Contacts of the helix formed by residues 39 - 52 (chain B) in PDB entry 3VOD
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 THR 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ASN* 3.3 13.7 - - - +
33B LEU* 4.0 1.3 - - - -
38B ILE* 1.3 77.9 - - - +
40B ALA* 1.3 58.7 + - - +
41B ALA* 3.7 8.7 + - - +
42B GLN* 3.1 38.7 + - - +
43B PHE* 2.9 27.2 + - - +
74B MET* 5.0 1.0 - - - +
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Residues in contact with ALA 40 (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 ASP* 4.0 12.8 - - + +
29B LEU* 3.7 33.4 - - + -
30B ASN* 2.9 28.0 + - - +
33B LEU* 3.8 12.1 - - - +
39B THR* 1.3 68.7 - - - +
41B ALA* 1.3 61.9 + - - +
43B PHE* 3.2 2.1 + - - +
44B LYS* 2.9 38.0 + - - +
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Residues in contact with ALA 41 (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 ASN* 5.5 0.2 - - - +
39B THR* 3.3 8.8 + - - +
40B ALA* 1.3 79.9 - - - +
42B GLN* 1.3 61.6 + - - +
44B LYS* 3.4 10.9 + - - +
45B VAL* 3.3 24.8 + - - +
64B LEU* 5.6 0.2 - - - +
74B MET* 4.1 19.5 - - + +
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Residues in contact with GLN 42 (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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37B ASP 4.2 4.0 - - - +
38B ILE* 3.5 22.7 - - + +
39B THR* 3.1 41.4 + - - +
41B ALA* 1.3 78.2 - - - +
43B PHE* 1.3 62.7 + - - +
45B VAL* 3.4 5.8 + - - +
46B LEU* 3.2 24.4 + - - +
74B MET* 4.0 27.3 - - + +
77B ARG* 4.3 24.5 - - - +
78B LEU* 4.3 16.3 - - + +
81B LYS* 4.2 18.1 + - - +
83B TRP* 4.6 0.7 - - - -
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Residues in contact with PHE 43 (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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29B LEU* 4.3 22.7 - - + -
33B LEU* 3.7 22.0 - - + -
38B ILE* 4.1 7.6 - - + +
39B THR 2.9 17.5 + - - +
40B ALA 3.2 5.6 + - - +
42B GLN* 1.3 75.1 - - - +
44B LYS* 1.3 69.0 + - + +
46B LEU* 3.1 11.0 + - + +
47B CYS* 3.0 47.7 + - - -
108B CYS* 3.8 11.7 - - - -
111B CYS* 3.2 42.2 - - + -
112B HIS* 3.9 23.3 - + - -
115B VAL* 5.3 4.0 - - + -
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Residues in contact with LYS 44 (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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19A HIS* 3.8 37.1 + - + +
22B ASN* 5.0 2.6 - - - +
25B LYS* 3.9 6.1 - - - +
26B ASP* 2.8 41.6 + - - -
29B LEU* 4.6 6.5 - - + -
40B ALA* 2.9 21.9 + - - +
41B ALA* 3.7 8.7 - - - +
43B PHE* 1.3 81.3 - - + +
45B VAL* 1.3 57.4 + - - +
47B CYS* 3.5 6.9 + - - +
48B SER* 2.7 34.3 + - - -
64B LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 45 (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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41B ALA 3.3 14.3 + - - +
42B GLN 3.4 8.5 - - - +
43B PHE 3.1 0.4 - - - -
44B LYS* 1.3 73.8 - - - +
46B LEU* 1.3 66.8 + - + +
48B SER* 3.1 4.3 + - - -
49B ILE* 3.0 40.8 + - + +
60B LEU* 4.3 10.5 - - + +
64B LEU* 3.7 24.9 - - + -
66B VAL* 6.1 1.1 - - + -
71B LEU* 4.1 9.4 - - + -
74B MET* 3.8 19.7 - - - -
75B LEU* 4.4 4.7 - - + -
78B LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 46 (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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38B ILE* 3.4 32.5 - - + -
42B GLN 3.2 8.7 + - - +
43B PHE* 3.1 11.2 + - + +
45B VAL* 1.3 78.7 - - - +
47B CYS* 1.3 56.9 + - - +
49B ILE* 3.4 3.1 + - - +
50B ARG* 2.8 29.3 + - - +
78B LEU* 4.3 9.6 - - + -
83B TRP* 4.1 17.7 - - + -
84B VAL* 4.0 15.9 - - + -
100B LEU* 3.6 28.9 - - + +
104B GLY 4.8 3.1 - - - +
107B ILE* 4.0 18.8 - - + -
108B CYS* 4.1 22.7 - - + -
111B CYS* 5.1 0.2 - - - -
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Residues in contact with CYS 47 (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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43B PHE* 3.0 51.4 + - - +
44B LYS* 3.7 10.8 - - - +
46B LEU* 1.3 73.6 - - - +
48B SER* 1.3 59.3 + - - +
50B ARG* 3.0 10.6 + - - +
51B CYS* 2.9 38.1 + - - -
108B CYS* 4.0 5.1 - - - -
112B HIS* 3.5 21.1 - - + -
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Residues in contact with SER 48 (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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44B LYS 2.7 22.6 + - - -
45B VAL 3.6 4.3 - - - -
47B CYS* 1.3 74.2 - - - +
49B ILE* 1.3 63.6 + - - +
51B CYS* 3.3 17.3 + - - +
52B ALA* 3.5 12.1 + - - +
55B ILE* 5.0 4.5 - - - +
60B LEU* 3.6 20.8 - - - +
63B VAL* 4.5 16.5 - - - +
64B LEU* 3.3 19.4 - - - +
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Residues in contact with ILE 49 (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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45B VAL* 3.0 33.9 + - + +
46B LEU 3.6 7.4 - - - +
48B SER* 1.3 74.8 - - - +
50B ARG* 1.3 54.2 + - - +
52B ALA 2.2 29.5 - - - +
53B ALA* 3.9 2.8 - - - +
55B ILE* 4.0 12.8 - - + -
60B LEU* 3.9 15.7 - - + -
75B LEU* 4.2 5.2 - - + -
84B VAL* 4.0 24.9 - - + -
98B VAL* 3.8 21.5 - - + +
99B LYS* 3.6 29.6 - - - -
100B LEU* 3.6 16.1 + - + +
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Residues in contact with ARG 50 (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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46B LEU 2.8 18.4 + - - +
47B CYS* 3.0 10.1 + - - +
49B ILE* 1.3 75.8 - - - +
51B CYS* 1.3 64.5 + - - +
52B ALA 4.1 3.1 - - - +
53B ALA* 4.7 2.3 + - - +
100B LEU* 3.7 18.6 - - + -
105B ALA* 4.0 23.4 + - + +
108B CYS* 3.9 20.1 - - - +
109B GLU* 4.4 26.0 + - - +
112B HIS* 5.0 13.3 + - - -
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Residues in contact with CYS 51 (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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47B CYS* 2.9 22.6 + - - -
48B SER* 3.3 11.4 + - - +
50B ARG* 1.3 80.8 - - - +
52B ALA* 1.3 59.1 + - - +
53B ALA 4.0 1.2 + - - -
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Residues in contact with ALA 52 (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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48B SER 3.5 6.8 + - - +
49B ILE 2.2 30.7 - - - +
50B ARG 4.2 1.3 - - - -
51B CYS* 1.3 77.0 - - - +
53B ALA* 1.3 63.8 + - - +
54B CYS* 3.1 19.9 + - - +
55B ILE* 4.3 18.4 - - + -
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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