Contacts of the helix formed by residues 29 - 55 (chain A) in PDB entry 3EXG
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 ARG 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.3 34.6 - - - -
2A ALA 3.9 12.3 - - - +
3A ASN* 2.7 22.1 + - - +
28A THR* 1.3 73.7 - - - +
30A GLU* 1.3 79.9 + - - +
31A ASP 3.0 0.5 + - - -
32A GLY* 3.1 1.4 + - - -
33A LEU* 3.0 38.2 + - + +
295A MET* 5.1 0.5 - - - +
300A LEU* 2.4 65.5 + - + +
301A ALA* 3.9 1.6 - - - +
305A GLU* 3.0 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.4 5.5 + - - +
29A ARG* 1.3 88.0 - - - +
31A ASP* 1.3 57.7 - - - +
33A LEU* 3.7 9.6 - - - +
34A LYS* 3.6 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.9 9.4 - - + -
28A THR* 2.9 39.6 + - - +
30A GLU* 1.3 74.3 + - - +
32A GLY* 1.3 56.5 + - - +
33A LEU 2.9 5.2 - - - -
34A LYS* 2.7 36.8 + - - +
35A TYR* 2.9 41.0 + - + -
234A ARG* 4.9 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.3 20.6 - - - +
28A THR 3.0 7.5 + - - -
29A ARG 3.7 2.5 - - - -
31A ASP* 1.3 80.2 - - - +
33A LEU* 1.3 59.6 + - - +
35A TYR* 4.0 8.3 - - - -
36A TYR* 3.3 15.2 + - - +
291A LEU* 4.0 4.1 - - - +
295A MET* 2.8 32.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.0 33.5 + - - +
30A GLU* 3.7 11.0 - - - +
31A ASP 2.9 0.8 - - - -
32A GLY* 1.3 78.4 - - - +
34A LYS* 1.3 63.6 + - - +
36A TYR* 3.5 3.3 + - - +
37A ARG* 3.2 22.7 + - - +
295A MET* 3.6 20.2 - - + -
300A LEU 4.5 1.1 - - - +
301A ALA* 3.9 20.2 - - + -
305A GLU* 4.0 16.6 - - - +
306A LEU* 4.8 4.5 - - + -
309A ILE* 4.2 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU 3.6 10.5 + - - +
31A ASP* 2.7 20.4 + - - +
33A LEU* 1.3 78.4 - - - +
35A TYR* 1.3 77.2 - - - +
36A TYR 3.4 0.2 + - - -
37A ARG* 3.4 5.8 + - + +
38A MET* 3.1 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.3 13.9 - - + -
31A ASP* 2.9 36.3 + - - +
32A GLY* 4.2 7.6 - - - +
34A LYS* 1.3 92.8 - - - +
36A TYR* 1.3 60.4 + - - +
38A MET* 3.9 4.1 - - + +
39A MET* 2.9 35.2 + - - +
73A VAL* 4.2 15.5 - - + -
77A ALA* 4.0 19.6 + - + +
230A ILE* 4.1 30.3 - - + -
231A LEU* 4.9 3.8 - - + -
234A ARG* 3.0 43.8 + - - -
238A ARG* 4.9 1.4 + - - -
291A LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY 3.3 17.0 + - - +
33A LEU 3.8 4.7 - - - +
34A LYS 3.2 0.6 - - - -
35A TYR* 1.3 77.0 - - - +
37A ARG* 1.3 61.1 + - - +
38A MET 3.1 0.2 + - - -
39A MET* 3.2 3.3 + - + +
40A GLN* 2.8 46.5 + - + +
288A ILE* 3.7 28.6 - - + +
291A LEU* 3.9 15.7 - - + +
292A LYS* 4.0 31.5 - - + +
295A MET* 4.3 5.2 - - + -
306A LEU* 3.9 43.9 - - + +
309A ILE* 4.3 15.3 - - + -
310A ASP* 3.2 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.2 14.6 + - - +
34A LYS* 3.4 5.1 + - - +
36A TYR* 1.3 79.6 - - - +
38A MET* 1.3 56.4 + - - +
40A GLN* 3.7 2.9 + - - -
41A THR* 2.9 36.6 + - - +
309A ILE* 3.2 55.3 + - + +
312A GLU* 3.7 38.4 + - - +
313A VAL* 3.9 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.1 56.9 + - + +
35A TYR* 4.6 3.8 - - + +
36A TYR 3.1 0.8 - - - -
37A ARG* 1.3 73.9 - - - +
39A MET* 1.3 70.1 + - - +
41A THR* 3.1 1.7 + - - -
42A VAL* 3.0 23.9 + - - +
73A VAL* 3.8 36.1 - - + +
76A GLU* 5.5 6.1 - - + -
96A PHE* 4.2 23.3 - - + -
97A THR* 4.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR 2.9 18.5 + - - +
36A TYR* 3.9 4.0 - - + +
38A MET* 1.3 74.0 - - - +
40A GLN* 1.3 65.5 + - - +
42A VAL* 3.1 2.1 + - - +
43A ARG* 2.9 20.6 + - - +
69A GLU* 3.6 33.3 - - + +
70A ALA* 4.0 8.7 - - - -
73A VAL* 3.8 19.3 - - + -
230A ILE* 4.2 14.6 - - + -
287A PRO 3.0 29.8 - - - +
288A ILE* 3.7 26.7 - - + +
291A LEU* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 2.8 37.1 + - + +
37A ARG* 4.5 0.9 - - - -
39A MET* 1.3 73.3 - - - +
41A THR* 1.3 57.1 + - - +
43A ARG* 3.6 11.0 - - - +
44A ARG* 2.8 60.6 + - - +
288A ILE* 3.5 27.9 - - + +
309A ILE* 5.6 0.7 - - + -
310A ASP* 3.5 37.8 - - - +
313A VAL* 3.7 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 2.9 25.1 + - - +
38A MET 3.1 2.2 + - - -
40A GLN* 1.3 73.1 - - - +
42A VAL* 1.3 61.0 + - - +
44A ARG* 3.4 0.3 + - - -
45A MET* 2.8 31.9 + - + +
96A PHE* 3.6 26.4 - - + -
102A VAL* 3.5 31.6 - - + -
313A VAL* 3.3 21.0 - - - +
316A GLU* 4.9 9.8 - - + +
317A ILE* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET 3.0 15.2 + - - +
39A MET* 3.7 5.8 - - - +
41A THR* 1.3 76.2 - - - +
43A ARG* 1.3 64.1 + - - +
45A MET* 3.5 7.9 - - - +
46A GLU* 3.1 24.4 + - + +
65A CYS* 3.9 26.0 - - - -
69A GLU* 3.6 21.1 - - + +
72A CYS* 4.5 11.2 - - - -
73A VAL* 5.0 1.6 - - + -
92A HIS 5.4 0.2 - - - -
93A GLY* 3.9 23.6 - - - +
96A PHE* 3.8 23.3 - - + -
97A THR* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET 2.9 12.2 + - - +
40A GLN* 3.6 17.9 - - - +
42A VAL* 1.3 79.1 - - - +
44A ARG* 1.3 68.5 + - - +
45A MET 3.0 0.9 + - - -
46A GLU* 3.2 2.3 + - - +
47A LEU* 3.1 38.8 + - + +
66A ASP* 3.6 17.2 + - - +
67A GLY 3.7 5.9 - - - +
69A GLU* 2.5 45.5 + - - +
260A TYR* 3.8 10.9 - - - -
282A ARG* 5.6 2.2 - - - +
286A ASP* 2.9 38.5 + - - -
287A PRO* 3.9 4.2 - - - +
288A ILE* 4.0 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 2.8 45.3 + - - +
43A ARG* 1.3 77.6 - - - +
45A MET* 1.3 63.1 + - - +
47A LEU* 3.3 35.7 + - - +
48A LYS* 3.1 22.3 + - - +
310A ASP 5.5 0.2 - - - +
313A VAL* 3.5 11.4 - - + +
314A ARG* 3.1 55.6 - - + +
317A ILE* 3.5 27.1 - - + +
289P ASP* 4.7 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.8 19.3 + - + +
42A VAL* 3.5 10.8 - - - +
43A ARG 3.0 0.4 - - - -
44A ARG* 1.3 81.5 - - - +
46A GLU* 1.3 63.4 + - - +
48A LYS* 3.2 4.2 + - - +
49A ALA* 2.9 25.3 + - + +
92A HIS* 4.1 27.6 - - - +
96A PHE* 4.6 7.4 - - + -
102A VAL* 3.2 42.2 - - + -
105A ILE* 3.3 43.3 - - + -
106A LEU* 4.4 12.4 - - + +
109A LEU* 6.0 0.9 - - + -
317A ILE* 3.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.1 19.0 + - + +
43A ARG 3.8 2.9 - - - +
45A MET* 1.3 81.0 - - + +
47A LEU* 1.3 61.5 + - - +
49A ALA* 3.4 5.2 - - - +
50A ASP* 2.8 32.1 + - - +
63A HIS 4.0 0.5 - - - +
64A LEU* 3.6 17.1 - - + +
65A CYS* 3.0 43.4 + - - +
66A ASP* 3.9 24.7 - - + +
92A HIS* 3.1 41.8 + - - +
93A GLY 5.0 0.2 - - - -
109A LEU* 5.4 0.3 - - - +
261A HIS* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.1 33.5 + - + +
44A ARG* 3.4 48.7 - - - +
45A MET 3.2 0.2 - - - -
46A GLU* 1.3 76.6 - - + +
48A LYS* 1.3 62.1 + - - +
50A ASP* 3.3 8.5 + - + +
51A GLN* 3.0 22.7 + - - +
66A ASP* 4.9 7.0 - - - +
261A HIS* 4.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 3.1 5.5 + - - -
45A MET 3.6 7.2 - - - +
47A LEU* 1.3 72.9 - - - +
49A ALA* 1.3 60.4 + - - +
51A GLN* 3.1 30.8 + - - +
52A LEU* 2.8 48.0 + - + +
106A LEU* 4.3 8.7 - - + -
317A ILE* 3.8 21.5 - - + -
318A GLU* 2.9 33.3 + - - -
321A ALA* 3.6 31.8 - - + +
286P ASN* 3.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A MET* 2.9 13.5 + - + +
46A GLU* 3.4 12.1 - - - +
48A LYS* 1.3 76.1 - - - +
50A ASP* 1.3 60.3 + - - +
52A LEU* 3.1 3.0 + - - +
53A TYR* 2.8 32.7 + - - +
58A ILE* 3.6 11.8 - - + +
62A CYS* 4.5 3.6 - - - -
64A LEU* 4.0 17.3 - - + -
106A LEU* 4.4 6.9 - - + +
109A LEU* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 2.8 16.8 + - - +
47A LEU* 3.5 11.1 - - + +
49A ALA* 1.3 76.8 - - - +
51A GLN* 1.3 60.7 + - - +
53A TYR* 3.4 13.5 + - - +
54A LYS* 2.7 58.7 + - - -
62A CYS* 5.3 0.2 - - - -
64A LEU* 3.4 22.9 - - + +
261A HIS* 3.6 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 3.0 15.8 + - - +
48A LYS* 3.1 36.2 + - - +
50A ASP* 1.3 73.4 - - - +
52A LEU* 1.3 67.8 + - - +
53A TYR 2.9 5.6 + - - -
54A LYS* 3.4 8.9 + - - +
55A GLN* 3.2 56.4 + - + +
286P ASN* 3.8 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 2.8 44.8 + - + +
49A ALA 3.6 4.7 - - - +
51A GLN* 1.3 77.0 - - - +
53A TYR* 1.3 57.4 + - - +
55A GLN* 3.9 13.7 - - - +
56A LYS 3.4 2.6 + - - -
57A ILE* 3.0 47.7 + - + +
58A ILE* 3.2 15.3 + - + -
106A LEU* 4.4 16.4 - - + -
110A THR* 4.1 18.6 - - + -
321A ALA* 4.7 11.4 - - + +
324A ALA* 5.4 0.2 - - + -
325A THR* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 2.8 15.9 + - - +
50A ASP* 3.8 14.4 - - - +
51A GLN 2.9 0.6 - - - -
52A LEU* 1.3 78.0 - - - +
54A LYS* 1.3 63.9 + - + +
55A GLN 3.1 4.5 - - - -
56A LYS* 3.4 15.3 + - - +
58A ILE* 3.2 39.2 - - + +
59A ARG* 4.6 1.1 - - - -
60A GLY 3.4 23.4 + - - -
61A PHE* 4.4 0.6 - - - -
62A CYS* 3.3 44.9 + - + +
64A LEU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 2.7 64.8 + - - +
51A GLN* 3.4 7.0 + - - +
53A TYR* 1.3 78.4 - - + +
55A GLN* 1.3 61.8 + - + +
56A LYS* 3.3 16.2 + - - +
261A HIS* 6.1 0.4 - - - -
289N ASP* 4.2 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.2 46.6 + - + +
52A LEU* 3.8 18.8 - - - +
53A TYR 3.1 0.6 - - - -
54A LYS* 1.3 80.1 - - + +
56A LYS* 1.3 74.8 + - - +
57A ILE* 3.5 18.3 + - + +
289N ASP* 3.1 41.1 + - + +
----------------------------------------------------------
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