Contacts of the helix formed by residues 32 - 43 (chain F) in PDB entry 1VQM
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 GLY 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2620 A 3.6 25.6 + - - -
2630 U 3.6 1.8 - - - -
2640 G 3.3 11.4 - - - -
31F LYS* 1.3 73.8 - - - +
33F THR* 1.3 57.7 + - - -
34F ASN 3.3 2.0 - - - -
36F THR* 2.5 38.5 + - - -
93F SER* 3.9 0.2 + - - -
95F ALA 3.4 14.0 + - - -
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Residues in contact with THR 33 (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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2620 A 4.2 0.2 + - - -
2630 U 2.7 32.5 + - - -
2640 G 3.9 0.4 + - - -
32F GLY* 1.3 69.9 - - - -
34F ASN* 1.3 57.3 + - - +
36F THR* 3.7 5.6 - - - -
37F THR* 2.6 38.7 + - - +
59F ILE* 3.2 36.8 - - + +
60F VAL* 4.1 4.8 - - + +
62F HIS* 3.8 15.7 - - + -
63F ILE* 4.8 2.5 - - + -
94F ALA* 3.6 16.3 - - - +
95F ALA* 4.0 11.1 + - + +
4M ALA* 3.9 8.1 - - + -
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Residues in contact with ASN 34 (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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2430 A 3.1 22.4 + - - -
2460 G 2.9 25.2 + - - +
2630 U 5.8 0.2 - - - -
2640 G 3.5 20.8 + - - +
32F GLY 3.3 0.4 - - - -
33F THR* 1.3 75.4 - - - +
35F GLU* 1.3 67.0 + - - +
37F THR* 2.9 14.2 + - - -
38F LYS* 3.0 23.2 + - - +
3M SER* 3.5 7.8 - - - -
4M ALA* 2.8 32.0 + - + +
5M TYR* 3.9 22.3 + - + -
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Residues in contact with GLU 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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2460 G 2.7 63.8 + - + +
2640 G 2.9 30.2 + - - +
30F LYS* 3.7 33.1 + - + +
31F LYS* 3.2 17.4 + - - +
34F ASN* 1.3 77.2 - - - +
36F THR* 1.3 63.6 - - - +
38F LYS* 3.3 9.9 + - - +
39F SER* 3.0 26.4 + - - -
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Residues in contact with THR 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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30F LYS* 4.1 4.6 + - - +
32F GLY 2.5 24.6 + - - -
33F THR* 3.7 6.7 - - - -
35F GLU* 1.3 75.0 - - - +
37F THR* 1.3 63.5 + - - +
39F SER* 3.2 5.1 + - - -
40F ILE* 3.2 27.3 + - + +
48F VAL* 4.0 13.0 - - + -
63F ILE* 4.4 7.2 - - + -
95F ALA* 3.6 12.2 + - + -
96F ALA* 3.5 29.9 - - - +
97F ALA* 3.8 25.6 + - + -
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Residues in contact with THR 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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33F THR 2.6 24.8 + - - -
34F ASN 2.9 4.9 + - - -
36F THR* 1.3 78.3 - - - +
38F LYS* 1.3 59.6 + - - +
40F ILE* 3.4 9.5 + - - +
41F GLU* 2.8 49.6 + - - +
62F HIS* 2.8 32.8 + - - +
63F ILE* 3.8 4.0 - - - +
66F LEU* 3.8 13.2 - - + +
2M ARG 4.3 2.0 - - - +
4M ALA* 3.4 13.0 - - - +
7M TYR* 3.9 10.3 - - + -
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Residues in contact with LYS 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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2430 A 3.1 16.7 + - - -
2440 C 2.8 34.0 + - - +
2450 C 5.3 0.9 - - - +
2460 G 5.0 4.3 - - - +
34F ASN* 3.0 24.0 + - - +
35F GLU* 3.9 8.7 - - - +
36F THR 3.3 0.2 - - - -
37F THR* 1.3 72.5 - - - +
39F SER* 1.3 54.7 + - - +
41F GLU* 3.0 14.0 + - - +
42F ARG* 2.6 64.9 + - - +
1M ALA* 3.3 11.2 + - + -
2M ARG 2.8 24.9 + - - +
3M SER* 3.2 16.2 - - - +
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Residues in contact with SER 39 (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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30F LYS* 3.3 26.5 - - - +
35F GLU 3.0 14.3 + - - -
36F THR* 3.4 11.2 - - - -
38F LYS* 1.3 76.3 - - - +
40F ILE* 1.3 52.2 + - - +
42F ARG* 3.1 2.3 + - - +
43F GLY* 2.7 31.2 + - - -
44F SER* 3.0 28.9 + - - -
45F ALA* 3.7 20.2 - - - -
97F ALA* 4.4 4.5 - - - -
99F THR* 5.0 0.8 - - - -
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Residues in contact with ILE 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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36F THR* 3.2 16.1 + - + +
37F THR 3.6 6.1 - - - +
39F SER* 1.3 76.0 - - - +
41F GLU* 1.3 61.4 + - - +
43F GLY* 3.3 11.3 + - - -
45F ALA* 4.2 2.0 - - + +
48F VAL* 3.8 37.2 - - + -
63F ILE* 4.1 29.4 - - + +
66F LEU* 3.9 36.8 - - + +
67F ALA* 4.1 11.9 - - + -
70F LYS* 3.8 24.0 - - + +
72F VAL* 4.1 16.8 - - + +
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Residues in contact with GLU 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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37F THR* 2.8 25.1 - - + +
38F LYS* 3.0 20.8 + - - +
40F ILE* 1.3 75.0 - - - +
42F ARG* 1.3 60.2 + - - +
43F GLY 3.1 5.5 + - - -
66F LEU* 4.2 12.8 - - + -
70F LYS* 4.0 22.7 + - - +
1M ALA* 3.3 15.4 - - + +
2M ARG* 2.6 44.7 - - - +
7M TYR* 2.9 25.8 + - - +
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Residues in contact with ARG 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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2440 C 2.7 42.8 + - - -
2450 C 2.8 39.5 + - - -
38F LYS* 2.6 38.6 + - - +
39F SER* 3.9 3.6 - - - +
41F GLU* 1.3 73.6 - - - +
43F GLY* 1.3 59.7 + - - +
44F SER* 3.1 18.2 + - - +
1M ALA* 4.6 10.1 - - + +
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Residues in contact with GLY 43 (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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39F SER 2.7 6.9 + - - -
40F ILE* 3.3 9.4 + - - -
41F GLU 3.1 4.8 - - - -
42F ARG* 1.3 78.7 - - - +
44F SER* 1.3 56.0 + - - +
45F ALA 3.2 14.4 + - - +
70F LYS* 6.1 1.3 - - - -
72F VAL* 5.3 6.0 - - - +
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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