Contacts of the helix formed by residues 58 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 2.8 44.4 - - + +
2A ALA* 3.9 5.9 - - - +
6A GLY 3.9 11.4 - - - +
7A GLU* 3.5 20.3 - - - +
10A GLU* 4.1 12.8 - - + -
49A LEU* 4.6 2.2 - - + -
19B PRO* 3.8 10.6 - - + +
56B SER* 3.0 13.6 + - - +
57B PRO* 1.3 79.0 - - - +
59B GLU* 1.3 72.2 + - - +
60B TRP* 2.9 34.6 + - - +
61B GLU* 3.0 26.3 + - + +
62B ALA* 3.1 19.4 + - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.9 0.6 + - - -
2A ALA* 4.4 15.6 - - + +
203A MSE 3.8 23.2 - - + +
56B SER 5.4 0.4 - - - -
57B PRO 3.4 5.4 + - - -
58B GLN* 1.3 72.9 + - - +
60B TRP* 1.3 62.5 + - - +
62B ALA* 3.1 7.7 + - - +
63B LEU* 2.8 41.2 + - + +
107B SER* 2.6 37.7 + - - +
109B LYS* 3.1 31.8 - - - +
110B VAL* 4.1 5.8 - - + +
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Residues in contact with TRP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA 5.7 0.2 + - - -
7A GLU* 3.5 20.4 - - - +
19B PRO* 2.9 26.9 + - + -
21B ASN 2.8 25.8 + - - -
22B ARG 4.6 1.8 - - - -
23B GLN* 4.1 26.5 - - - -
24B GLU* 4.3 22.7 - - - -
58B GLN* 2.9 14.4 + - - +
59B GLU* 1.3 77.6 + - - +
61B GLU* 1.3 62.8 + - - +
63B LEU* 3.2 23.6 + - + -
64B GLN* 2.9 70.1 + - + +
67B THR* 6.4 1.1 - - + -
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 2.7 41.8 - - - +
14A ASN* 3.6 8.3 + - - +
52A HIS* 5.2 2.8 - - - -
17B THR* 3.6 26.8 + - - +
19B PRO* 3.8 16.5 - - + +
53B LYS* 3.6 32.7 + - + +
56B SER* 2.7 28.8 + - - +
58B GLN* 3.0 16.2 - - + +
60B TRP* 1.3 75.9 - - - +
62B ALA* 1.3 62.3 + - - +
64B GLN* 3.6 0.8 + - - +
65B ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS 3.6 14.8 + - - +
54B ILE* 3.5 24.2 - - - +
56B SER 4.3 9.0 - - - +
58B GLN 3.1 12.4 + - - +
59B GLU* 3.1 9.3 + - - +
61B GLU* 1.3 75.0 - - - +
63B LEU* 1.3 64.8 + - - +
65B ALA* 3.0 13.8 + - - +
66B LEU* 3.0 18.2 + - - +
110B VAL* 4.1 15.7 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 2.8 40.8 + - + +
60B TRP* 3.5 27.6 - - + +
62B ALA* 1.3 73.5 - - - +
64B GLN* 1.3 61.6 + - - +
66B LEU* 3.2 21.7 + - + +
67B THR* 3.3 18.9 + - + +
109B LYS* 4.3 18.8 - - + +
110B VAL* 3.5 35.4 - - + +
113B LYS* 5.1 4.3 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.2 26.4 - - - +
17B THR* 3.7 13.7 + - - -
18B ASN 2.8 30.3 + - - -
21B ASN* 3.4 15.9 - - - +
23B GLN 4.4 3.8 - - - +
24B GLU* 4.5 11.3 - - + +
25B ASP 4.8 0.2 + - - -
60B TRP* 2.9 65.9 + - + +
61B GLU 4.0 0.9 - - - +
63B LEU* 1.3 72.8 - - - +
65B ALA* 1.3 66.7 + - - +
67B THR* 3.2 11.1 + - - +
68B VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.6 9.6 - - + +
50B LEU* 3.9 8.0 - - + +
53B LYS* 3.7 28.7 - - + -
54B ILE* 3.8 19.1 - - + +
61B GLU 3.1 14.3 + - - +
62B ALA 3.0 11.3 + - - +
64B GLN* 1.3 76.8 - - - +
66B LEU* 1.3 57.1 + - - +
68B VAL* 3.0 7.2 + - - +
69B LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.6 34.3 - - + -
62B ALA 3.0 15.1 + - - +
63B LEU* 3.2 13.4 + - + +
65B ALA* 1.3 76.6 - - - +
67B THR* 1.3 62.5 + - + +
69B LEU* 3.2 9.3 + - + +
70B GLU* 3.0 26.4 + - - +
93B LEU* 5.3 1.3 - - + -
110B VAL* 3.8 29.2 - - + +
113B LYS* 3.3 40.8 - - + -
114B VAL* 4.3 8.7 - - + -
117B LEU* 3.8 20.8 - - + +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.7 34.9 - - - +
26B TRP* 5.0 9.7 - - - -
29B ILE* 4.1 11.7 - - - +
60B TRP* 6.4 0.9 - - + -
63B LEU 3.4 16.6 - - - +
64B GLN* 3.2 9.3 + - - +
66B LEU* 1.3 76.8 - - + +
68B VAL* 1.3 59.3 + - - +
70B GLU* 3.3 21.5 + - - +
71B ALA* 2.9 26.9 + - - +
113B LYS* 5.3 4.7 - - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.0 2.5 - - + -
16B ALA* 4.1 25.4 - - + +
17B THR* 4.1 9.6 - - + -
29B ILE* 4.1 27.1 - - + +
32B PHE* 3.5 33.4 - - + -
50B LEU* 3.7 15.0 - - + -
64B GLN* 3.0 20.3 + - + +
65B ALA 3.3 7.6 - - - +
67B THR* 1.3 75.2 - - - +
69B LEU* 1.3 60.5 + - - +
71B ALA* 3.1 4.0 + - - +
72B CYS* 2.9 28.4 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.8 20.2 - - + +
54B ILE* 4.0 21.5 - - + -
65B ALA 2.9 12.0 + - - +
66B LEU* 3.3 10.3 - - + +
68B VAL* 1.3 77.2 - - - +
70B GLU* 1.3 62.3 + - - +
72B CYS* 3.0 6.4 + - - +
73B MSE 2.9 25.3 + - - +
80B PHE* 3.8 27.1 - - + -
84B VAL* 4.6 2.2 - - + -
89B PHE* 4.2 19.7 - - + -
93B LEU* 5.2 3.1 - - + -
117B LEU* 4.2 14.8 - - + -
121B TRP* 3.6 36.3 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU 3.0 13.0 + - - +
67B THR* 3.3 27.7 - - - +
68B VAL 3.2 0.2 - - - -
69B LEU* 1.3 76.3 - - - +
71B ALA* 1.3 63.4 + - - +
73B MSE 2.9 22.6 + - - +
74B LYS* 3.2 14.9 + - - +
113B LYS* 2.4 38.0 + - - -
116B GLU* 4.0 1.6 - - - +
117B LEU* 3.4 28.6 - - + +
151B PRO* 5.5 1.9 - - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TRP* 4.4 12.3 - - + -
29B ILE* 3.5 29.6 - - + -
30B ILE* 5.2 2.9 - - + -
33B CYS* 3.8 8.5 - - - -
67B THR 2.9 10.4 + - - +
68B VAL 3.1 8.9 + - - +
70B GLU* 1.3 75.7 - - - +
72B CYS* 1.3 58.7 + - - +
74B LYS* 3.1 5.9 + - - -
75B ASN* 2.9 38.3 + - - +
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Residues in contact with CYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 3.9 28.3 - - - -
33B CYS* 3.6 22.7 - - - -
36B ILE* 4.7 2.0 - - - -
50B LEU* 4.4 2.0 - - - -
68B VAL* 2.9 17.9 + - - -
69B LEU* 3.0 10.3 + - - +
71B ALA* 1.3 77.4 - - - +
73B MSE 1.3 57.3 + - - +
76B CYS* 2.9 43.8 + - - +
80B PHE* 3.5 32.5 - - + -
81B HIS* 5.0 0.2 + - - -
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Residues in contact with MSE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 2.9 19.4 + - + +
70B GLU* 2.9 12.4 + - - +
72B CYS* 1.3 76.6 - - - +
74B LYS* 1.3 62.0 + - + +
77B GLY* 4.7 2.4 + - - -
80B PHE* 3.5 24.9 - - - -
81B HIS* 2.8 37.1 + - + +
84B VAL* 3.7 19.7 - - + -
121B TRP* 3.5 47.8 - - + +
125B LEU* 3.4 34.5 - - + -
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU 3.2 9.3 + - - +
71B ALA* 3.1 9.4 + - - +
73B MSE 1.3 83.0 - - + +
75B ASN* 1.3 66.1 + - - +
77B GLY* 4.9 2.2 + - - -
153B ASP* 3.0 28.2 + - - -
155B THR* 4.8 14.3 + - + +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 4.6 25.0 - - - +
33B CYS* 4.0 23.1 - - + +
37B ASN* 3.4 18.3 + - - +
71B ALA* 2.9 23.9 + - - +
74B LYS* 1.3 85.6 - - - +
76B CYS* 1.3 61.1 + - - +
77B GLY 3.4 3.6 + - - -
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Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B CYS* 3.8 24.9 - - - -
36B ILE* 3.9 17.9 - - + -
37B ASN* 3.4 20.4 - - - +
72B CYS* 2.9 40.5 + - - +
75B ASN* 1.3 74.8 - - - +
77B GLY* 1.3 65.4 + - - +
78B ARG 3.9 0.3 + - - -
79B ARG* 4.0 14.4 - - - +
80B PHE* 3.5 27.2 + - + +
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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