Contacts of the helix formed by residues 26 - 48 (chain A) in PDB entry 2WMN
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 ASP 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 2.8 29.0 + - - +
24A ASN* 3.4 27.2 + - - +
25A GLY* 1.3 76.6 - - - +
27A LEU* 1.3 63.5 + - - +
28A SER 3.3 2.2 - - - -
29A GLU* 3.2 21.7 - - - +
30A ALA 3.1 16.5 + - - -
177A LYS 5.4 1.6 - - - +
179A PRO* 4.4 19.8 - - - +
292A LYS* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.4 29.6 - - + +
25A GLY* 3.3 21.9 + - - +
26A ASP* 1.3 74.5 - - - +
28A SER* 1.3 57.7 + - - +
30A ALA* 3.1 6.4 + - + +
31A ALA* 2.8 28.1 + - - +
97A GLY 4.8 1.6 - - - +
100A LYS* 3.6 33.9 - - + +
101A ALA* 3.9 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 3.3 0.8 - - - -
27A LEU* 1.3 77.9 - - - +
29A GLU* 1.3 53.7 + - - +
31A ALA* 3.3 3.9 + - - +
32A MET* 2.9 38.7 + - - +
101A ALA* 3.2 24.5 + - - +
103A ARG* 2.9 32.8 + - - -
152A LEU* 5.0 2.4 + - - +
177A LYS* 4.3 16.2 + - - -
288A PRO* 4.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.6 23.1 - - + +
26A ASP* 3.2 30.9 - - + +
28A SER* 1.3 78.0 + - - +
30A ALA* 1.3 63.3 + - - +
32A MET* 3.5 2.4 + - - +
33A CYS* 3.1 26.3 + - - -
177A LYS* 2.8 40.8 + - - +
287A PHE* 5.4 0.3 - - - -
288A PRO* 4.7 4.5 - - - +
289A TYR 3.2 24.2 + - - +
291A LYS 3.9 20.5 - - - +
292A LYS* 4.0 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.0 4.5 - - - +
21A HIS* 3.8 17.1 - - + +
22A VAL* 3.8 29.2 - - + +
26A ASP 3.1 8.3 + - - +
27A LEU* 3.1 14.6 + - + +
29A GLU* 1.3 77.7 - - - +
31A ALA* 1.3 62.3 + - - +
33A CYS* 3.0 10.4 + - - +
34A TYR* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 2.8 15.7 + - - +
28A SER* 3.4 13.5 - - - +
30A ALA* 1.3 68.8 - - - +
32A MET* 1.3 69.6 + - + +
34A TYR* 3.0 18.0 + - - +
35A VAL* 2.9 25.7 + - - +
94A CYS* 5.4 0.4 - - - -
97A GLY 4.0 17.9 - - - +
98A LEU* 3.9 26.2 - - + +
101A ALA* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 2.9 20.9 + - - +
29A GLU 3.8 0.4 - - - +
30A ALA 3.2 0.2 - - - -
31A ALA* 1.3 76.1 - - + +
33A CYS* 1.3 62.5 + - - +
35A VAL* 3.2 4.1 + - + +
36A HIS* 2.9 35.4 + - + +
61A ILE* 4.4 13.5 - - + +
62A THR* 4.0 33.7 - - - -
98A LEU* 4.0 25.8 - - + -
103A ARG* 5.1 2.7 - - - -
250A HIS* 4.5 6.1 - - + -
288A PRO* 3.6 43.7 - - + +
289A TYR* 3.5 23.1 - - - +
290A VAL* 4.0 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.6 32.2 - - + +
17A MET* 3.8 21.3 - - - -
18A ALA* 3.8 9.2 - - + -
21A HIS* 3.9 7.0 - - - -
29A GLU 3.1 18.5 + - - -
30A ALA 3.0 10.3 + - - +
32A MET* 1.3 76.1 - - - +
34A TYR* 1.3 64.0 + - - +
35A VAL 3.3 0.2 + - - -
36A HIS* 3.3 2.8 + - - +
37A VAL* 3.0 28.3 + - - +
290A VAL* 3.7 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 5.4 5.6 - - - -
18A ALA* 3.6 23.5 - - + +
22A VAL* 3.5 24.9 - - - +
30A ALA* 3.0 22.1 + - + +
31A ALA* 3.0 12.3 + - - +
33A CYS* 1.3 77.0 - - - +
35A VAL* 1.3 50.5 + - - +
37A VAL* 3.3 6.3 + - + +
38A THR* 2.7 40.8 + - - +
93A GLN* 3.7 53.4 + - + +
94A CYS* 3.6 17.3 - - - -
97A GLY* 3.8 19.5 - - - -
100A LYS* 5.2 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 2.9 20.2 + - - +
32A MET* 3.2 14.3 + - + +
34A TYR* 1.3 75.0 - - - +
36A HIS* 1.3 54.3 + - + +
38A THR* 3.3 1.8 + - - -
39A ALA* 2.7 34.0 + - - +
58A PHE* 4.1 21.2 - - + -
61A ILE* 4.1 31.2 - - + -
62A THR* 4.2 15.0 - - + -
65A ILE* 4.2 4.5 - - + -
94A CYS* 3.8 21.8 - - + -
98A LEU* 4.9 8.3 - - + -
110A ILE* 4.9 4.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
10A ARG* 5.3 0.2 + - - -
14A LEU* 3.9 15.3 - - + +
32A MET* 2.9 34.1 + - - +
33A CYS 3.7 3.6 - - - +
35A VAL* 1.3 73.4 - - + +
37A VAL* 1.3 66.6 + - - +
39A ALA* 3.4 1.7 + - - +
40A LEU* 3.1 26.3 + - - +
62A THR* 4.0 17.1 + - + +
64A ASN* 3.5 38.8 + - + +
65A ILE* 3.8 19.2 - - + +
67A GLU* 4.6 7.8 + - - -
68A GLU* 3.0 32.2 + - - +
289A TYR* 4.6 4.3 - + - -
290A VAL* 3.7 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.0 28.0 - - + +
14A LEU* 3.4 36.3 - - + -
15A ASP* 4.0 21.8 - - - +
33A CYS 3.0 12.0 + - - +
34A TYR* 3.6 8.7 - - + +
36A HIS* 1.3 77.3 - - - +
38A THR* 1.3 64.0 + - - +
40A LEU* 3.0 16.1 + - - +
41A VAL* 3.0 14.6 + - + +
90A LEU* 3.6 29.4 - - + -
93A GLN* 5.8 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
34A TYR 2.7 27.3 + - - -
35A VAL 3.6 3.4 - - - -
37A VAL* 1.3 76.0 - - - +
39A ALA* 1.3 60.8 + - - +
41A VAL* 3.4 2.9 + - - +
42A ALA* 3.0 22.0 + - - +
58A PHE* 3.7 21.1 - - + -
87A LEU* 3.8 12.1 - - + +
90A LEU* 3.5 22.0 + - + +
91A LEU* 3.7 25.4 - - + -
93A GLN* 5.6 0.3 + - - -
94A CYS* 2.8 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL 2.7 21.5 + - - +
36A HIS 3.9 2.5 - - - +
38A THR* 1.3 73.5 - - - +
40A LEU* 1.3 61.2 + - - +
42A ALA* 3.8 1.1 - - - +
43A GLU* 3.1 24.8 + - - +
55A CYS* 3.9 13.7 + - - -
58A PHE* 3.7 26.9 - - + -
65A ILE* 3.5 31.2 - - + -
68A GLU* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.7 43.3 - - + +
10A ARG* 4.7 12.1 - - + -
11A LYS* 6.0 2.5 - - + +
14A LEU* 5.9 0.9 - - + -
36A HIS 3.1 9.8 + - - +
37A VAL* 3.0 13.1 + - - +
39A ALA* 1.3 75.8 - - - +
41A VAL* 1.3 67.0 + - + +
42A ALA 3.3 0.2 + - - -
43A GLU* 3.3 7.5 + - + +
44A TYR* 3.2 22.8 + - + +
55A CYS* 5.7 0.2 - - - -
68A GLU* 3.3 45.8 - - + +
82A PHE* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.7 1.1 - - + -
37A VAL* 3.0 14.2 + - + +
38A THR 3.8 4.3 - - - +
40A LEU* 1.3 78.6 - - + +
42A ALA* 1.3 55.7 + - - +
44A TYR* 3.5 1.6 + - - +
45A LEU* 2.9 48.9 + - + +
82A PHE* 3.9 50.0 - - + -
83A ASN 5.0 0.2 - - - +
86A VAL* 4.8 1.6 - - + -
87A LEU* 4.0 11.7 - - + +
90A LEU* 3.4 34.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
38A THR 3.0 17.6 + - - +
39A ALA 3.8 1.3 - - - +
40A LEU 3.2 0.2 - - - -
41A VAL* 1.3 74.0 - - - +
43A GLU* 1.3 54.2 + - - +
45A LEU* 3.5 1.8 + - - +
46A THR* 2.7 40.5 + - - -
51A PHE* 3.9 17.9 - - + -
54A GLY* 3.6 9.4 - - - -
58A PHE* 3.6 27.8 - - + -
87A LEU* 4.1 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.1 17.8 + - - +
40A LEU* 3.6 9.0 - - + +
42A ALA* 1.3 73.7 - - - +
44A TYR* 1.3 66.3 + - - +
46A THR* 3.2 6.0 + - - +
47A ARG* 3.0 58.7 + - - +
53A GLN 4.2 3.1 - - - +
54A GLY* 3.4 8.4 - - - -
55A CYS* 3.0 39.9 + - - +
56A THR* 5.7 0.7 - - - +
68A GLU 5.3 4.3 - - - +
69A ALA 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 5.2 13.2 - - + -
40A LEU* 3.2 19.0 + - + +
41A VAL* 3.7 4.3 - - - +
43A GLU* 1.3 79.7 - - - +
45A LEU* 1.3 80.7 + - + +
47A ARG* 3.1 25.9 + - + +
48A LYS* 3.2 52.5 + - + +
81A HIS* 6.6 0.4 - - + -
82A PHE* 4.2 33.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 2.9 39.8 + - + +
42A ALA 3.9 1.1 - - - +
44A TYR* 1.3 89.9 - - + +
46A THR* 1.3 58.3 + - - +
48A LYS* 3.4 4.7 + - + -
49A GLY 3.3 2.8 + - - -
50A VAL* 2.9 47.5 + - + +
51A PHE* 3.1 17.5 + - + +
82A PHE 3.6 23.6 - - - +
83A ASN* 3.8 24.7 - - - -
84A GLU* 4.1 3.1 - - - +
87A LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 2.7 26.3 + - - -
43A GLU* 3.5 10.1 - - - +
44A TYR 3.1 0.2 - - - -
45A LEU* 1.3 72.4 - - - +
47A ARG* 1.3 65.9 + - + +
49A GLY* 3.0 14.7 + - - -
51A PHE* 3.4 17.5 - - - +
52A ARG 4.1 8.1 - - - +
53A GLN 3.0 43.4 + - - +
54A GLY 3.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.0 38.9 + - - +
44A TYR* 3.3 15.7 - - + +
46A THR* 1.3 77.6 - - + +
48A LYS* 1.3 60.8 + - + +
49A GLY 3.4 0.9 + - - -
----------------------------------------------------------
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 TYR* 3.2 54.8 + - + +
45A LEU* 3.4 8.7 + - + +
46A THR 3.2 0.4 - - - -
47A ARG* 1.3 77.8 - - + +
49A GLY* 1.3 61.9 + - - +
50A VAL* 3.5 14.6 + - + +
----------------------------------------------------------
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