Contacts of the helix formed by residues 58 - 76 (chain A) in PDB entry 1JPL
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 GLN 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.1 24.9 - - - +
56A SER* 3.1 12.8 + - - +
57A PRO* 1.3 77.9 - - - +
59A GLU* 1.3 80.5 + - - +
60A TRP* 3.7 10.0 + - - +
61A GLU* 3.3 11.9 + - + +
62A ALA* 3.1 19.8 + - - +
1B MSE 2.9 37.4 - - + +
2B ALA* 4.1 4.5 - - - +
6B GLY 3.6 17.5 - - - +
7B GLU* 3.0 36.0 - - - +
10B GLU* 4.3 7.0 - - + -
49B LEU* 4.5 5.4 - - + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 3.5 5.3 + - - -
58A GLN* 1.3 76.8 + - - +
60A TRP* 1.3 57.5 + - - +
62A ALA* 3.2 7.7 + - - +
63A LEU* 2.9 45.5 + - + +
107A SER* 3.0 40.5 + - - +
109A LYS* 3.5 24.6 + - - +
110A VAL* 4.1 3.3 - - + +
1B MSE 4.6 1.2 + - - -
2B ALA* 4.1 33.3 - - + +
203B MSE 6.1 0.4 - - + -
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Residues in contact with TRP 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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19A PRO* 3.1 28.0 - - + -
21A ASN 2.9 27.9 + - - -
22A ARG 5.2 0.2 - - - -
23A GLN* 4.0 26.0 - - - -
24A GLU* 3.7 24.9 - - - -
58A GLN* 3.6 14.0 + - - +
59A GLU* 1.3 78.8 + - - +
61A GLU* 1.3 57.4 + - - +
63A LEU* 4.1 20.2 - - + -
64A GLN* 3.0 64.0 + - + +
7B GLU* 4.0 19.5 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.8 19.8 + - - +
19A PRO* 3.7 18.6 - - + +
53A LYS* 3.9 30.7 + - + +
56A SER* 2.6 31.4 + - - +
58A GLN* 3.3 13.2 + - + +
59A GLU 3.2 0.8 - - - -
60A TRP* 1.3 75.9 - - - +
62A ALA* 1.3 67.1 + - - +
64A GLN* 3.5 2.5 + - - +
65A ALA* 3.0 23.2 + - - +
10B GLU* 2.6 43.3 - - - +
14B ASN* 3.9 4.0 - - - +
52B HIS* 5.2 2.9 - - - -
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Residues in contact with ALA 62 (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 LYS 3.6 13.7 + - - +
54A ILE* 3.4 23.5 - - - +
56A SER 4.2 8.7 - - - +
58A GLN 3.1 9.8 + - - +
59A GLU* 3.6 7.2 - - - +
61A GLU* 1.3 81.2 - - - +
63A LEU* 1.3 55.8 + - - +
65A ALA* 3.1 5.3 + - - +
66A LEU* 2.9 33.3 + - - +
110A VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 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 GLU* 2.9 45.6 + - + +
60A TRP* 3.8 22.7 - - + +
62A ALA* 1.3 74.3 - - - +
64A GLN* 1.3 64.6 + - - +
66A LEU* 3.0 23.6 + - + +
67A THR* 3.0 15.8 + - - -
109A LYS* 4.2 23.1 - - + +
110A VAL* 3.9 29.6 - - + +
113A LYS* 4.6 8.3 - - + -
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Residues in contact with GLN 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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16A ALA 3.2 17.1 + - - +
17A THR* 3.8 10.6 - - - +
18A ASN 3.1 13.1 - - - +
21A ASN* 2.6 35.1 - - - +
23A GLN 4.2 4.4 + - - -
24A GLU* 4.6 12.7 - - + +
25A ASP 4.9 0.4 - - - +
29A ILE* 5.6 1.3 - - + +
60A TRP* 3.0 68.5 + - + +
61A GLU 3.9 3.8 - - - +
63A LEU* 1.3 76.2 - - - +
65A ALA* 1.3 57.2 + - - +
67A THR* 3.0 10.2 + - - -
68A VAL* 2.9 32.9 + - - +
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Residues in contact with ALA 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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17A THR* 3.9 11.4 - - + +
50A LEU* 3.6 8.0 - - + +
53A LYS* 3.6 27.8 - - + -
54A ILE* 3.6 17.9 - - + +
61A GLU 3.0 15.8 + - - +
62A ALA 3.1 10.7 + - - +
64A GLN* 1.3 77.6 - - - +
66A LEU* 1.3 56.5 + - - +
68A VAL* 3.3 4.6 + - - +
69A LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 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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54A ILE* 3.5 26.7 - - + -
62A ALA 2.9 17.4 + - - +
63A LEU* 3.0 16.8 + - + +
65A ALA* 1.3 78.1 - - - +
67A THR* 1.3 57.3 + - - +
69A LEU* 3.6 6.9 + - + +
70A GLU* 3.1 24.6 + - - +
93A LEU* 5.0 1.6 - - + -
110A VAL* 3.8 34.3 - - + +
113A LYS* 3.9 28.2 - - + -
114A VAL* 3.8 21.5 - - + -
117A LEU* 3.8 26.1 - - + +
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Residues in contact with THR 67 (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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24A GLU* 4.3 17.2 + - + +
26A TRP* 3.6 33.3 - - + -
29A ILE* 4.1 12.3 - - + -
63A LEU 3.0 12.0 + - - -
64A GLN* 3.0 12.4 + - - -
66A LEU* 1.3 75.6 - - - +
68A VAL* 1.3 60.2 + - - +
70A GLU* 3.0 17.2 + - - +
71A ALA* 2.8 26.5 + - - +
113A LYS* 5.3 7.2 - - - +
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Residues in contact with VAL 68 (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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13A LEU* 4.2 4.0 - - + -
16A ALA* 3.9 29.2 - - + +
17A THR* 4.3 5.8 - - + -
29A ILE* 4.0 28.3 - - + +
32A PHE* 3.5 41.1 - - + -
50A LEU* 3.9 9.9 - - + -
64A GLN 2.9 18.1 + - - +
65A ALA* 3.6 7.2 - - - +
67A THR* 1.3 76.7 - - - +
69A LEU* 1.3 57.0 + - - +
71A ALA* 3.1 2.8 + - - +
72A CYS* 2.8 29.4 + - - -
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Residues in contact with LEU 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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47A VAL* 5.8 0.2 - - + -
50A LEU* 4.0 26.2 - - + +
54A ILE* 3.6 25.8 - - + -
65A ALA 2.9 17.2 + - - +
66A LEU* 3.6 7.6 - - + +
67A THR 3.2 0.2 - - - -
68A VAL* 1.3 76.2 - - - +
70A GLU* 1.3 62.3 + - - +
72A CYS* 3.4 2.0 + - - +
73A MSE 3.1 27.1 + - + +
80A PHE* 4.1 16.4 - - + -
84A VAL* 4.4 7.2 - - + -
89A PHE* 3.9 21.5 - - + -
93A LEU* 4.8 2.9 - - + -
117A LEU* 4.2 11.7 - - + -
121A TRP* 3.7 31.2 - - + -
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Residues in contact with GLU 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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26A TRP* 5.9 1.4 - - - -
66A LEU 3.1 13.5 + - - +
67A THR* 3.0 19.5 + - - +
69A LEU* 1.3 75.3 - - - +
71A ALA* 1.3 65.8 + - - +
73A MSE 3.0 20.4 + - + +
74A LYS* 3.2 13.5 + - + +
113A LYS* 4.3 19.8 + - - -
116A GLU* 4.6 3.5 - - - +
117A LEU* 3.9 29.0 - - + +
121A TRP* 5.7 1.3 - - - +
151A PRO* 5.4 5.9 - - - +
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Residues in contact with ALA 71 (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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26A TRP* 4.3 11.4 - - + -
29A ILE* 3.6 28.3 - - + -
30A ILE* 4.6 0.9 - - + -
33A CYS* 3.9 10.5 - - - -
67A THR 2.8 9.7 + - - +
68A VAL 3.4 7.6 - - - +
70A GLU* 1.3 77.6 - - - +
72A CYS* 1.3 56.7 - - - +
74A LYS* 3.1 11.0 + - - +
75A ASN* 2.8 43.3 + - - +
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Residues in contact with CYS 72 (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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32A PHE* 3.7 33.2 - - - -
33A CYS* 3.8 11.0 - - - -
36A ILE* 3.7 15.7 - - - -
50A LEU* 4.3 2.0 - - - -
68A VAL* 2.8 21.0 + - - +
69A LEU 3.7 2.2 - - - +
70A GLU 3.2 0.2 - - - -
71A ALA* 1.3 73.2 - - - +
73A MSE 1.3 61.4 + - - +
76A CYS* 2.9 42.6 + - - +
80A PHE* 3.3 31.3 - - + +
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Residues in contact with MSE 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 LEU* 3.1 17.3 + - + +
70A GLU* 3.0 10.6 + - + +
72A CYS* 1.3 77.8 - - - +
74A LYS* 1.3 59.8 + - + +
76A CYS 4.4 1.2 + - - -
77A GLY* 4.7 0.9 + - - -
80A PHE* 3.6 24.2 - - - -
81A HIS* 2.7 36.1 + - + +
84A VAL* 3.8 23.3 - - + -
121A TRP* 3.6 49.6 - - + +
125A LEU* 3.4 33.4 - - + -
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Residues in contact with LYS 74 (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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26A TRP* 4.5 13.7 - - - -
30A ILE* 4.6 5.0 - - - +
70A GLU* 3.2 5.3 + - + +
71A ALA* 3.1 26.0 + - - +
73A MSE 1.3 81.2 - - - +
75A ASN* 1.3 82.4 + - - +
76A CYS 3.9 0.2 - - - -
77A GLY 5.3 0.7 - - - -
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Residues in contact with ASN 75 (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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30A ILE* 3.9 22.2 - - + +
33A CYS* 4.1 17.1 - - + -
37A ASN* 3.2 19.9 + - - +
71A ALA* 2.8 25.8 + - - +
74A LYS* 1.3 115.4 - - - +
76A CYS* 1.3 59.7 + - - +
77A GLY 3.7 2.5 - - - -
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Residues in contact with CYS 76 (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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33A CYS* 3.7 24.9 - - - -
36A ILE* 4.2 12.8 - - + -
37A ASN* 3.4 20.6 - - - +
72A CYS* 2.9 38.3 + - - +
74A LYS 3.9 0.2 - - - -
75A ASN* 1.3 82.9 - - - +
77A GLY* 1.3 66.5 + - - +
79A ARG* 3.2 24.7 - - + +
80A PHE* 3.3 19.3 - - + +
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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
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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