33.2 - - + -
122A ARG* 4.3 9.4 - - - +
49B PHE* 4.4 17.9 - - + -
52B VAL* 3.8 21.1 - - + +
53B ASP* 4.2 20.0 - - - +
56B VAL* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 2.6 18.2 + - - -
40A GLU 3.8 1.1 - - - -
42A LEU* 1.3 73.4 - - - +
44A ASP* 1.3 62.7 + - - +
46A LEU* 3.7 4.2 - - - +
47A VAL* 3.0 30.5 + - - +
110A GLU* 3.4 30.3 - - - -
113A TRP 5.1 0.2 - - - -
114A ALA* 3.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 2.9 30.6 + - - +
41A PHE* 3.3 15.3 - - + +
43A GLY* 1.3 76.3 - - - +
45A ALA* 1.3 57.8 + - - +
47A VAL* 4.3 1.8 - - - +
48A ASN* 3.0 31.2 + - - +
75A ILE* 5.6 5.2 - - - +
110A GLU* 3.2 9.2 - - - +
222A MG 3.0 25.9 - - - -
223A MG 3.9 0.9 - - - -
1C C 4.3 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 3.8 1.4 + - - +
42A LEU 3.1 8.8 + - - +
44A ASP* 1.3 77.1 - - - +
46A LEU* 1.3 65.5 + - - +
48A ASN* 3.3 3.3 + - - +
49A PHE* 3.0 24.8 + - - +
45B ALA 5.1 1.0 - - - +
48B ASN* 3.9 26.1 + - - +
49B PHE* 3.9 24.7 - - + +
52B VAL* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.2 11.5 + - + +
43A GLY* 3.7 8.5 - - - +
45A ALA* 1.3 79.9 - - - +
47A VAL* 1.3 59.1 + - + +
49A PHE* 3.2 6.3 + - - +
50A PHE* 3.0 62.3 + - + -
113A TRP* 3.2 33.4 - - + +
114A ALA* 4.5 1.8 - - - -
117A TYR* 3.8 24.9 - - + -
124A ALA* 4.8 2.5 - - + -
127A THR* 3.8 7.0 - - + -
49B PHE* 3.5 41.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.0 16.6 + - - +
44A ASP* 4.3 2.2 - - - +
46A LEU* 1.3 73.2 - - + +
48A ASN* 1.3 68.3 + - - +
50A PHE* 2.9 20.1 + - + +
51A ILE* 2.9 22.6 + - + +
75A ILE* 5.2 0.4 - - + -
80A PHE* 3.4 38.1 - - + -
109A PHE* 5.1 2.2 - - + -
110A GLU* 4.9 8.1 - - + -
113A TRP* 4.2 24.2 - - + -
131A PHE* 4.2 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.0 24.5 + - - +
45A ALA* 3.4 8.3 - - - +
47A VAL* 1.3 75.3 - - - +
49A PHE* 1.3 58.1 + - - +
51A ILE* 3.3 1.9 + - - +
52A VAL* 2.9 34.0 + - - +
71A LYS* 2.9 39.9 + - - +
75A ILE* 3.3 25.9 - - + +
45B ALA* 3.8 22.4 - - - +
48B ASN* 4.9 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 3.0 12.4 + - - +
46A LEU 3.2 8.5 - - - +
48A ASN* 1.3 77.3 - - - +
50A PHE* 1.3 88.9 + + - +
53A ASP* 3.0 25.7 + - + +
124A ALA* 5.2 1.6 - - + -
128A ARG* 5.0 4.7 - - - -
42B LEU* 4.9 6.3 - - + -
45B ALA* 3.9 17.5 - - + +
46B LEU* 3.7 38.6 - - + -
49B PHE* 4.1 29.4 - + + -
117B TYR* 3.7 35.7 - + - -
124B ALA* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.0 49.0 + - + -
47A VAL* 2.9 16.0 + - + +
49A PHE* 1.3 101.6 - + - +
51A ILE* 1.3 63.4 + - - +
53A ASP* 4.7 0.4 - - - -
54A LEU* 3.4 9.5 + - - +
113A TRP* 5.1 1.6 - + + -
124A ALA 4.1 4.7 - - - -
127A THR* 4.0 11.0 - - + -
128A ARG* 3.4 47.3 - - + -
131A PHE* 3.7 41.5 - + + -
132A TYR* 3.0 28.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 2.9 23.3 + - + +
48A ASN 3.7 5.6 - - - +
50A PHE* 1.3 74.2 - - - +
52A VAL* 1.3 67.2 + - + +
54A LEU* 3.1 6.6 + - - +
55A LEU* 2.9 25.4 + - + +
71A LYS* 5.4 2.5 - - + +
74A LEU* 3.4 49.8 - - + +
75A ILE* 4.0 20.4 - - + -
79A PHE* 5.1 2.2 - - + -
80A PHE* 5.2 1.8 - - + -
131A PHE* 4.0 13.7 - - + -
139A ILE* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 2.9 25.4 + - - +
49A PHE 4.0 0.7 - - - +
51A ILE* 1.3 77.6 - - + +
53A ASP* 1.3 65.8 + - - +
55A LEU* 3.1 7.4 + - - +
56A VAL* 3.0 22.7 + - + +
71A LYS* 3.6 38.6 - - + -
41B PHE* 4.1 21.8 - - + +
42B LEU* 3.7 35.9 - - + -
45B ALA* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.0 22.9 + - + +
50A PHE* 4.7 0.2 - - - -
51A ILE 3.3 0.2 - - - -
52A VAL* 1.3 75.8 - - - +
54A LEU* 1.3 61.1 + - - +
56A VAL* 3.2 6.2 - - - +
57A GLN* 2.8 40.4 + - - +
128A ARG* 4.0 4.9 + - - -
132A TYR* 3.6 17.5 + - - +
42B LEU* 3.9 16.4 - - + +
117B TYR* 2.4 39.7 + - - -
122B ARG* 3.1 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE 3.4 3.0 + - - +
51A ILE* 3.1 8.7 + - - +
53A ASP* 1.3 74.9 - - - +
55A LEU* 1.3 68.5 + - - +
57A GLN* 2.9 9.0 + - - +
58A TYR* 2.9 52.3 + - + +
132A TYR* 3.6 41.5 - - + +
136A LYS* 4.1 27.6 - - + +
139A ILE* 3.7 38.4 - - + -
140A LEU* 4.2 4.0 - - + -
143A ILE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 2.9 16.6 + - + +
52A VAL* 3.1 6.9 + - - +
54A LEU* 1.3 76.2 - - - +
56A VAL* 1.3 59.0 + - - +
59A SER* 2.8 47.4 + - - -
67A LEU* 3.9 13.7 - - + +
70A LEU* 3.4 31.6 - - + -
71A LYS* 3.7 42.0 - - + +
74A LEU* 3.8 18.8 - - + -
143A ILE* 3.9 11.3 - - + +
41B PHE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.0 15.8 + - + +
53A ASP* 3.2 23.3 - - - +
55A LEU* 1.3 76.0 - - - +
57A GLN* 1.3 64.4 + - + +
59A SER* 5.2 0.4 - - - -
62A LYS* 3.1 26.8 + - - +
67A LEU* 5.2 4.3 - - + -
38B THR* 4.5 19.1 - - + +
41B PHE* 3.2 35.9 - - + -
42B LEU* 4.3 25.8 - - + -
118B ILE* 6.3 0.2 - - + -
122B ARG* 4.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 2.8 41.7 + - - +
54A LEU* 2.9 12.5 + - - +
56A VAL* 1.3 83.6 - - + +
58A TYR* 1.3 84.5 + - + +
59A SER 3.8 0.2 - - - -
62A LYS* 4.2 6.3 + - - -
132A TYR* 5.1 1.2 + - - -
122B ARG* 3.2 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.9 38.8 + - + +
57A GLN* 1.3 100.6 + - + +
59A SER* 1.3 67.6 + - - +
60A PRO* 3.2 6.9 - - - +
136A LYS* 3.0 25.9 + - - -
140A LEU* 3.5 38.1 - - + +
143A ILE* 4.2 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 2.8 36.0 + - - +
57A GLN 3.8 0.8 - - - -
58A TYR* 1.3 71.0 - - - +
60A PRO* 1.3 74.8 - - - +
61A ASN 2.7 25.8 + - - -
62A LYS* 2.8 28.1 + - - +
66A PHE* 3.6 12.0 - - - -
67A LEU* 3.6 15.3 - - - +
70A LEU* 4.3 0.3 - - - +
143A ILE* 3.8 6.8 - - - +
----------------------------------------------------------
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