Contacts of the helix formed by residues 36 - 58 (chain B) in PDB entry 2NUG
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS 3.1 7.6 + - - +
24B ALA* 3.3 19.3 - - - +
26B THR 3.0 24.9 + - - -
27B HIS* 3.3 40.9 + + + -
28B VAL 5.3 0.2 - - - -
35B HIS* 1.3 73.9 - - - +
37B GLU* 1.3 85.1 + - - +
38B THR 3.4 2.9 - - - -
39B LEU* 3.2 6.9 + - - +
40B GLU* 2.8 34.5 + - + -
104B ILE* 3.7 13.2 - - + +
107B ASP* 3.4 38.4 + - + +
108B VAL* 3.6 27.6 - - + -
111B ALA* 3.6 10.8 - - + -
3D A 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 3.4 19.8 + - - +
64A GLU* 3.6 28.5 - - - +
27B HIS* 5.0 0.5 - - - -
28B VAL* 4.4 17.3 + - + +
35B HIS* 3.2 27.9 - - + +
36B TYR* 1.3 97.2 + - - +
38B THR* 1.3 60.7 + - - +
40B GLU* 3.1 7.0 + - - +
41B PHE* 3.3 19.4 + - - +
107B ASP* 5.3 0.3 - - - +
510B MG 2.1 32.5 - - - -
3D A 4.7 8.0 + - - -
18F G 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.9 28.5 - - + -
60A PRO 3.8 21.9 + - - +
61A ASN 5.0 1.0 - - - -
62A LYS 3.0 27.1 + - - +
63A ARG* 4.3 10.0 - - - -
64A GLU* 5.3 2.7 - - - +
67A LEU* 4.6 4.9 - - + -
35B HIS* 4.9 3.8 + - - -
36B TYR 3.4 0.4 - - - -
37B GLU* 1.3 73.7 - - - +
39B LEU* 1.3 68.8 + - + +
41B PHE* 3.2 9.6 + - + +
42B LEU* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.0 14.4 - - + +
23B LYS* 4.0 20.0 - - + +
24B ALA* 3.7 36.1 - - + +
35B HIS 4.9 2.2 + - - +
36B TYR* 3.2 9.9 + - - +
38B THR* 1.3 79.9 - - + +
40B GLU* 1.3 52.7 + - - +
42B LEU* 3.3 2.5 + - + +
43B GLY* 2.7 31.9 + - - -
111B ALA* 3.8 16.1 - - + +
114B ALA* 3.1 19.6 - - + +
115B ALA* 4.3 9.2 - - + +
118B ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 2.8 20.7 + - + +
37B GLU* 3.1 7.7 - - - +
38B THR 3.2 0.2 - - - -
39B LEU* 1.3 75.1 - - - +
41B PHE* 1.3 64.7 + - - +
43B GLY* 3.7 0.2 - - - -
44B ASP* 2.9 25.5 + - - +
107B ASP* 3.2 43.3 - - - +
110B GLU* 3.5 7.4 - - - +
111B ALA* 3.8 10.7 - - + +
508B MG 2.0 32.3 - - - -
510B MG 2.0 32.7 - - - -
17F A 2.8 9.4 + - - +
18F G 4.4 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.8 22.7 - - + +
55A LEU* 4.8 4.0 - - + -
56A VAL* 3.7 20.9 - - + -
64A GLU* 4.4 17.5 - - + -
67A LEU* 3.6 29.8 - - + -
68A SER* 3.9 24.0 - - - -
71A LYS* 3.8 32.2 + - + -
37B GLU 3.3 10.0 + - - +
38B THR* 3.2 10.9 + - - +
40B GLU* 1.3 83.0 - - - +
42B LEU* 1.3 60.4 + - - +
44B ASP* 3.7 11.0 + - - +
45B ALA* 3.8 7.4 + - - +
17F A 3.8 37.2 - - - +
18F G 5.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.5 12.6 - - + -
52A VAL* 3.8 14.6 - - + +
53A ASP* 3.7 46.2 - - + +
56A VAL* 4.3 17.0 - - + -
38B THR 3.2 9.3 + - - +
39B LEU* 3.7 7.2 - - + +
41B PHE* 1.3 78.1 - - - +
43B GLY* 1.3 60.8 + - - +
45B ALA* 3.2 4.9 + - - +
46B LEU* 3.0 25.3 + - + +
114B ALA* 4.0 12.3 - - + -
117B TYR* 4.0 13.5 - - + -
118B ILE* 3.9 28.5 - - + -
122B ARG* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 2.7 17.1 + - - -
40B GLU 3.3 1.5 + - - -
42B LEU* 1.3 70.7 - - - +
44B ASP* 1.3 58.9 + - - +
46B LEU* 4.2 5.4 - - - -
47B VAL* 2.8 36.3 + - - +
110B GLU* 3.2 30.1 - - - -
114B ALA* 3.5 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 4.2 9.7 + - - -
40B GLU 2.9 17.1 + - - +
41B PHE* 3.8 6.8 - - - +
43B GLY* 1.3 74.3 - - - +
45B ALA* 1.3 61.1 + - - +
47B VAL* 4.2 0.6 - - - -
48B ASN* 2.9 44.3 + - - +
110B GLU* 3.1 20.5 - - - +
507B MG 2.1 30.0 - - - -
12C G 2.8 17.6 + - - -
17F A 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 4.5 2.4 - - - +
48A ASN* 4.5 4.0 - - + +
49A PHE* 4.0 21.1 - - + +
52A VAL* 3.9 35.0 - - + -
71A LYS* 5.3 2.9 - - - +
41B PHE 3.8 2.3 + - - +
42B LEU 3.2 9.2 + - - +
44B ASP* 1.3 84.7 + - - +
46B LEU* 1.3 63.2 + - - +
48B ASN* 3.8 6.3 - - - +
49B PHE* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.6 38.3 - - + -
42B LEU* 3.0 17.1 + - + +
43B GLY* 3.3 4.0 + - - +
45B ALA* 1.3 73.9 - - - +
47B VAL* 1.3 66.5 + - - +
49B PHE* 3.1 8.7 + - + +
50B PHE* 3.0 61.4 + - + -
113B TRP* 3.4 35.9 - - + +
114B ALA* 4.1 4.0 - - - -
117B TYR* 3.6 26.9 - - + -
124B ALA* 5.0 2.0 - - + -
127B THR* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 2.8 23.8 + - - +
44B ASP 4.4 0.9 - - - +
46B LEU* 1.3 70.0 - - + +
48B ASN* 1.3 68.0 + - - +
50B PHE* 3.0 10.2 + - + +
51B ILE* 2.9 24.6 + - + +
80B PHE* 3.5 33.7 - - + -
109B PHE* 4.5 2.9 - - + -
110B GLU* 4.7 8.1 - - + -
113B TRP* 3.7 37.9 - - + -
131B PHE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 4.6 5.8 - - + -
44B ASP* 2.9 35.7 + - - +
45B ALA* 3.8 6.5 - - - +
46B LEU 3.3 0.2 - - - -
47B VAL* 1.3 75.7 - - - +
49B PHE* 1.3 58.7 + - - +
51B ILE* 3.3 1.4 + - - +
52B VAL* 2.9 37.9 + - + +
71B LYS* 5.4 3.9 - - - +
75B ILE* 3.4 41.2 - - + +
80B PHE* 4.4 7.1 - - - -
12C G 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.4 8.3 - - + -
45A ALA* 3.9 20.1 - - + +
46A LEU* 3.5 38.4 - - + -
49A PHE* 4.4 19.7 - + + -
117A TYR* 3.3 41.5 - + - -
124A ALA* 4.2 15.0 - - + -
45B ALA 3.1 11.6 + - - +
46B LEU* 3.1 8.4 + - + +
47B VAL 3.1 0.4 - - - -
48B ASN* 1.3 79.3 - - - +
50B PHE* 1.3 89.0 + + - +
52B VAL 3.3 0.3 + - - -
53B ASP* 2.9 31.3 + - + +
124B ALA* 5.3 1.6 - - + -
128B ARG* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.0 54.7 + - + -
47B VAL* 3.0 13.7 + - + +
49B PHE* 1.3 92.8 - + - +
51B ILE* 1.3 62.6 + - - +
53B ASP* 4.7 0.7 - - - -
54B LEU* 3.1 10.0 + - - +
113B TRP* 4.6 2.5 - + - -
124B ALA* 4.1 4.5 - - - -
127B THR* 3.8 26.2 - - + -
128B ARG* 3.5 40.4 - - + -
131B PHE* 3.6 42.4 - + + -
132B TYR* 2.7 29.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 2.9 23.3 + - + +
48B ASN 3.8 3.4 - - - +
50B PHE* 1.3 74.6 - - - +
52B VAL* 1.3 66.1 + - - +
54B LEU* 3.2 7.7 + - - +
55B LEU* 3.0 29.7 + - + +
71B LYS* 4.9 1.6 - - + -
74B LEU* 3.0 61.2 - - + +
75B ILE* 3.7 18.4 - - + -
79B PHE* 5.3 1.6 - - + -
80B PHE* 3.8 16.2 - - + -
83B LEU* 5.6 0.4 - - + -
131B PHE* 4.4 15.0 - - + -
139B ILE* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 25.4 - - + +
42A LEU* 3.7 31.0 - - + -
45A ALA* 3.9 16.4 - - + -
48B ASN 2.9 20.5 + - - +
49B PHE 3.9 1.1 - - - +
51B ILE* 1.3 75.0 - - - +
53B ASP* 1.3 64.5 + - - +
55B LEU* 3.3 8.9 + - - +
56B VAL* 3.0 22.4 + - + +
71B LYS* 3.7 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.8 16.3 - - + +
117A TYR* 2.6 36.8 + - - -
122A ARG* 2.8 35.0 + - - -
49B PHE* 2.9 24.6 + - + +
50B PHE* 4.7 0.4 - - - -
52B VAL* 1.3 76.4 - - - +
54B LEU* 1.3 58.4 + - - +
56B VAL* 3.3 1.9 + - - +
57B GLN* 2.8 32.0 + - - +
128B ARG* 3.9 6.2 - - - -
132B TYR* 3.7 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE 3.1 15.2 + - - +
51B ILE* 3.2 9.2 + - - +
53B ASP* 1.3 77.1 - - - +
55B LEU* 1.3 62.4 + - + +
57B GLN* 3.4 5.9 + - - +
58B TYR* 3.2 56.0 + - + +
132B TYR* 3.4 21.7 + - + +
136B LYS* 4.0 33.0 - - + +
139B ILE* 3.8 46.0 - - + -
140B LEU* 4.1 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.5 5.6 - - + -
51B ILE* 3.0 23.4 + - + +
52B VAL* 3.6 11.9 - - - +
54B LEU* 1.3 79.1 - - + +
56B VAL* 1.3 61.1 + - - +
58B TYR* 3.4 2.5 + - - +
59B SER* 3.2 26.7 + - - -
67B LEU* 3.7 36.7 - - + +
70B LEU* 4.1 15.7 - - + -
71B LYS* 3.7 26.7 - - + +
74B LEU* 3.9 10.8 - - + -
139B ILE* 5.4 2.2 - - + -
140B LEU* 6.0 1.1 - - - -
143B ILE* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.8 23.6 - - + +
39A LEU* 6.1 1.1 - - + -
41A PHE* 3.8 26.7 - - + -
42A LEU* 4.1 25.8 - - + -
118A ILE* 5.1 6.1 - - + -
122A ARG* 4.4 12.1 - - - +
52B VAL* 3.0 17.2 + - + +
53B ASP* 3.9 4.0 - - - +
55B LEU* 1.3 73.0 - - - +
57B GLN* 1.3 62.2 + - - +
59B SER 4.4 1.1 - - - -
60B PRO* 2.9 36.1 - - + +
67B LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 3.8 40.5 + - - +
53B ASP* 2.8 21.8 + - - +
54B LEU* 3.6 7.6 - - - +
56B VAL* 1.3 77.5 - - - +
58B TYR* 1.3 89.2 + - + +
60B PRO* 3.5 13.5 - - - +
132B TYR* 4.7 13.2 - - - -
136B LYS* 4.3 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.2 32.9 + - + +
55B LEU* 3.4 2.2 + - - +
57B GLN* 1.3 102.1 + - + +
59B SER* 1.3 65.7 + - - +
60B PRO* 3.6 3.7 - - - +
136B LYS* 2.5 44.4 + - - -
140B LEU* 4.1 26.7 - - + -
----------------------------------------------------------
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