Contacts of the helix formed by residues 39 - 52 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 4.7 6.1 - - - -
33A LEU* 4.4 2.5 - - - -
38A ILE* 1.3 80.3 - - - +
40A ALA* 1.3 58.9 + - - +
41A ALA* 3.7 7.1 + - - +
42A GLN* 3.2 42.3 + - - +
43A PHE* 2.9 27.5 + - - +
74A MET* 5.3 0.2 - - - -
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Residues in contact with ALA 40 (chain A).
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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26A ASP* 4.7 3.4 - - + +
29A LEU* 4.0 21.3 - - + +
30A ASN* 3.3 39.3 + - - +
33A LEU* 4.1 10.9 - - - +
39A THR* 1.3 72.0 - - - +
41A ALA* 1.3 60.9 + - - +
43A PHE* 3.4 3.3 + - - +
44A LYS* 3.0 39.5 + - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 3.3 6.4 + - - +
40A ALA* 1.3 77.9 - - - +
42A GLN* 1.3 65.0 + - - +
44A LYS* 3.3 10.4 + - - +
45A VAL* 3.2 26.7 + - - +
74A MET* 3.7 22.7 - - + +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.7 20.1 - - + +
39A THR* 3.2 44.3 + - - +
41A ALA* 1.3 78.9 - - - +
43A PHE* 1.3 60.0 + - - +
45A VAL* 3.5 6.5 - - - +
46A LEU* 3.2 27.0 + - - +
74A MET* 4.1 21.3 - - + -
77A ARG* 4.7 18.5 - - - +
78A LEU* 3.9 25.3 - - + +
81A LYS* 4.2 17.0 + - - +
83A TRP* 4.3 1.2 - - - -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.4 25.8 - - + -
33A LEU* 3.8 20.6 - - + -
38A ILE* 4.1 11.1 - - + +
39A THR 2.9 18.3 + - - +
40A ALA 3.6 3.6 - - - +
41A ALA 3.2 0.4 - - - -
42A GLN* 1.3 74.3 - - - +
44A LYS* 1.3 68.1 + - + +
46A LEU* 3.3 5.6 + - + +
47A CYS* 3.2 48.2 + - - -
108A CYS* 3.9 14.6 - - - -
111A CYS* 3.4 38.8 - - + -
112A HIS* 3.7 24.7 - + - -
115A VAL* 5.9 2.5 - - + -
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.7 14.6 - - - +
26A ASP* 3.3 29.6 + - - -
29A LEU* 4.0 10.2 - - - +
40A ALA* 3.0 25.5 + - - +
41A ALA* 3.3 8.0 + - - +
43A PHE* 1.3 79.2 - - + +
45A VAL* 1.3 65.7 - - - +
47A CYS* 3.2 7.6 + - - +
48A SER* 3.0 26.9 + - - -
64A LEU* 4.2 15.7 - - + -
19B HIS* 4.6 19.7 + - + -
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Residues in contact with VAL 45 (chain A).
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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41A ALA 3.2 13.8 + - - +
42A GLN 3.5 8.3 - - - +
43A PHE 3.3 0.2 - - - -
44A LYS* 1.3 76.2 - - - +
46A LEU* 1.3 63.7 + - - +
48A SER* 3.2 2.9 + - - -
49A ILE* 2.9 45.3 + - + +
60A LEU* 4.3 9.4 - - + +
64A LEU* 3.6 24.9 - - + +
71A LEU* 4.1 5.4 - - + -
74A MET* 3.5 28.5 - - + -
75A LEU* 4.4 6.5 - - + -
78A LEU* 3.6 22.7 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.7 26.9 - - + -
42A GLN 3.2 12.3 + - - +
43A PHE* 3.3 8.0 + - + +
45A VAL* 1.3 79.1 - - + +
47A CYS* 1.3 58.2 + - - +
49A ILE* 3.7 1.2 - - - +
50A ARG* 2.8 28.9 + - - +
78A LEU* 3.9 17.9 - - + -
83A TRP* 4.2 17.7 - - + -
84A VAL* 3.7 30.5 - - + -
100A LEU* 3.8 18.2 - - + +
104A GLY 4.4 13.9 - - - +
107A ILE* 4.9 2.0 - - + -
108A CYS* 4.1 23.1 - - + +
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 3.2 52.1 + - - -
44A LYS* 3.6 10.8 - - - +
45A VAL 3.2 0.6 - - - -
46A LEU* 1.3 74.2 - - - +
48A SER* 1.3 60.9 + - - +
50A ARG* 3.3 5.0 + - - +
51A CYS* 3.0 38.3 + - - -
108A CYS* 3.7 15.9 - - - -
112A HIS* 4.5 11.2 - - - -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS 3.0 12.3 + - - -
45A VAL 3.2 1.8 + - - -
47A CYS* 1.3 74.5 - - - +
49A ILE* 1.3 63.6 + - - +
51A CYS* 3.3 7.0 + - - +
52A ALA* 3.2 25.8 + - - +
55A ILE* 5.0 1.7 - - - +
60A LEU* 3.6 24.1 - - - +
63A VAL* 3.9 18.9 - - - +
64A LEU* 3.4 21.4 - - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 2.9 38.9 + - + +
46A LEU* 3.8 4.3 - - - +
48A SER* 1.3 74.8 - - - +
50A ARG* 1.3 55.6 + - - +
52A ALA 2.2 28.2 - - - +
53A ALA 3.5 5.5 - - - +
55A ILE* 4.1 10.1 - - + -
60A LEU* 4.0 19.1 - - + -
75A LEU* 4.2 3.1 - - + -
84A VAL* 4.0 22.2 - - + -
98A VAL* 3.8 24.0 - - + +
99A LYS* 3.6 35.0 - - - -
100A LEU* 3.9 8.6 - - + +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU 2.8 19.4 + - - +
47A CYS* 3.4 7.6 - - - +
49A ILE* 1.3 79.5 - - - +
51A CYS* 1.3 66.6 + - - +
52A ALA 3.9 2.9 - - - +
53A ALA* 4.1 5.4 + - - -
100A LEU* 3.9 15.9 - - + +
105A ALA* 3.6 32.7 + - - +
108A CYS* 3.9 15.4 - - - +
109A GLU* 3.8 32.5 + - - +
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A CYS* 3.0 27.9 + - - +
48A SER* 3.3 7.2 + - - +
50A ARG* 1.3 82.2 - - - +
52A ALA* 1.3 58.2 + - - +
53A ALA 3.7 1.7 + - - -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER 3.2 10.2 + - - +
49A ILE* 2.2 30.8 - - - +
51A CYS* 1.3 76.8 - - - +
53A ALA* 1.3 59.3 + - - +
54A CYS* 3.3 12.9 + - - +
55A ILE* 4.0 24.5 - - + -
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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