Contacts of the strand formed by residues 39 - 52 (chain C) in PDB entry 5JTM
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 GLU 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C GLN 5.3 2.2 - - - +
38C PRO* 1.3 71.6 - - - +
40C VAL* 1.3 60.1 + - - +
41C LYS* 3.3 10.0 + - + +
65C THR 4.3 0.5 - - - -
66C ALA* 3.7 1.0 - - - -
67C SER* 2.9 36.9 + - - +
69C GLY* 3.8 27.6 + - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PRO* 3.6 21.9 + - + +
39C GLU* 1.3 68.1 - - - +
41C LYS* 1.3 61.1 + - - +
42C LEU* 3.6 1.8 + - - +
64C VAL* 3.7 22.2 - - + -
65C THR 3.2 14.4 - - - +
66C ALA* 5.1 1.1 - - + -
126C LEU* 3.9 32.8 - - + -
5G THR* 6.2 1.8 - - + -
6G ILE* 3.2 50.1 - - + +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLU* 3.3 7.4 + - + +
40C VAL* 1.3 69.9 - - - +
42C LEU* 1.3 89.1 + - - +
43C ASP* 3.3 25.3 + - + +
63C THR 3.8 0.3 - - - +
65C THR* 2.9 57.3 + - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.6 3.8 + - - +
41C LYS* 1.3 97.1 + - - +
43C ASP* 1.3 66.2 + - - +
44C LEU* 4.9 2.0 - - + +
63C THR 3.4 6.5 - - - +
64C VAL* 4.7 5.6 - - + +
128C LEU* 6.0 0.2 - - + -
6G ILE* 3.6 38.8 - - + +
7G ALA 3.4 32.1 - - - +
8G LEU* 3.7 31.6 - - + +
9G ALA 5.5 1.6 - - - +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.3 19.9 + - + +
42C LEU* 1.3 78.4 - - - +
44C LEU* 1.3 73.7 + - - +
45C ASP* 4.0 11.8 - - - +
61C ARG* 3.5 5.5 - - - +
62C VAL* 3.8 2.8 - - - +
63C THR* 2.8 54.1 + - + +
65C THR* 5.9 1.1 - - - +
8G LEU* 5.0 1.5 - - - +
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.9 3.2 - - + +
43C ASP* 1.3 78.7 + - - +
45C ASP* 1.3 59.5 + - - +
46C THR* 4.6 0.7 - - + -
60C LEU* 3.6 45.5 - - + -
61C ARG 3.5 13.2 - - - +
62C VAL* 4.3 10.8 - - + -
133C PHE* 4.1 15.3 - - + -
8G LEU* 3.8 36.1 - - + -
9G ALA 5.4 3.1 - - - +
11G LEU* 3.7 30.9 - - + +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ASP* 4.0 8.9 + - - +
44C LEU* 1.3 73.9 - - - +
46C THR* 1.3 77.3 + - - +
47C ALA* 5.1 3.8 - - - +
60C LEU* 3.8 7.3 - - - +
61C ARG* 2.9 73.4 + - - +
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ASP* 1.3 91.5 + - - +
47C ALA* 1.3 62.8 + - - +
59C VAL 4.2 3.4 - - - -
60C LEU* 3.9 11.0 - - + -
11G LEU* 3.7 42.0 - - + -
13G LEU 5.9 0.2 - - - +
15G PHE* 3.4 25.1 - - + +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ASP* 4.4 4.9 + - - +
46C THR* 1.3 75.6 - - - +
48C SER* 1.3 69.2 + - - +
59C VAL* 2.9 50.5 + - + +
61C ARG* 5.5 4.0 - - + +
79C GLN* 5.3 5.8 - - - +
15G PHE* 3.4 4.2 - - - -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA* 1.3 82.9 + - - +
49C SER* 1.3 64.4 + - - +
57C GLU* 3.3 23.2 + - - +
59C VAL* 4.6 1.1 - - - +
15G PHE* 3.1 22.9 - - - -
17G PRO* 3.5 27.2 - - - +
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 5.0 1.2 + - - -
48C SER* 1.3 79.4 - - - +
50C GLN* 1.3 63.2 + - - +
51C LEU* 3.5 16.3 + - - +
56C TYR* 3.8 3.9 - - - +
57C GLU* 3.0 56.6 + - - +
29D PRO* 4.7 1.4 - - - +
17G PRO* 5.6 1.1 - - - -
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C SER* 1.3 72.1 - - - +
51C LEU* 1.3 63.4 + - - +
52C ALA* 3.3 28.7 + - - +
53C ASP* 4.3 10.3 + - - +
56C TYR* 3.3 40.7 + - + -
17G PRO* 5.5 0.9 - - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C SER* 3.5 28.0 - - - +
50C GLN* 1.3 77.2 - - - +
52C ALA* 1.3 63.3 + - - +
55C VAL* 3.3 17.2 + - + +
57C GLU* 4.3 4.7 - - + +
83C ILE* 3.6 48.9 - - + -
29D PRO* 3.8 24.7 - - + -
30D HIS* 5.3 6.1 - - + +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLN* 3.3 22.9 + - - +
51C LEU* 1.3 78.4 - - - +
53C ASP* 1.3 66.9 + - - +
54C ASP 3.5 1.7 + - - -
55C VAL* 3.0 34.8 + - + +
56C TYR* 4.1 1.0 - - - -
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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