Contacts of the helix formed by residues 46 - 66 (chain A) in PDB entry 1J7H
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 46 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.1 2.4 - - + +
45A ALA* 1.3 75.3 - - - +
47A ILE* 1.3 55.9 + - - +
48A VAL* 2.9 10.9 - - - +
49A ALA* 2.6 50.7 + - + +
50A GLN* 2.7 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.7 14.6 + - - +
46A ASP* 1.3 69.6 - - - +
48A VAL* 1.3 56.4 + - + +
50A GLN* 3.2 27.9 - - - +
51A ALA* 2.7 36.9 + - - +
81A ASP* 6.0 2.0 - - + -
84A ASP* 3.2 44.6 - - + +
87A ALA* 5.3 1.8 - - + -
88A VAL* 3.8 24.7 - - + -
120A GLY* 5.1 9.9 - - - +
121A LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 2.7 12.8 + - - +
47A ILE* 1.3 76.8 - - + +
49A ALA* 1.3 58.9 + - - +
51A ALA* 3.3 4.0 + - - +
52A ARG* 2.9 30.6 + - + +
87A ALA* 4.4 24.5 - - + +
88A VAL* 5.9 1.1 - - - +
91A GLU* 5.0 21.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
44A PRO* 4.4 8.5 - - + -
46A ASP* 2.6 34.3 + - + +
48A VAL* 1.3 75.8 - - - +
50A GLN* 1.3 56.8 + - - +
52A ARG* 3.2 4.7 + - - +
53A GLN* 3.0 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.1 31.0 - - + +
43A VAL* 3.0 25.9 - - - +
44A PRO* 2.5 38.8 - - + +
45A ALA* 3.2 16.6 - - - +
46A ASP 2.7 15.2 + - - +
47A ILE* 3.2 26.1 - - - +
49A ALA* 1.3 73.7 - - - +
51A ALA* 1.3 58.7 + - - +
53A GLN* 4.5 1.1 - - - -
54A SER* 3.1 23.0 + - - -
120A GLY* 3.8 15.6 - - - -
121A LEU* 3.4 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE 2.7 23.6 + - - +
48A VAL* 3.6 7.2 - - - +
49A ALA 3.2 0.2 - - - -
50A GLN* 1.3 79.3 - - - +
52A ARG* 1.3 59.1 + - - +
54A SER* 3.8 3.5 + - - -
55A LEU* 3.5 28.4 + - + +
88A VAL* 4.0 30.4 - - + +
91A GLU* 5.4 3.6 - - + +
121A LEU* 3.7 15.0 - - + -
123A ILE* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.9 18.8 + - + +
49A ALA* 3.6 5.8 - - - +
51A ALA* 1.3 76.1 - - - +
53A GLN* 1.3 75.3 + - - +
55A LEU* 3.2 16.9 + - - +
56A GLU* 3.1 62.7 + - - +
59A LYS* 5.9 2.2 - - - +
91A GLU* 3.7 29.3 + - - +
95A PHE* 5.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 4.7 10.8 - - + -
36A VAL 5.7 1.1 - - - +
38A PRO* 4.1 31.6 - - + +
44A PRO* 4.6 8.2 - - + +
49A ALA* 3.0 31.7 + - - +
50A GLN* 4.0 6.7 - - - +
52A ARG* 1.3 86.7 - - - +
54A SER* 1.3 61.2 + - - +
56A GLU* 3.1 8.5 + - + +
57A ASN* 2.5 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.5 0.2 - - - +
34A ILE* 3.8 10.5 + - - -
35A PRO* 3.8 17.3 - - - +
50A GLN 3.1 19.0 + - - -
51A ALA 4.0 2.5 - - - -
52A ARG 3.3 0.2 - - - -
53A GLN* 1.3 76.2 - - - +
55A LEU* 1.3 59.8 + - - +
57A ASN* 3.5 6.6 + - - +
58A VAL* 2.8 31.7 + - - +
121A LEU* 3.3 17.2 - - - +
123A ILE* 2.9 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.5 16.0 + - + +
52A ARG* 3.2 23.4 + - - +
53A GLN 3.2 0.4 - - - -
54A SER* 1.3 76.4 - - - +
56A GLU* 1.3 60.6 + - - +
58A VAL* 3.6 5.8 + - + +
59A LYS* 3.1 28.8 + - - +
88A VAL* 6.2 2.5 - - + -
91A GLU* 4.6 12.3 - - - +
92A TYR* 3.8 27.6 - - + -
95A PHE* 3.2 51.0 - - + -
96A PHE* 4.7 0.9 - - + -
123A ILE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 4.4 24.9 - - + -
52A ARG* 3.1 41.7 + - - +
53A GLN* 3.1 13.6 + - + +
55A LEU* 1.3 75.8 - - - +
57A ASN* 1.3 56.4 + - - +
59A LYS* 3.5 10.1 - - - +
60A ALA* 2.6 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 3.5 24.2 + - - -
11A ALA* 3.7 9.2 - - - +
12A PRO* 3.7 15.9 - - + +
33A GLN* 4.1 13.7 - - + -
34A ILE 4.5 10.2 + - - +
36A VAL* 5.3 10.5 + - - +
53A GLN* 2.5 38.4 + - - +
54A SER* 3.8 6.3 - - - +
56A GLU* 1.3 79.2 - - - +
58A VAL* 1.3 61.1 + - - +
60A ALA* 3.3 7.2 + - - +
61A ILE* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.3 33.1 - - + +
33A GLN* 3.4 31.4 - - + -
54A SER 2.8 24.4 + - - +
55A LEU* 3.9 7.2 - - + +
56A GLU 3.3 0.2 - - - -
57A ASN* 1.3 76.2 - - - +
59A LYS* 1.3 58.3 + - - +
61A ILE* 3.8 1.6 + - - +
62A ILE* 3.0 36.5 + - + +
72A ILE* 5.8 3.1 - - + -
123A ILE* 3.4 30.5 - - + -
125A ALA* 5.0 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 5.9 2.5 - - - +
55A LEU 3.1 18.4 + - - +
56A GLU* 3.8 11.4 - - - +
58A VAL* 1.3 74.1 - - - +
60A ALA* 1.3 56.6 + - - +
61A ILE 3.2 0.4 - - - -
62A ILE* 3.6 7.1 - - + -
63A GLU* 2.6 68.8 + - + +
68A THR* 4.2 12.5 - - - +
69A ALA* 4.0 39.3 - - + +
95A PHE* 5.8 3.8 - - + -
99A ASN* 3.4 25.0 + - - +
101A HIS* 4.2 9.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 4.0 3.2 + - - -
10A LYS* 3.3 44.8 - - + +
11A ALA 4.6 0.7 - - - +
56A GLU* 2.6 23.9 + - + +
57A ASN* 3.3 7.6 + - - +
59A LYS* 1.3 73.8 - - - +
61A ILE* 1.3 56.1 + - - +
63A GLU* 3.8 7.9 - - - +
64A LYS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.5 15.1 - - + +
8A THR* 3.9 15.9 - - + -
11A ALA* 3.1 29.8 - - + -
20A GLN 4.1 6.7 - - - +
21A ALA* 3.2 34.8 - - + -
30A THR* 5.1 0.9 - - + -
33A GLN* 3.2 39.0 - - + +
57A ASN 3.0 18.6 - - - +
58A VAL* 3.9 4.5 - - - +
59A LYS 3.2 0.6 - - - -
60A ALA* 1.3 74.1 - - - +
62A ILE* 1.3 65.0 + - + +
64A LYS* 3.3 3.8 + - - +
65A ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 6.0 2.2 - - + -
28A VAL* 4.4 9.2 - - + -
30A THR* 3.2 29.4 - - + -
58A VAL* 3.0 29.6 - - + +
59A LYS* 3.3 7.5 + - + +
61A ILE* 1.3 76.5 - - - +
63A GLU* 1.3 60.3 + - - +
65A ALA* 3.3 8.2 + - + +
66A GLY 3.2 6.4 + - - -
67A LEU* 3.0 50.0 + - + -
68A THR* 4.2 6.7 - - - +
69A ALA* 5.4 1.8 - - - -
72A ILE* 4.6 23.6 - - + -
125A ALA* 5.5 1.3 - - + +
127A ALA* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 2.6 51.5 + - + +
60A ALA* 3.8 8.7 - - - +
62A ILE* 1.3 70.1 - - - +
64A LYS* 1.3 61.1 + - - +
65A ALA 3.0 4.5 - - - -
66A GLY* 3.1 14.0 + - - -
67A LEU 3.6 13.6 + - - +
68A THR* 4.3 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.4 23.3 + - - +
8A THR* 3.8 25.1 - - - +
9A GLU* 4.8 4.3 - - - +
60A ALA 2.9 18.8 + - - +
61A ILE 3.3 5.4 + - - +
63A GLU* 1.3 76.8 - - - +
65A ALA* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.2 21.5 - - + -
23A ASP* 4.4 16.8 - - - +
28A VAL* 5.1 5.4 - - + -
61A ILE 3.2 11.8 + - - +
62A ILE* 3.5 12.3 - - - +
63A GLU 3.0 0.4 - - - -
64A LYS* 1.3 80.1 - - - +
66A GLY* 1.3 57.4 + - - +
67A LEU* 5.7 1.1 - - + -
129A ARG* 4.0 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE 3.2 0.8 + - - -
63A GLU 3.1 10.0 + - - -
64A LYS 3.5 0.2 - - - -
65A ALA* 1.3 80.9 - - - +
67A LEU* 1.3 69.2 + - - +
129A ARG* 3.7 15.9 + - - +
----------------------------------------------------------
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