Contacts of the helix formed by residues 30 - 53 (chain A) in PDB entry 2J3W
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 SER 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.4 25.2 - - - +
28A ALA 3.1 0.2 - - - -
29A GLU* 1.3 79.1 - - - +
31A LYS* 1.3 59.0 + - - +
32A ASP 3.5 1.1 - - - -
33A ASP* 3.4 10.6 + - - +
34A HIS* 3.1 53.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 5.4 4.5 - - - -
23A LEU* 6.2 4.5 - - + -
26A GLY 5.3 2.5 - - - +
27A LYS* 2.9 11.2 + - - +
28A ALA* 3.1 17.9 - - - +
30A SER* 1.3 74.4 - - - +
32A ASP* 1.3 74.1 + - - +
34A HIS* 3.3 6.9 + - - +
35A ARG* 3.0 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 4.6 0.8 + - - -
29A GLU* 3.7 28.4 - - - +
30A SER 3.5 1.0 - - - +
31A LYS* 1.3 89.1 - - - +
33A ASP* 1.3 65.2 + - - +
35A ARG* 3.2 12.8 + - - +
36A HIS* 3.2 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 4.3 12.5 + - - +
30A SER* 3.4 10.5 + - - +
31A LYS 3.3 0.6 - - - -
32A ASP* 1.3 79.6 - - - +
34A HIS* 1.3 60.2 + - + +
36A HIS* 3.4 14.6 + - - +
37A LEU* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 6.1 2.7 - - + -
27A LYS* 5.4 3.9 - - + +
30A SER* 3.1 41.0 + - - +
31A LYS* 3.7 6.5 - - - +
32A ASP 3.3 0.2 - - - -
33A ASP* 1.3 76.6 - - + +
35A ARG* 1.3 53.4 + - - +
37A LEU* 3.8 19.8 - - + +
38A ASN* 2.7 53.5 + - - +
70A TRP* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 5.0 4.5 - - - -
19A GLU* 5.9 0.7 - - - -
21A GLU* 2.8 52.8 + - - +
31A LYS* 3.0 34.5 + - + +
32A ASP* 3.4 16.7 + - - +
33A ASP 3.2 0.4 - - - -
34A HIS* 1.3 73.6 - - - +
36A HIS* 1.3 65.2 + - + +
38A ASN* 3.2 9.6 + - - +
39A GLN* 2.9 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 3.2 28.3 + - + +
33A ASP* 3.6 15.9 - - - +
35A ARG* 1.3 82.2 - - + +
37A LEU* 1.3 64.2 + - - +
39A GLN* 3.1 21.8 + - - +
40A PHE* 2.9 42.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 3.0 14.9 + - - +
34A HIS* 3.8 21.3 - - + +
36A HIS* 1.3 81.3 - - - +
38A ASN* 1.3 58.1 + - - +
40A PHE* 3.3 12.1 + - + +
41A ILE* 2.8 56.5 + - + +
67A PHE* 4.8 9.2 - - + -
68A ASN* 5.1 7.4 - - - +
70A TRP* 6.2 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.9 28.1 - - + -
21A GLU* 5.0 0.4 + - - -
23A LEU* 4.4 19.6 - - - +
34A HIS* 2.7 41.5 + - - +
35A ARG* 3.2 7.9 + - - +
37A LEU* 1.3 76.1 - - - +
39A GLN* 1.3 56.7 + - - +
41A ILE* 3.3 2.1 + - - +
42A ALA* 2.9 29.5 + - - +
70A TRP* 2.6 43.9 + - - -
86A LEU* 3.4 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.1 24.2 - - + +
19A GLU* 3.9 14.2 - - - +
35A ARG* 2.9 38.2 + - + +
36A HIS* 3.4 24.4 + - - +
38A ASN* 1.3 74.4 - - - +
40A PHE* 1.3 63.4 + - + +
42A ALA* 3.2 5.0 + - - +
43A HIS* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 2.9 37.9 + + + +
37A LEU* 3.3 14.1 + - + +
39A GLN* 1.3 79.6 - - + +
41A ILE* 1.3 60.5 + - - +
43A HIS* 3.2 10.1 + + + +
44A ALA* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.8 46.9 + - + +
38A ASN* 3.7 4.5 - - - +
40A PHE* 1.3 73.0 - - + +
42A ALA* 1.3 63.8 + - - +
44A ALA* 3.4 7.3 + - - +
45A ALA* 3.0 22.2 + - - +
67A PHE* 3.5 55.4 - - + -
68A ASN* 4.5 1.3 - - - +
70A TRP* 3.6 27.6 - - + +
72A VAL* 4.5 6.3 - - + -
86A LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.8 22.4 - - + +
8A VAL* 4.0 17.5 - - + -
10A VAL* 5.8 0.2 - - - +
38A ASN 2.9 13.9 + - - +
39A GLN* 3.2 9.9 - - - +
41A ILE* 1.3 78.5 - - - +
43A HIS* 1.3 61.5 + - - +
45A ALA* 3.3 15.8 + - - +
46A LEU* 3.8 7.8 + - - +
84A ILE* 4.1 20.8 - - + +
86A LEU* 4.3 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.4 0.7 - - - -
14A ASP* 4.1 31.2 + - + +
16A PRO* 6.3 0.7 - - + -
39A GLN 2.8 19.9 + - - +
40A PHE* 3.6 12.9 - + + +
42A ALA* 1.3 72.8 - - - +
44A ALA* 1.3 66.9 + - - +
46A LEU* 3.1 40.3 + - + +
47A ASP* 4.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE 2.8 21.7 + - - +
41A ILE* 3.7 7.9 - - - +
43A HIS* 1.3 77.9 + - - +
45A ALA* 1.3 62.1 + - - +
46A LEU 3.1 1.6 + - - -
47A ASP* 3.4 22.0 + - - +
48A LEU* 4.5 1.6 + - - +
67A PHE* 6.2 5.2 - - + -
----------------------------------------------------------
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 ILE 3.0 14.0 + - - +
42A ALA* 3.4 11.9 - - - +
43A HIS 3.2 0.4 - - - -
44A ALA* 1.3 75.7 - - - +
46A LEU* 1.3 63.4 + - - +
47A ASP 3.3 0.2 - - - -
48A LEU* 3.4 10.5 + - - +
49A VAL* 3.0 25.3 + - + +
64A VAL* 5.0 2.1 - - + +
65A ASP* 6.1 4.3 - - + +
72A VAL* 3.6 32.5 - - + -
84A ILE* 4.4 9.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
10A VAL* 4.0 36.8 - - + -
14A ASP* 4.0 20.4 - - + +
42A ALA 4.1 2.7 - - - +
43A HIS* 3.2 41.7 - - + +
44A ALA 3.1 1.0 - - - -
45A ALA* 1.3 75.1 - - - +
47A ASP* 1.3 59.1 + - - +
49A VAL* 3.0 3.8 + - + -
50A ASP* 2.7 40.3 + - - +
82A ARG* 3.9 30.7 - - + +
84A ILE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS* 5.0 4.9 - - - +
44A ALA* 3.4 15.1 + - - +
45A ALA 3.3 0.2 - - - -
46A LEU* 1.3 81.7 - - - +
48A LEU* 1.3 63.4 + - + +
50A ASP* 3.4 6.8 + - - +
51A GLU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 4.5 0.4 + - - -
45A ALA* 3.4 11.4 + - - +
47A ASP* 1.3 82.5 - - + +
49A VAL* 1.3 58.0 + - - +
51A GLU* 3.4 23.5 + - - +
52A ASN* 3.0 43.7 + - - +
64A VAL* 3.4 30.1 - - + +
65A ASP* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 3.0 20.2 + - + +
46A LEU* 3.0 11.5 + - - +
48A LEU* 1.3 72.7 - - - +
50A ASP* 1.3 58.1 + - - +
51A GLU 3.0 4.7 - - - -
52A ASN* 4.8 0.4 - - - -
53A MET* 2.9 38.6 + - + +
61A LEU* 4.0 9.0 - - + -
64A VAL* 4.4 10.5 - - + -
74A ALA* 3.6 26.5 - - + -
76A VAL* 3.9 27.1 - - + -
82A ARG* 4.2 14.4 - - + -
84A ILE* 3.8 14.6 - - + -
----------------------------------------------------------
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 LEU* 2.7 26.5 + - - +
47A ASP* 3.8 6.7 - - - +
49A VAL* 1.3 72.4 - - - +
51A GLU* 1.3 56.3 + - - +
53A MET* 3.3 14.3 - - + +
54A TRP* 3.3 27.4 + - - -
82A ARG* 2.9 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP 3.2 11.5 + - - +
48A LEU* 3.4 30.1 - - - +
49A VAL 3.0 0.4 - - - -
50A ASP* 1.3 77.0 - - - +
52A ASN* 1.3 76.8 + - - +
53A MET 3.3 1.1 + - - -
54A TRP* 3.4 14.8 + - - +
55A LEU* 3.9 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.0 24.9 + - - +
49A VAL* 4.3 1.3 - - - +
51A GLU* 1.3 92.2 + - - +
53A MET* 1.3 65.1 + - - +
54A TRP 3.2 0.2 - - - -
55A LEU* 3.1 26.7 + - - +
56A SER* 3.5 12.3 + - - -
61A LEU* 4.5 14.7 - - + +
64A VAL* 3.9 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.9 26.6 + - + +
50A ASP* 3.3 41.3 - - - +
52A ASN* 1.3 77.7 - - - +
54A TRP* 1.3 83.2 + - + +
56A SER 2.7 17.0 - - - +
61A LEU* 4.2 9.1 - - + +
76A VAL* 4.1 18.4 - - + -
80A HIS* 3.9 26.7 - - + +
82A ARG* 4.0 14.6 - - + -
78B ARG* 2.4 35.2 + - - +
80B THR* 3.8 1.0 - - - +
----------------------------------------------------------
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