Contacts of the helix formed by residues 49 - 73 (chain A) in PDB entry 1E7J
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 LYS 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 3.8 55.2 - - + +
44A ARG* 3.9 16.7 + - - +
45A ALA* 6.3 0.2 - - - -
46A MET* 4.3 6.5 - - + +
47A LYS 3.9 3.1 + - - +
48A ASP* 1.4 71.0 - - - +
50A SER* 1.4 57.9 - - - +
51A GLU 3.2 3.1 - - - -
52A TRP* 3.2 14.0 + - - +
53A GLU* 3.1 35.0 + - + +
24C T 5.1 4.8 + - - -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 3.4 9.8 - - - -
49A LYS* 1.4 74.6 - - - +
51A GLU* 1.4 62.5 + - - +
53A GLU* 3.9 10.7 - - - +
54A ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 6.0 2.3 - - - +
48A ASP* 4.0 22.6 + - + +
50A SER* 1.4 78.4 - - - +
52A TRP* 1.3 95.2 + - + +
54A ALA* 3.6 4.3 + - - +
55A LYS* 3.4 47.7 + - - +
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Residues in contact with TRP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 3.3 26.3 - - + +
14A LEU* 3.5 40.2 - - + +
15A TRP* 3.6 24.0 - + + -
18A SER* 3.4 27.4 - - - -
43A TRP* 3.7 20.2 - + + -
46A MET* 3.8 2.6 - - - +
47A LYS* 6.3 3.3 - - - +
48A ASP 3.4 26.2 + - - -
49A LYS 3.2 5.7 + - - +
51A GLU* 1.3 99.0 + - + +
53A GLU* 1.4 59.9 + - - +
55A LYS* 3.5 18.8 + - + +
56A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 3.1 23.4 - - + +
43A TRP* 4.7 6.2 - - - -
49A LYS* 3.1 29.9 + - + +
50A SER* 3.9 9.6 - - - +
51A GLU 3.4 0.2 - - - -
52A TRP* 1.4 76.0 - - - +
54A ALA* 1.4 57.7 + - - +
56A ALA* 3.5 4.0 + - - +
57A ALA* 3.0 29.6 + - - +
24C T 4.4 3.8 - - - +
25C C 3.5 29.7 + - - +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER 3.1 18.7 + - - +
51A GLU* 3.7 6.7 - - - +
52A TRP 3.3 0.4 - - - -
53A GLU* 1.4 76.2 - - - +
55A LYS* 1.4 57.3 + - + +
57A ALA* 3.5 5.9 + - - +
58A LYS* 3.1 34.2 + - + +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.1 14.5 - - + +
51A GLU* 3.4 38.8 + - - +
52A TRP* 4.0 22.6 - - + +
53A GLU 3.4 0.2 - - - -
54A ALA* 1.4 77.1 - - + +
56A ALA* 1.4 58.9 + - - +
58A LYS* 3.9 7.0 - - - +
59A ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 5.4 0.2 - - - +
9A LEU 3.5 24.4 - - - +
10A SER* 4.1 2.2 - - - -
11A ALA* 3.8 19.3 - - + +
14A LEU* 4.2 4.2 - - + +
52A TRP 3.0 18.9 + - - +
53A GLU* 3.8 6.1 - - - +
55A LYS* 1.4 73.5 - - - +
57A ALA* 1.4 64.0 + - - +
59A ALA* 3.5 4.7 + - - +
60A LYS* 3.2 26.9 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 3.0 18.2 + - - +
54A ALA* 3.7 6.7 - - - +
56A ALA* 1.4 74.5 - - - +
58A LYS* 1.4 63.1 + - + +
60A LYS* 3.3 13.3 + - - +
61A ASP* 3.1 23.8 - - - +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 3.1 21.9 + - + +
55A LYS* 3.9 7.4 - - - +
57A ALA* 1.4 78.6 - - + +
59A ALA* 1.4 55.1 + - - +
61A ASP* 3.5 5.9 + - + +
62A ASP* 3.0 31.5 + - + +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 4.6 4.8 - - + +
7A ARG 4.4 4.5 - - - +
8A PRO* 3.8 21.5 - - + +
9A LEU* 4.4 10.8 - - + +
14A LEU* 6.5 0.2 - - + -
55A LYS 3.0 18.6 + - - +
56A ALA* 3.8 7.4 - - - +
57A ALA 3.3 0.4 - - - -
58A LYS* 1.4 73.0 - - - +
60A LYS* 1.4 62.9 + - - +
62A ASP* 4.0 7.1 - - - +
63A TYR* 3.2 24.8 + - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.2 21.3 - - + -
9A LEU 5.6 2.7 - - - -
56A ALA* 3.2 16.4 + - - +
57A ALA* 3.4 14.9 - - - +
58A LYS 3.2 0.2 - - - -
59A ALA* 1.4 78.0 - - - +
61A ASP* 1.4 66.1 + - - +
63A TYR* 3.6 4.0 + - - +
64A ASP* 3.3 22.9 + - - +
26C G 4.1 28.3 + - - -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 3.1 14.6 + - - +
58A LYS* 3.5 7.7 + - + +
60A LYS* 1.4 79.1 - - - +
62A ASP* 1.4 64.9 + - - +
64A ASP* 3.5 5.9 + - - +
65A ARG* 3.1 27.0 + - - +
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 5.1 1.7 - - - +
6A LYS* 4.7 16.5 + - - +
58A LYS 3.0 20.9 + - - +
59A ALA* 4.2 6.1 - - - +
61A ASP* 1.4 75.7 - - - +
63A TYR* 1.4 59.7 + - - +
65A ARG* 4.0 2.7 - - - +
66A ALA* 3.0 41.5 + - - +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.7 7.6 - - + -
6A LYS 3.3 24.7 + - - +
7A ARG* 4.0 28.9 + - + -
8A PRO* 3.7 29.4 - - + -
59A ALA 3.2 18.5 + - - +
60A LYS 3.7 4.7 - - - +
62A ASP* 1.4 78.9 + - - +
64A ASP* 1.4 65.3 + - + +
66A ALA* 3.9 2.2 - - - -
67A VAL* 3.0 58.8 + - + +
4B T 5.4 7.4 + - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS 3.3 14.7 + - - +
61A ASP* 3.8 7.4 - - - +
62A ASP 3.4 0.2 - - - -
63A TYR* 1.4 82.1 - - + +
65A ARG* 1.4 63.2 + - - +
67A VAL* 3.5 16.6 - - - +
68A LYS* 4.0 7.1 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP 3.1 18.1 + - - +
62A ASP* 4.1 3.1 - - - +
64A ASP* 1.4 78.1 + - - +
66A ALA* 1.4 62.6 + - - +
68A LYS* 3.4 19.8 - - - +
69A GLU* 3.9 13.2 + - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.7 24.1 - - + +
62A ASP* 3.0 27.0 + - - +
65A ARG* 1.4 76.3 - - - +
67A VAL* 1.4 58.9 + - - +
68A LYS 3.2 2.0 - - - -
69A GLU* 3.3 9.5 + - - +
70A PHE* 3.1 27.8 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.8 13.7 - - + -
63A TYR* 3.0 59.8 + - + +
64A ASP* 3.5 14.4 - - - +
66A ALA* 1.4 73.0 - - - +
68A LYS* 1.4 61.8 + - - +
70A PHE* 3.8 9.4 - - + -
71A GLU* 3.0 49.9 + - + +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP 4.2 7.4 - - - +
65A ARG* 3.4 14.1 + - - +
66A ALA 3.2 0.6 - - - -
67A VAL* 1.4 81.6 - - + +
69A GLU* 1.4 69.1 + - - +
71A GLU* 4.7 2.5 - - - +
72A ALA* 3.2 28.4 + - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.9 16.7 - - + +
66A ALA* 3.3 8.7 + - - +
67A VAL 3.3 0.2 - - - -
68A LYS* 1.4 87.3 - - - +
70A PHE* 1.4 58.9 + - - +
72A ALA* 3.8 4.4 - - - +
73A ASN* 3.0 34.1 + - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 5.7 3.1 - - - -
3A ASP* 3.4 31.0 - - - -
4A LYS* 4.1 31.9 - - + -
5A PRO* 3.9 20.4 - - + -
66A ALA 3.1 17.5 + - - +
67A VAL* 3.8 9.6 - - + +
68A LYS 3.4 0.2 - - - -
69A GLU* 1.4 77.2 - - - +
71A GLU* 1.4 70.3 + - + +
73A ASN 3.1 20.8 - - - +
74A GLY* 3.7 11.0 - - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.0 38.6 + - + +
68A LYS* 4.7 2.0 - - - +
70A PHE* 1.4 83.8 - - + +
72A ALA* 1.4 65.0 + - - +
73A ASN 4.9 0.2 - - - -
74A GLY* 5.0 3.0 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.2 23.9 + - + +
69A GLU* 3.8 5.8 - - - +
70A PHE 3.3 0.2 - - - -
71A GLU* 1.4 81.0 - - - +
73A ASN* 1.4 61.4 + - + +
74A GLY 3.7 2.6 + - - -
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU 3.0 12.6 + - - +
70A PHE* 3.1 13.0 - - - +
72A ALA* 1.4 76.8 - - + +
74A GLY* 1.3 62.6 + - - +
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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