Contacts of the helix formed by residues 40 - 65 (chain A) in PDB entry 4DJ9
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 LEU 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.8 23.3 - - + -
38A PRO 3.2 19.2 + - - +
39A ASP* 1.3 77.2 + - - +
41A THR* 1.4 57.2 + - - +
42A ALA 3.6 1.8 - - - -
43A PRO* 3.4 6.5 - - - +
44A VAL* 2.9 38.3 + - + +
92A ALA* 4.3 14.5 + - + +
95A LEU* 3.8 16.4 - - + +
108A LEU* 3.8 29.2 - - + -
2094B LEU* 3.9 12.8 - - + -
2097B ALA* 3.9 34.3 - - + +
2098B THR* 3.8 8.3 - - + -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 2.8 29.1 + - - -
40A LEU* 1.4 75.4 - - - +
42A ALA* 1.4 57.5 + - - +
44A VAL* 3.9 1.4 - - - +
45A ALA* 3.0 31.4 + - + +
92A ALA* 4.6 11.0 + - - +
96A GLN* 3.1 25.6 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP 5.3 0.2 + - - -
41A THR* 1.4 75.8 - - - +
43A PRO* 1.4 71.9 - - + +
45A ALA* 3.2 9.6 + - - +
46A ALA* 3.1 19.6 + - - +
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Residues in contact with PRO 43 (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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39A ASP 4.6 4.7 - - - +
40A LEU* 3.4 20.9 - - - +
42A ALA* 1.4 92.6 - - + +
44A VAL* 1.4 59.3 + - - +
46A ALA* 3.2 11.2 + - + +
47A VAL* 3.1 23.9 + - - +
2090B ALA 4.6 1.2 - - - +
2093B ASP* 4.5 6.5 - - + +
2094B LEU* 3.7 35.2 - - + +
2097B ALA* 3.9 19.7 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 2.9 29.9 + - + +
41A THR* 4.0 2.9 - - - +
43A PRO* 1.4 67.8 - - - +
45A ALA* 1.4 59.2 + - - +
47A VAL* 2.9 10.6 + - + +
48A GLN* 2.9 29.5 + - + +
85A CYS* 5.9 0.7 - - - -
88A LEU* 4.0 11.7 - - + +
89A VAL* 3.9 39.5 - - + +
92A ALA* 3.7 21.3 - - + -
108A LEU* 5.8 0.7 - - + -
2094B LEU* 3.5 28.0 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.0 16.7 + - + +
42A ALA* 3.4 11.4 - - - +
44A VAL* 1.4 74.3 - - - +
46A ALA* 1.4 56.5 + - - +
48A GLN* 3.2 19.5 + - - +
49A ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.1 11.8 + - - +
43A PRO* 3.4 13.0 - - + +
44A VAL 3.2 0.2 - - - -
45A ALA* 1.4 75.8 - - - +
47A VAL* 1.4 61.5 + - - +
49A ALA* 3.6 6.2 + - - +
50A ALA* 3.1 23.6 + - - +
2090B ALA* 3.8 14.2 - - + +
2093B ASP* 6.0 3.1 - - + +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.1 14.8 + - - +
44A VAL* 2.9 11.2 + - + +
46A ALA* 1.4 75.7 - - - +
48A GLN* 1.4 56.2 + - - +
50A ALA* 3.2 3.5 + - - +
51A VAL* 2.9 33.5 + - + +
85A CYS* 4.4 5.4 - - - -
88A LEU* 4.0 11.4 - - + -
115A ILE* 3.8 29.2 - - + -
2087B VAL* 5.3 3.4 - - + +
2090B ALA* 3.5 34.8 - - + +
2091B LEU* 3.9 10.5 - - + +
2094B LEU* 4.1 16.2 - - + -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 2.9 15.3 + - - +
45A ALA* 3.2 24.3 + - - +
47A VAL* 1.4 75.9 - - - +
49A ALA* 1.4 56.4 + - - +
51A VAL* 3.5 2.1 + - - +
52A SER* 3.0 31.6 + - - -
85A CYS* 3.9 15.5 - - - -
89A VAL* 3.5 41.6 - - + +
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Residues in contact with ALA 49 (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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45A ALA 2.9 16.6 + - - +
46A ALA* 3.8 7.6 - - - +
48A GLN* 1.4 73.6 - - - +
50A ALA* 1.4 61.7 + - - +
52A SER* 3.6 5.7 + - - -
53A ASN* 3.3 32.1 + - - +
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Residues in contact with ALA 50 (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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46A ALA 3.1 15.3 + - - +
47A VAL 3.2 6.7 + - - +
49A ALA* 1.4 73.1 - - - +
51A VAL* 1.3 59.1 + - - +
53A ASN* 3.4 10.3 + - - +
54A LEU* 3.0 23.4 + - - +
2083B ALA 4.7 1.7 - - - +
2086B ASP* 3.8 16.6 - - + +
2087B VAL* 3.5 39.9 - - + +
2090B ALA* 4.4 4.0 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 2.9 26.5 + - + +
48A GLN 3.9 3.8 - - - +
50A ALA* 1.3 73.9 - - - +
52A SER* 1.3 58.6 + - - +
54A LEU* 3.1 4.2 + - - +
55A VAL* 2.9 39.9 + - + +
81A VAL* 3.8 34.3 - - + +
82A GLU* 4.5 6.5 - - + -
85A CYS* 4.0 31.4 - - + -
115A ILE* 4.2 2.2 - - + -
2087B VAL* 4.0 20.4 - - + -
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN 3.0 18.8 + - - -
49A ALA* 3.8 7.4 - - - -
51A VAL* 1.3 77.5 - - - +
53A ASN* 1.4 59.0 + - - +
55A VAL* 3.6 5.0 + - - +
56A ARG* 3.1 32.2 + - - +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.3 17.4 + - - +
50A ALA* 3.6 10.6 - - - +
52A SER* 1.4 78.8 + - - +
54A LEU* 1.4 63.4 + - - +
56A ARG* 2.9 28.9 + - - +
57A VAL* 3.1 31.9 + - + +
2083B ALA* 5.0 6.5 - - + -
2086B ASP* 5.3 7.2 + - - +
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Residues in contact with LEU 54 (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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50A ALA 3.0 17.6 + - - +
51A VAL 3.1 4.0 + - - +
53A ASN* 1.4 74.6 - - - +
55A VAL* 1.3 53.9 + - + +
57A VAL* 4.1 1.3 - - - +
58A GLY* 2.9 30.7 + - - -
78A PHE* 4.4 5.2 - - + -
81A VAL* 4.5 14.1 - - + -
119A THR* 4.4 11.9 - - + -
122A LEU* 3.9 27.6 - - + -
2080B LEU* 4.0 18.4 - - + -
2083B ALA* 4.1 19.0 - - + +
2084B VAL* 3.8 29.2 - - + -
2087B VAL* 3.8 22.4 - - + -
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Residues in contact with VAL 55 (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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51A VAL* 2.9 28.0 + - + +
52A SER* 4.1 4.9 - - - +
54A LEU* 1.3 76.7 - - + +
56A ARG* 1.4 51.5 + - - +
58A GLY* 3.4 0.5 + - - -
59A LYS* 2.8 66.6 + - + +
78A PHE* 4.4 25.4 - - + +
81A VAL* 5.3 3.4 - - + -
82A GLU* 3.7 37.9 - - + +
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Residues in contact with ARG 56 (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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52A SER* 3.1 19.8 + - - +
53A ASN* 2.9 40.0 + - - +
55A VAL* 1.4 70.4 - - - +
57A VAL* 1.3 87.6 + - - +
59A LYS* 3.5 8.2 + - - +
60A GLU* 3.2 44.5 + - - +
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Residues in contact with VAL 57 (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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53A ASN* 3.1 19.1 + - + +
54A LEU* 4.1 3.1 - - - +
56A ARG* 1.3 96.2 - - - +
58A GLY* 1.3 59.1 + - - +
60A GLU* 3.2 15.9 + - - +
61A THR* 3.0 33.1 + - - +
2079B VAL* 4.9 15.5 - - + +
2080B LEU* 3.9 29.6 - - + +
2083B ALA* 5.2 5.6 - - + -
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Residues in contact with GLY 58 (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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54A LEU 2.9 17.0 + - - -
56A ARG 3.3 0.2 - - - -
57A VAL* 1.3 77.2 - - - +
59A LYS* 1.4 56.0 + - - +
61A THR* 3.3 4.4 + - - -
62A VAL* 3.1 32.1 + - - +
74A MET* 3.6 2.6 - - - +
78A PHE* 3.3 27.4 - - - -
2080B LEU* 3.9 13.0 - - - -
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Residues in contact with LYS 59 (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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55A VAL* 2.8 45.7 + - + +
56A ARG* 3.8 7.6 - - - +
58A GLY* 1.4 71.1 - - - +
60A GLU* 1.4 62.6 + - - +
62A VAL* 3.5 9.6 + - + +
63A GLN* 3.2 30.0 + - + +
78A PHE* 3.9 13.4 - - + -
82A GLU* 4.0 16.3 + - - -
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Residues in contact with GLU 60 (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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56A ARG* 3.2 40.2 + - - +
57A VAL* 3.2 20.6 + - - +
59A LYS* 1.4 73.2 - - + +
61A THR* 1.4 65.3 + - - +
63A GLN* 3.5 5.6 + - - +
64A THR* 3.2 31.7 + - + +
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Residues in contact with THR 61 (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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57A VAL* 3.0 15.7 + - - +
58A GLY 3.3 8.9 + - - -
60A GLU* 1.4 73.4 - - - +
62A VAL* 1.4 57.3 + - - +
64A THR* 3.2 8.2 + - - +
65A THR* 2.8 46.0 + - - +
70A LEU* 5.1 5.8 - - + -
74A MET* 3.9 13.5 - - + -
2080B LEU* 3.4 32.4 - - + +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.1 16.6 + - - +
59A LYS* 3.6 12.1 - - + +
61A THR* 1.4 76.3 - - - +
63A GLN* 1.3 62.3 + - - +
65A THR* 3.7 6.8 - - - +
70A LEU 4.5 3.4 - - - +
71A LYS* 2.8 48.4 + - + +
74A MET* 4.0 12.1 - - + -
75A PRO* 3.9 31.9 - - + -
78A PHE* 3.9 18.4 - - + -
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Residues in contact with GLN 63 (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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59A LYS* 3.2 18.7 + - + +
60A GLU* 3.9 5.8 - - - +
61A THR 3.3 0.2 - - - -
62A VAL* 1.3 87.8 - - - +
64A THR* 1.3 61.6 + - + +
71A LYS* 3.5 12.0 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 3.2 20.7 + - + +
61A THR* 3.3 8.3 + - - +
63A GLN* 1.3 78.3 - - + +
65A THR* 1.4 68.3 + - - +
66A GLU* 3.8 1.0 + - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 2.8 31.3 + - + +
62A VAL* 3.7 3.6 - - - +
64A THR* 1.4 76.8 + - - +
66A GLU* 1.3 63.2 + - - +
67A ASP* 3.2 24.6 + - - +
68A GLN* 5.4 0.2 + - - -
70A LEU* 3.7 22.8 - - + +
71A LYS* 2.8 53.3 + - + +
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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) + - + + + + + -
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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