Contacts of the helix formed by residues 32 - 49 (chain G) in PDB entry 1V8O
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 32 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.9 15.5 - - + +
31G ILE* 1.3 86.0 - - - +
33G HIS* 1.3 65.7 + - - +
34G LEU* 3.0 8.1 - - + +
35G THR* 2.8 26.5 + - - +
36G ILE* 3.9 0.7 + - - +
70G VAL* 3.7 5.3 - - - +
71G LEU* 4.2 12.6 - - + +
72G GLU 4.7 5.6 - - - +
73G ASP* 5.4 0.2 - - - +
74G PRO* 4.8 0.2 - - + -
94G SER* 3.9 33.9 - - - +
95G TYR* 3.7 32.8 - - + -
98G VAL* 3.6 28.5 - - + -
37H TYR* 4.1 16.2 - - + +
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Residues in contact with HIS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 1.3 74.7 - - - +
34G LEU* 1.3 61.5 + - - +
35G THR 3.4 0.3 + - - -
36G ILE* 3.4 12.5 + - - +
37G TYR* 3.2 21.5 - - - -
70G VAL* 3.6 23.1 + - + +
71G LEU 3.6 18.0 + - - -
72G GLU* 5.2 1.6 - - - -
73G ASP* 3.3 26.4 + - - +
33H HIS* 3.5 54.3 - + + -
37H TYR* 4.5 1.3 - - + -
73H ASP* 2.7 26.3 + - - +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 4.4 6.3 - - + -
33G HIS* 1.3 77.9 - - - +
35G THR* 1.3 65.7 + - - +
37G TYR* 3.0 14.4 + - + -
38G GLU* 3.0 50.7 + - + +
91G TYR* 3.4 42.0 - - + +
94G SER* 4.6 0.9 - - - -
95G TYR* 4.3 7.0 - - + +
34H LEU* 5.6 3.8 - - + -
37H TYR* 3.4 50.1 - - + +
91H TYR* 4.9 4.0 - - + +
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Residues in contact with THR 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL 3.9 6.1 - - - +
8G ASP 3.8 7.2 - - - +
9G ALA* 3.8 28.3 - - - +
12G LEU* 4.4 11.7 - - + -
31G ILE* 3.3 17.0 - - + +
32G LEU* 2.8 30.5 + - - -
34G LEU* 1.3 77.4 - - - +
36G ILE* 1.3 65.8 + - - +
38G GLU* 3.0 4.0 + - - +
39G ALA* 2.7 27.0 + - + +
65G MSE 4.5 1.8 - - + -
95G TYR* 3.1 18.4 + - - +
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Residues in contact with ILE 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ILE* 4.0 22.9 - - + -
32G LEU 4.3 0.4 - - - +
33G HIS* 3.6 17.0 - - - +
35G THR* 1.3 75.1 - - - +
37G TYR* 1.3 64.7 + - + +
39G ALA* 3.4 2.1 + - - +
40G GLY* 2.8 26.5 + - - -
65G MSE 3.7 23.8 - - + -
70G VAL* 4.7 10.8 - - + -
73H ASP* 3.2 34.5 - - + +
74H PRO* 5.1 9.4 - - + +
76H LEU* 4.2 19.8 - - + +
90H PHE* 4.3 3.4 - - + -
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Residues in contact with TYR 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G HIS 3.2 27.8 - - - -
34G LEU* 3.0 11.4 + - + +
36G ILE* 1.3 76.4 - - + +
38G GLU* 1.3 62.0 + - - +
40G GLY* 3.6 0.7 - - - -
41G ASN* 2.7 31.5 + - - +
32H LEU* 4.1 14.1 - - + +
33H HIS* 4.6 0.7 - - + -
34H LEU* 3.6 45.5 - - + -
73H ASP* 2.9 31.0 + - + -
74H PRO* 3.1 25.2 - - + +
90H PHE* 3.6 13.6 - + - -
91H TYR* 3.4 17.8 - + + -
94H SER* 3.4 33.2 - - - -
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Residues in contact with GLU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ALA* 3.4 22.1 + - + +
34G LEU* 3.0 43.8 + - + +
35G THR 3.5 5.8 - - - +
37G TYR* 1.3 75.1 - - - +
39G ALA* 1.3 64.6 + - - +
41G ASN* 3.2 3.5 + - - +
42G ALA* 2.9 24.3 + - - +
91G TYR* 3.7 18.4 - - + +
92G ASP* 5.5 0.7 - - - +
95G TYR* 2.7 30.9 + - - -
91H TYR* 4.0 14.4 - - - +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ALA* 4.2 8.7 - - + +
12G LEU* 4.2 12.6 - - + -
13G TYR* 4.3 8.3 - - + -
35G THR 2.7 20.0 + - - +
36G ILE 3.7 3.4 - - - +
38G GLU* 1.3 72.5 - - - +
40G GLY* 1.3 62.4 + - - +
42G ALA* 3.3 7.4 + - - +
43G LEU* 3.1 18.0 + - - +
61G LEU* 3.7 28.1 - - + +
65G MSE 4.2 16.6 - - + -
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Residues in contact with GLY 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE 2.8 16.0 + - - -
37G TYR 3.6 3.1 - - - -
39G ALA* 1.3 76.3 - - - +
41G ASN* 1.3 62.5 + - - +
43G LEU* 3.3 4.7 + - - +
44G TRP* 2.9 21.8 + - - +
61G LEU* 4.4 1.8 - - - -
76H LEU* 3.9 13.2 - - - +
80H MSE 4.3 1.4 - - - +
90H PHE* 3.5 28.8 - - - -
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Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TYR 2.7 20.8 + - - +
38G GLU* 3.7 4.0 - - - +
40G GLY* 1.3 72.0 - - - +
42G ALA* 1.3 64.0 + - - +
44G TRP* 3.1 24.0 + - - +
45G LYS* 3.0 51.8 + - - +
89H THR* 4.4 4.8 - - - +
90H PHE* 3.5 22.7 - - + +
91H TYR* 3.8 29.3 + - + +
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Residues in contact with ALA 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ALA* 6.3 0.9 - - + -
13G TYR* 4.0 23.1 - - + -
38G GLU 2.9 13.6 + - - +
39G ALA* 3.5 10.5 - - - +
40G GLY 3.3 0.2 - - - -
41G ASN* 1.3 79.2 + - - +
43G LEU* 1.3 61.6 + - - +
45G LYS* 3.1 21.6 + - - +
46G GLU* 3.2 14.7 + - - +
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.5 15.6 + - + +
39G ALA 3.1 9.7 + - - +
40G GLY* 3.6 7.9 - - - +
42G ALA* 1.3 78.6 - - - +
44G TRP* 1.3 61.9 + - - +
46G GLU* 3.2 16.8 + - + -
47G ALA* 3.0 17.2 + - - +
51G ARG* 4.3 9.9 - - - +
54G TRP* 4.3 8.3 - - - +
57G ALA* 3.9 21.1 - - + +
58G SER* 3.6 40.8 - - - +
61G LEU* 4.0 17.7 - - + -
76H LEU* 4.9 1.8 - - + -
80H MSE 4.3 11.2 - - - -
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Residues in contact with TRP 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLY 2.9 13.6 + - - +
41G ASN* 3.1 28.7 + - - +
43G LEU* 1.3 77.8 - - - +
45G LYS* 1.3 81.4 + - + +
47G ALA* 3.1 4.3 + - + +
48G ARG* 2.8 75.0 + - + +
1004G CL 4.7 2.0 - - + -
80H MSE 3.2 38.8 - - + -
83H ALA* 3.5 18.9 + - + +
84H VAL* 4.7 3.6 - - + +
88H LEU 2.9 29.4 + - - -
89H THR* 3.3 28.0 - - + -
90H PHE* 3.8 12.6 - - + -
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Residues in contact with LYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS* 5.5 9.3 - - - +
41G ASN* 3.0 38.1 + - - +
42G ALA* 3.1 12.8 + - - +
44G TRP* 1.3 90.9 - - + +
46G GLU* 1.3 65.2 + - - +
48G ARG* 3.2 8.4 + - - +
49G LEU* 3.0 32.7 + - + +
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.4 31.5 + - - +
42G ALA 3.3 15.7 - - - +
43G LEU* 3.2 17.3 - - + +
45G LYS* 1.3 79.0 - - - +
47G ALA* 1.3 64.5 + - - +
49G LEU* 3.3 12.8 + - - +
50G GLY 3.4 15.4 + - - +
51G ARG* 3.7 27.9 + - + +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ARG* 4.8 4.2 - - - +
43G LEU* 3.0 8.0 + - - +
44G TRP 3.4 8.1 - - - +
46G GLU* 1.3 77.8 - - - +
48G ARG* 1.3 67.2 + - - +
50G GLY* 3.0 13.9 + - - -
51G ARG* 3.9 13.3 + - - +
54G TRP* 3.5 34.4 - - + -
80H MSE 4.0 12.8 - - + -
84H VAL* 4.5 6.5 - - + -
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ASP* 5.0 6.1 + - - -
110E ASP* 3.0 33.2 + - - -
111E ARG* 3.2 33.8 + - - +
112E GLU* 3.4 43.9 + - - +
44G TRP* 2.8 57.3 + - + +
45G LYS* 3.2 11.4 + - - +
47G ALA* 1.3 73.1 - - - +
49G LEU* 1.3 63.0 + - + +
50G GLY 2.9 6.2 + - - -
1004G CL 3.6 26.1 - - - +
87H GLY* 4.7 6.3 + - - -
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E SER* 3.8 30.7 - - - -
109E GLN* 3.5 27.8 - - + +
110E ASP* 4.0 25.4 - - + +
111E ARG* 4.0 0.2 + - - -
45G LYS* 3.0 23.0 + - + +
46G GLU* 3.3 5.3 + - - +
48G ARG* 1.3 77.0 - - + +
50G GLY* 1.3 62.9 + - - +
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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