Contacts of the helix formed by residues 58 - 76 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MSE 3.0 35.6 - - - +
2C ALA* 3.7 9.9 - - - +
6C GLY 3.7 20.2 - - - +
7C GLU* 3.6 25.9 + - - +
10C GLU* 4.4 6.7 - - + -
49C LEU* 4.4 7.4 - - + -
19D PRO* 4.0 4.2 - - - +
56D SER* 3.2 12.5 + - - +
57D PRO* 1.3 76.6 - - - +
59D GLU* 1.3 68.8 + - - +
60D TRP* 3.1 16.4 + - - +
61D GLU* 3.0 52.0 + - + +
62D ALA* 3.1 10.2 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 4.3 28.3 - - + +
203C MSE 4.8 6.6 - - + +
56D SER 5.3 0.7 - - - -
57D PRO 3.5 6.2 + - - -
58D GLN* 1.3 70.1 + - - +
60D TRP* 1.3 56.9 + - - +
62D ALA* 3.1 8.1 + - - +
63D LEU* 2.7 55.8 + - + +
107D SER* 2.7 38.2 + - - +
109D LYS* 4.2 16.6 - - - +
110D VAL* 4.1 2.9 - - + +
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ALA 5.9 0.2 + - - -
7C GLU* 4.3 17.3 - - - +
19D PRO* 3.2 25.8 + - + -
21D ASN 2.7 25.7 + - - -
22D ARG 4.4 4.3 - - - -
23D GLN* 4.2 17.9 - - - -
24D GLU* 4.1 22.4 - - + -
58D GLN* 3.1 14.7 + - - +
59D GLU* 1.3 78.8 - - - +
61D GLU* 1.3 63.2 + - - +
63D LEU* 3.1 22.3 + - + -
64D GLN* 2.8 65.8 + - + +
67D THR* 6.5 0.7 - - + -
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLU* 2.8 40.1 - - - +
14C ASN* 3.7 4.3 + - - +
52C HIS* 5.3 2.9 - - - -
17D THR* 3.6 25.3 - - - +
19D PRO* 3.8 16.8 - - + +
53D LYS* 3.7 32.5 + - + +
56D SER* 2.5 30.9 + - - +
58D GLN* 3.0 17.5 - - + +
60D TRP* 1.3 76.3 - - - +
62D ALA* 1.3 58.4 + - - +
64D GLN* 3.6 1.3 + - - -
65D ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LYS 3.6 14.1 - - - +
54D ILE* 3.5 24.0 - - - +
56D SER* 4.1 10.8 - - - +
58D GLN 3.1 8.8 + - - +
59D GLU* 3.1 9.1 + - - +
61D GLU* 1.3 78.8 - - - +
63D LEU* 1.3 65.7 + - - +
65D ALA* 3.3 3.7 + - - +
66D LEU* 3.0 27.6 + - - +
106D VAL* 6.3 0.4 - - + -
110D VAL* 4.1 14.8 - - + -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 2.7 57.0 + - + +
60D TRP* 3.5 25.1 - - + +
62D ALA* 1.3 68.7 - - - +
64D GLN* 1.3 66.7 + - - +
66D LEU* 2.9 22.5 + - + +
67D THR* 3.1 19.1 + - + +
109D LYS* 4.3 26.9 - - + +
110D VAL* 3.9 26.7 - - + +
113D LYS* 4.7 9.2 - - + -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 3.5 11.5 + - - +
17D THR* 3.5 20.2 - - - +
18D ASN 3.2 9.8 + - - +
19D PRO* 4.1 0.2 - - - +
21D ASN* 2.9 37.6 + - - +
23D GLN 4.2 3.4 + - - -
24D GLU* 4.8 10.4 - - + +
29D ILE* 6.0 0.4 - - + -
60D TRP* 2.8 67.8 + - + +
61D GLU 3.8 3.8 - - - +
63D LEU* 1.3 78.8 - - - +
65D ALA* 1.3 63.4 + - - +
67D THR* 2.9 27.7 + - - -
68D VAL* 3.0 10.2 + - - +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 3.5 13.8 - - + +
50D LEU* 3.5 11.6 - - + +
53D LYS* 3.4 33.4 - - + -
54D ILE* 3.9 14.0 - - + +
61D GLU 3.0 16.0 + - - +
62D ALA 3.5 6.7 - - - +
63D LEU 3.2 0.2 - - - -
64D GLN* 1.3 75.5 - - - +
66D LEU* 1.3 57.7 + - - +
68D VAL* 3.3 6.3 + - - +
69D LEU* 3.0 23.6 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.5 34.3 - - + -
62D ALA 3.0 16.5 + - - +
63D LEU* 2.9 14.1 + - + +
65D ALA* 1.3 75.2 - - - +
67D THR* 1.3 64.2 + - + +
69D LEU* 3.2 6.9 + - + +
70D GLU* 3.1 20.8 + - - +
93D LEU* 5.2 1.6 - - + -
110D VAL* 3.7 41.3 - - + +
113D LYS* 3.7 27.3 - - + -
114D VAL* 4.0 9.4 - - + -
117D LEU* 3.8 25.8 - - + +
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Residues in contact with THR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLU* 4.4 30.9 + - - +
26D TRP* 5.1 11.5 - - - -
29D ILE* 4.8 8.8 - - - +
60D TRP* 6.5 0.4 - - + -
63D LEU* 3.6 15.3 - - + +
64D GLN* 2.9 18.3 + - - -
66D LEU* 1.3 74.8 - - - +
68D VAL* 1.3 62.5 + - - +
70D GLU* 3.3 14.3 + - - +
71D ALA* 2.9 27.0 + - - +
113D LYS* 4.9 12.6 - - - +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 4.0 4.0 - - + -
16D ALA* 4.0 11.9 - - + +
17D THR* 4.2 10.8 - - + -
29D ILE* 3.3 42.6 - - + +
32D PHE* 3.5 38.4 - - + -
50D LEU* 3.8 8.5 - - + -
64D GLN 3.0 17.5 + - - +
65D ALA* 3.4 8.1 - - - +
67D THR* 1.3 75.8 - - - +
69D LEU* 1.3 58.8 + - - +
71D ALA* 3.3 1.9 + - - +
72D CYS* 2.9 28.8 + - - -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 4.0 17.7 - - + +
54D ILE* 3.9 22.0 - - + -
65D ALA 3.0 13.3 + - - +
66D LEU* 3.4 10.8 - - + +
67D THR 3.2 0.2 - - - -
68D VAL* 1.3 76.7 - - - +
70D GLU* 1.3 61.8 + - - +
72D CYS* 3.1 2.6 + - - +
73D MSE 3.0 27.8 + - + +
80D PHE* 3.8 28.3 - - + -
84D VAL* 4.7 1.8 - - + -
89D PHE* 4.1 20.4 - - + -
93D LEU* 5.0 3.1 - - + -
117D LEU* 4.1 11.9 - - + -
121D TRP* 3.5 34.1 - - + -
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU 3.1 7.7 + - - +
67D THR* 3.4 15.7 - - - +
68D VAL 3.2 0.2 - - - -
69D LEU* 1.3 80.2 - - - +
71D ALA* 1.3 62.1 + - - +
73D MSE 3.2 19.5 + - + +
74D LYS* 3.5 18.3 + - + +
113D LYS* 2.8 34.4 + - - -
116D GLU* 5.2 1.2 - - - +
117D LEU* 4.0 20.6 - - + +
121D TRP* 5.8 0.9 - - - +
151D PRO* 5.8 3.6 - - - +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TRP* 4.3 11.9 - - + -
29D ILE* 3.5 32.1 - - + -
30D ILE* 5.1 3.1 - - + -
33D CYS* 3.9 8.3 - - - -
67D THR 2.9 10.5 + - - +
68D VAL 3.3 4.9 + - - +
70D GLU* 1.3 75.8 - - - +
72D CYS* 1.3 58.1 + - - +
74D LYS* 3.2 6.6 + - - +
75D ASN* 2.7 40.1 + - - +
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Residues in contact with CYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE* 3.7 13.5 - - - -
33D CYS* 3.7 14.6 - - - -
36D ILE* 3.5 30.5 - - - -
50D LEU* 4.1 7.0 - - - -
68D VAL 2.9 22.3 + - - +
69D LEU 3.1 8.7 + - - +
71D ALA* 1.3 72.9 - - - +
73D MSE 1.3 59.8 + - - +
74D LYS 3.0 2.0 - - - -
76D CYS* 2.9 43.4 + - - +
80D PHE* 3.5 23.0 - - + -
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Residues in contact with MSE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.0 20.1 + - + +
70D GLU* 3.2 11.2 + - + +
72D CYS* 1.3 76.7 - - - +
74D LYS* 1.3 62.0 + - + +
77D GLY 4.8 0.7 + - - -
80D PHE* 3.8 10.8 - - + -
81D HIS* 2.8 35.6 + - + +
84D VAL* 3.7 33.9 - - + -
121D TRP* 3.4 56.8 - - + +
125D LEU* 3.6 26.7 - - + -
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 3.5 15.0 + - + +
71D ALA* 3.2 10.2 + - - +
72D CYS 3.0 0.4 - - - -
73D MSE 1.3 83.6 - - + +
75D ASN* 1.3 68.0 + - - +
76D CYS 3.6 0.7 - - - -
77D GLY* 4.6 3.3 + - - -
153D ASP* 2.7 30.3 + - - -
155D THR* 3.3 18.6 + - - -
156D LEU* 5.7 2.4 - - - +
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.3 27.5 - - + +
33D CYS* 4.0 18.8 - - + -
37D ASN* 2.8 23.0 - - - +
71D ALA* 2.7 28.9 + - - +
74D LYS* 1.3 85.8 + - - +
76D CYS* 1.3 59.4 + - - +
77D GLY 3.6 1.1 - - - -
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Residues in contact with CYS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS* 3.8 21.3 - - - -
36D ILE* 4.1 15.3 - - + -
37D ASN* 3.3 27.8 + - - +
43D PRO* 5.8 0.4 - - + +
72D CYS* 2.9 36.7 + - - +
75D ASN* 1.3 82.0 - - - +
77D GLY* 1.3 67.3 + - - +
79D ARG* 4.0 12.0 - - - +
80D PHE* 3.4 25.7 + - + -
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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
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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