Contacts of the helix formed by residues 32 - 49 (chain F) in PDB entry 1V8P
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TYR* 4.2 12.8 - - - +
6F LEU* 4.1 16.2 - - + -
31F ILE* 1.3 89.4 - - - +
33F HIS* 1.3 66.7 + - - +
34F LEU* 3.9 8.7 - - + +
35F THR* 3.1 24.1 + - - +
36F ILE 4.0 0.5 + - - -
70F VAL* 4.0 5.2 - - - -
71F LEU* 4.3 12.3 - - + +
72F GLU 4.4 9.0 - - - +
74F PRO* 4.9 0.4 - - + -
94F SER* 4.1 23.3 - - - -
95F TYR* 3.8 39.0 - - + +
98F VAL* 3.9 26.0 - - + -
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Residues in contact with HIS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E HIS* 3.3 54.2 - + + -
37E TYR* 4.7 0.4 - - + -
73E ASP* 2.5 31.5 + - - +
32F LEU* 1.3 73.8 - - - +
34F LEU* 1.3 63.6 + - - +
35F THR 3.2 0.9 + - - -
36F ILE* 3.2 15.5 + - - +
37F TYR* 3.3 16.8 - - - -
70F VAL* 3.6 28.4 + - + +
71F LEU 3.8 11.0 + - - -
72F GLU* 5.0 1.8 - - - -
73F ASP* 3.4 25.8 + - - +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 5.2 3.8 - - + -
37E TYR* 3.6 53.2 - - + -
91E TYR* 4.9 2.0 - - - +
32F LEU* 3.0 6.0 - - + +
33F HIS* 1.3 78.4 - - - +
35F THR* 1.3 60.7 + - - +
37F TYR* 3.1 22.9 + - + +
38F GLU* 3.2 32.3 + - + +
91F TYR* 3.7 33.9 - - + +
94F SER* 4.4 1.6 - - - +
95F TYR* 3.8 27.1 - - + +
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Residues in contact with THR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL 3.9 0.4 + - - +
8F ASP 4.1 5.4 - - - +
9F ALA* 3.8 27.1 - - - +
12F LEU* 4.4 8.5 - - + -
31F ILE* 3.6 23.6 - - + +
32F LEU 3.1 27.8 + - - -
34F LEU* 1.3 74.5 - - - +
36F ILE* 1.3 65.9 - - - +
38F GLU* 4.0 3.1 - - - +
39F ALA* 2.9 24.5 + - + +
65F LEU* 4.5 6.1 - - + -
95F TYR* 3.0 20.8 + - - -
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Residues in contact with ILE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASP* 3.1 38.6 - - + +
74E PRO* 4.6 12.3 - - + +
76E LEU* 3.8 18.8 - - + +
90E PHE* 4.4 2.7 - - + -
31F ILE* 4.5 12.3 - - + -
32F LEU 4.5 0.2 - - - +
33F HIS* 3.2 12.0 + - - +
35F THR* 1.3 77.1 - - - +
37F TYR* 1.3 65.9 + - + +
39F ALA* 3.4 1.9 + - - +
40F GLY* 2.9 25.5 + - - -
65F LEU* 4.1 31.6 - - + +
70F VAL* 5.3 8.1 - - + -
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Residues in contact with TYR 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.2 13.4 - - + +
33E HIS* 4.7 0.2 - - + -
34E LEU* 3.5 43.2 + - + -
73E ASP* 2.9 30.0 + - + -
74E PRO* 3.2 24.7 - - + +
79E VAL* 6.2 0.2 - - + -
90E PHE* 3.6 14.8 - + - -
91E TYR* 3.4 22.2 - + + -
94E SER* 3.4 33.7 - - - -
33F HIS 3.3 23.8 - - - -
34F LEU* 3.1 11.3 + - + +
36F ILE* 1.3 79.3 - - + +
38F GLU* 1.3 54.5 + - - +
41F ASN* 2.7 35.7 + - - +
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E TYR* 3.5 17.3 - - - +
9F ALA* 3.4 23.5 + - + +
34F LEU* 3.2 33.5 + - + +
35F THR* 4.0 1.3 - - - +
37F TYR* 1.3 72.2 - - - +
39F ALA* 1.3 67.5 + - - +
41F ASN* 3.2 2.7 + - - +
42F ALA* 2.9 25.1 + - - +
91F TYR* 3.8 22.4 - - + +
92F ASP* 5.1 2.9 - - - +
95F TYR* 2.5 34.1 + - - -
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Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA* 4.1 8.4 - - + +
12F LEU* 4.6 8.3 - - + -
13F TYR* 4.0 9.2 - - + -
35F THR 2.9 19.1 + - - +
36F ILE 3.7 3.4 - - - +
38F GLU* 1.3 76.0 - - - +
40F GLY* 1.3 64.2 + - - +
42F ALA* 3.1 16.4 + - - +
43F LEU 3.2 10.2 + - - -
61F LEU* 3.8 36.2 - - + +
65F LEU* 4.3 9.9 - - + -
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Residues in contact with GLY 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 3.6 22.6 - - - +
80E LEU* 5.1 0.5 - - - +
90E PHE* 3.6 26.5 - - - -
36F ILE 2.9 11.1 + - - -
37F TYR 3.7 0.7 - - - -
39F ALA* 1.3 78.6 - - - +
41F ASN* 1.3 61.5 + - - +
42F ALA 3.1 0.3 + - - -
43F LEU* 3.1 3.8 + - - +
44F TRP* 2.9 23.9 + - - +
61F LEU* 4.6 0.7 - - - -
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Residues in contact with ASN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR* 4.6 1.4 - - - -
90E PHE* 3.6 20.0 - - + +
91E TYR* 3.2 42.3 + - + +
37F TYR 2.7 20.5 + - - +
38F GLU* 3.2 4.5 + - - +
40F GLY* 1.3 73.2 - - - +
42F ALA* 1.3 61.0 + - - +
44F TRP* 3.4 22.9 - - - +
45F LYS* 3.2 53.0 + - - +
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA* 6.3 0.9 - - + -
13F TYR* 3.9 23.1 - - + -
38F GLU 2.9 13.1 + - - +
39F ALA* 3.3 10.1 - - - +
40F GLY 3.1 0.4 - - - -
41F ASN* 1.3 75.6 - - - +
43F LEU* 1.3 62.5 + - - +
45F LYS* 3.6 11.7 + - - +
46F GLU* 3.3 25.1 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LEU* 4.6 1.6 - - + -
80E LEU* 4.4 8.7 - - + -
13F TYR* 3.7 13.6 + - - +
39F ALA 3.2 10.2 + - - +
40F GLY* 3.1 7.9 + - - +
42F ALA* 1.3 72.7 - - - +
44F TRP* 1.3 67.0 + - - +
46F GLU* 3.1 15.5 + - + +
47F ALA* 2.9 21.5 + - - +
51F ARG* 4.3 10.1 - - - +
54F TRP* 3.8 17.0 - - + +
57F ALA* 3.9 18.8 - - + -
58F SER* 3.4 45.5 - - - +
61F LEU* 4.1 16.6 - - + -
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Residues in contact with TRP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 3.8 20.8 - - + +
83E ALA* 3.9 21.3 + - + +
84E VAL* 4.6 8.8 - - + +
88E LEU 3.3 26.4 + - - -
89E THR* 3.5 25.8 - - + -
90E PHE* 3.7 15.3 - - + -
40F GLY 2.9 16.8 + - - +
41F ASN* 3.4 32.1 - - - +
43F LEU* 1.3 78.1 - - - +
45F LYS* 1.3 69.8 + - + +
47F ALA* 3.1 4.8 + - + +
48F ARG* 2.8 77.2 + - + +
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Residues in contact with LYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F ASN* 3.2 33.0 + - - +
42F ALA* 3.8 11.9 - - - +
43F LEU 3.2 0.4 - - - -
44F TRP* 1.3 90.8 - - + +
46F GLU* 1.3 61.8 + - + +
48F ARG* 3.5 8.2 + - - +
49F LEU* 3.0 37.9 + - + +
45H LYS* 3.9 22.5 - - - +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 2.6 37.4 + - - -
42F ALA 3.3 10.5 - - - +
43F LEU* 3.1 10.9 + - - +
45F LYS* 1.3 75.1 - - + +
47F ALA* 1.3 67.6 + - - +
49F LEU* 3.0 14.5 + - - +
50F GLY 3.3 0.5 + - - -
51F ARG* 3.0 58.3 + - + +
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Residues in contact with ALA 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.9 1.3 - - + -
84E VAL* 4.4 18.6 - - + -
43F LEU 2.9 13.4 + - - +
44F TRP* 3.3 12.3 - - + +
46F GLU* 1.3 77.0 - - - +
48F ARG* 1.3 58.0 + - - +
50F GLY* 2.8 23.2 + - - -
51F ARG* 3.7 12.8 + - - +
54F TRP* 3.8 30.3 - - + +
111H ARG* 4.3 6.3 - - - +
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Residues in contact with ARG 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 5.9 0.2 - - - +
87E GLY* 5.0 5.1 + - - -
1001E CL 3.9 22.6 - - - +
44F TRP* 2.8 61.0 + - + +
45F LYS* 3.6 10.3 - - - +
47F ALA* 1.3 71.9 - - - +
49F LEU* 1.3 58.3 + - + +
50F GLY 3.4 0.4 - - - -
88H LEU* 5.5 2.0 - - - +
89H THR* 5.8 1.8 - - - +
92H ASP* 4.3 13.1 + - - -
109H GLN 3.4 0.2 - - - +
110H ASP* 2.5 47.0 + - - +
111H ARG* 2.9 36.2 + - - -
112H GLU* 3.2 41.5 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LYS* 3.0 22.9 + - + +
46F GLU* 3.4 10.8 - - - +
47F ALA 2.9 1.8 + - - -
48F ARG* 1.3 78.5 - - + +
50F GLY* 1.3 55.4 + - - +
51F ARG 3.6 0.4 + - - -
10H SER* 3.4 35.0 - - - +
109H GLN* 3.4 41.1 - - + +
110H ASP* 4.2 9.2 - - + +
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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
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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