Contacts of the helix formed by residues 44 - 62 (chain A) in PDB entry 3J2I
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 44 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 3.8 2.6 + - - -
43A VAL* 1.3 73.9 - - - +
45A VAL* 1.3 60.8 + - - +
46A LEU* 3.3 3.6 + - - +
47A SER* 2.6 48.4 + - - -
48A LEU* 3.1 11.9 + - - +
97A ASP* 2.6 24.1 + - - -
99A ILE* 3.8 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL 3.6 0.2 + - - -
44A SER* 1.3 68.7 - - - +
46A LEU* 1.3 67.3 + - - +
48A LEU* 3.1 9.5 + - + +
49A CYS* 2.9 28.5 + - - -
80A ILE* 3.8 29.2 - - + +
82A VAL* 4.6 3.6 - - + -
89A PHE* 3.6 33.7 - - + -
91A PRO* 4.3 1.3 - - + -
97A ASP* 3.9 2.2 - - - +
98A TYR* 2.9 34.8 + - + +
100A LEU* 3.8 28.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
44A SER* 3.3 5.1 + - - +
45A VAL* 1.3 76.9 - - - +
47A SER* 1.3 56.1 + - - +
49A CYS* 3.2 3.6 + - - +
50A GLU* 2.9 52.8 + - + +
91A PRO* 3.4 38.5 - - + +
92A LEU 4.6 3.8 - - - +
93A LYS* 4.2 23.8 - - + +
97A ASP* 2.9 27.5 + - + +
281A ARG* 3.6 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.9 8.1 - - - +
44A SER* 2.6 41.0 + - - -
46A LEU* 1.3 77.0 - - - +
48A LEU* 1.3 57.2 + - - +
50A GLU* 3.4 11.2 + - - +
51A LYS* 2.8 31.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
35A LEU* 3.6 26.1 - - + +
38A ALA* 3.7 30.3 - - + +
39A SER* 3.6 19.1 - - - +
43A VAL* 3.7 24.7 - - + -
44A SER 3.6 9.6 - - - +
45A VAL* 3.1 9.9 + - + +
47A SER* 1.3 81.4 + - - +
49A CYS* 1.3 59.8 + - - +
51A LYS* 4.3 6.3 - - + -
52A GLY* 2.9 26.0 + - - -
78A THR* 4.2 1.7 - - - +
80A ILE* 3.3 28.9 - - + -
100A LEU* 3.9 14.1 - - + -
108A ILE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 2.9 29.8 + - - -
46A LEU* 3.6 6.7 - - - +
48A LEU* 1.3 77.3 - - - +
50A GLU* 1.3 60.6 + - - +
52A GLY 3.4 0.2 + - - -
53A ASP* 3.1 29.5 + - - -
78A THR* 3.5 32.4 - - - +
80A ILE* 4.1 17.5 - - - -
89A PHE 4.1 2.5 - - - -
90A SER* 4.1 4.3 - - - -
91A PRO* 4.1 14.1 - - - -
281A ARG* 3.9 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 2.9 38.7 + - + +
47A SER* 3.8 9.1 - - - +
49A CYS* 1.3 74.1 - - - +
51A LYS* 1.3 64.5 + - - +
53A ASP* 3.5 3.6 + - - +
54A ALA* 3.0 27.1 + - - +
93A LYS* 3.9 19.2 - - - +
281A ARG* 3.7 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.7 20.8 + - - -
35A LEU* 4.1 12.3 - - + -
38A ALA* 4.6 20.2 - - + -
47A SER 2.8 21.5 + - - +
48A LEU* 3.7 8.3 - - + +
50A GLU* 1.3 74.0 - - - +
52A GLY* 1.3 63.2 + - - +
54A ALA* 3.3 5.4 + - - +
55A MET* 2.9 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.8 9.0 - - - +
35A LEU* 3.8 19.0 - - - +
48A LEU 2.9 15.6 + - - -
51A LYS* 1.3 76.9 - - - +
53A ASP* 1.3 62.0 + - - +
55A MET* 3.2 3.9 + - - +
56A ILE* 2.9 26.5 + - - +
78A THR* 3.5 16.8 - - - -
----------------------------------------------------------
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 CYS 3.1 14.5 + - - +
50A GLU* 4.0 4.0 - - - +
51A LYS 3.3 0.2 - - - -
52A GLY* 1.3 74.8 - - - +
54A ALA* 1.3 64.2 + - - +
56A ILE* 3.2 8.8 + - - +
57A MET* 3.0 26.5 + - - +
74A ILE* 3.6 25.4 - - + +
77A PRO* 3.8 12.0 - - - +
78A THR* 2.8 37.3 + - - -
279A THR* 4.2 5.5 - - - +
281A ARG* 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU 3.0 18.4 + - - +
51A LYS* 3.7 5.2 - - - +
53A ASP* 1.3 77.5 - - - +
55A MET* 1.3 58.1 + - + +
57A MET* 3.3 7.9 + - - +
58A GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 5.3 2.7 - - + +
31A VAL* 4.0 21.5 - - + +
34A SER* 3.6 31.2 - - - +
35A LEU* 5.1 1.3 - - - -
51A LYS* 2.9 53.1 + - + +
52A GLY* 3.2 4.5 + - - +
54A ALA* 1.3 73.4 - - + +
56A ILE* 1.3 61.8 + - - +
58A GLU* 3.8 5.8 - - - -
59A GLU* 2.9 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.6 2.9 - - - -
31A VAL* 4.2 17.7 - - + -
52A GLY 2.9 20.2 + - - +
53A ASP* 3.2 8.7 + - - +
55A MET* 1.3 76.5 - - - +
57A MET* 1.3 57.1 - - - +
59A GLU* 4.0 0.5 - - - +
60A THR* 2.9 35.2 + - + +
73A GLY 3.5 33.0 - - - +
74A ILE* 3.7 15.3 - - + -
76A PHE 4.8 2.0 - - - +
78A THR* 4.2 14.1 - - - +
110A LEU* 4.3 15.7 - - + -
111A GLY 4.0 15.9 - - - +
112A VAL* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 3.0 19.2 + - - +
54A ALA* 3.8 8.1 - - - +
56A ILE* 1.3 75.5 - - - +
58A GLU* 1.3 57.5 + - - +
60A THR* 3.3 5.0 + - - +
61A GLY* 2.9 25.8 + - - -
72A LYS 4.3 15.5 - - - +
73A GLY* 3.8 12.3 - - - -
74A ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA 2.9 17.9 + - - +
55A MET* 3.8 7.2 - - - +
57A MET* 1.3 76.3 - - - +
59A GLU* 1.3 65.3 + - + +
61A GLY* 3.3 9.6 + - - -
62A LYS* 3.4 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.6 34.8 - - + +
30A ARG* 3.0 45.9 + - - +
31A VAL* 4.0 9.1 - - - +
55A MET* 2.9 44.5 + - - +
58A GLU* 1.3 77.0 - - + +
60A THR* 1.3 65.8 + - - +
62A LYS* 3.2 39.5 + - - +
63A ILE* 3.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.9 12.8 - - + -
56A ILE* 2.9 24.3 + - + +
57A MET* 3.3 8.5 + - - +
59A GLU* 1.3 75.5 - - - +
61A GLY* 1.3 61.6 + - - +
62A LYS 3.2 1.0 + - - -
63A ILE* 3.3 10.4 + - - +
72A LYS* 3.0 37.9 + - + +
73A GLY* 3.5 32.7 + - - +
112A VAL* 3.7 30.5 - - + -
113A HIS 4.1 4.0 - - - +
114A VAL* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 2.9 18.8 + - - -
58A GLU* 3.3 4.0 + - - -
59A GLU 3.2 0.6 - - - -
60A THR* 1.3 78.9 + - - +
62A LYS* 1.3 56.2 + - - +
63A ILE 3.4 0.2 - - - -
65A LYS* 3.5 18.9 - - - +
72A LYS* 3.7 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 5.0 6.9 - - - +
58A GLU* 3.4 21.3 - - + +
59A GLU* 3.5 41.3 + - - +
60A THR 3.1 1.0 - - - -
61A GLY* 1.3 78.8 - - - +
63A ILE* 1.3 64.8 + - + +
65A LYS* 3.2 33.3 + - - +
----------------------------------------------------------
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