Contacts of the helix formed by residues 39 - 52 (chain C) in PDB entry 1MBU
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 PRO 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 TYR 3.6 8.5 - - - +
38C THR* 1.3 93.9 - - + +
40C MET* 1.3 65.8 + - - +
41C GLU* 4.2 12.3 - - + +
42C PHE* 3.0 20.8 + - + +
43C VAL* 3.2 9.7 + - - +
97C HIS* 3.9 27.4 - - + +
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Residues in contact with MET 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 THR 3.7 2.5 + - - +
39C PRO* 1.3 71.8 - - - +
41C GLU* 1.3 58.2 + - - +
43C VAL* 3.2 6.8 + - - +
44C ILE* 2.9 35.4 + - + +
62C MET* 3.4 45.0 - - + +
63C LEU* 5.1 4.5 - - - -
66C HIS* 4.3 26.7 - - + +
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Residues in contact with GLU 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 PRO* 3.0 9.2 - - + +
40C MET* 1.3 80.6 - - - +
42C PHE* 1.3 57.0 + - - +
44C ILE* 3.4 10.8 + - + +
45C ASP* 2.8 27.4 + - + +
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Residues in contact with PHE 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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38C THR* 3.8 17.0 - - + -
39C PRO* 3.0 17.7 + - + +
41C GLU* 1.3 75.4 - - - +
43C VAL* 1.3 66.3 + - - +
45C ASP* 3.1 12.7 + - + +
46C VAL* 2.9 33.8 + - + +
91C TYR* 3.4 42.4 - + - -
92C ALA* 3.8 22.9 - - + -
95C ASN* 3.7 21.1 - - + -
97C HIS* 3.4 31.9 - + + +
99C LEU* 3.9 13.2 - - + -
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Residues in contact with VAL 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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32C LEU* 4.3 16.2 - - + -
38C THR* 3.9 19.5 - - + +
39C PRO 3.2 13.9 + - - +
40C MET* 3.2 10.9 + - - +
42C PHE* 1.3 76.1 - - - +
44C ILE* 1.3 57.4 + - - +
46C VAL* 3.3 7.4 + - - +
47C LEU* 3.0 42.6 + - + +
62C MET* 3.9 23.6 - - + -
65C VAL* 4.8 13.7 - - + -
99C LEU* 4.5 15.0 - - + -
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Residues in contact with ILE 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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40C MET* 2.9 22.5 + - + +
41C GLU* 3.6 10.8 - - + +
43C VAL* 1.3 73.8 - - - +
45C ASP* 1.3 65.3 - - - +
47C LEU* 3.1 4.2 + - - +
48C GLN* 3.0 37.7 + - - +
55C VAL* 5.0 8.1 - - + +
58C ALA* 4.0 18.2 - - + +
59C THR* 3.9 27.6 - - + +
62C MET* 3.9 32.8 - - + -
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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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41C GLU* 2.8 16.9 + - + +
42C PHE* 3.3 18.9 - - - +
44C ILE* 1.3 76.8 - - - +
46C VAL* 1.3 52.5 + - - +
48C GLN* 3.2 5.7 + - - +
49C LYS* 2.8 43.2 + - - +
91C TYR* 2.6 36.4 + - - -
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Residues in contact with VAL 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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32C LEU* 4.2 19.1 - - + -
42C PHE* 2.9 41.2 + - + +
43C VAL 3.5 7.9 - - - +
45C ASP* 1.3 76.3 - - - +
47C LEU* 1.3 57.0 + - - +
49C LYS* 4.6 0.2 - - - -
50C PHE* 2.9 38.9 + - + +
51C PHE* 3.8 4.2 - - + -
88C VAL* 3.9 35.2 - - + +
91C TYR* 3.9 17.9 - - + -
99C LEU* 3.9 9.4 - - + -
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Residues in contact with LEU 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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32C LEU* 3.7 24.0 - - + -
43C VAL* 3.0 37.3 + - + +
44C ILE* 3.1 4.7 + - - +
46C VAL* 1.3 74.4 - - - +
48C GLN* 1.3 61.4 + - - +
51C PHE* 3.2 33.1 + - + +
52C SER 3.3 3.8 + - - -
53C TYR* 3.3 24.4 + - + -
58C ALA* 3.4 35.4 - - + +
61C LEU* 3.7 20.4 - - + -
62C MET* 4.0 2.0 - - - +
65C VAL* 5.8 0.7 - - + -
73C CYS* 3.8 18.6 - - + -
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Residues in contact with GLN 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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44C ILE* 3.0 28.2 + - + +
45C ASP* 3.7 6.1 - - - +
47C LEU* 1.3 77.4 - - - +
49C LYS* 1.3 67.0 + - - +
52C SER* 3.2 19.2 + - - -
53C TYR 3.2 22.4 + - - +
54C ASP* 3.3 2.4 - - - +
55C VAL* 3.1 47.0 - - - +
58C ALA* 3.9 11.7 - - + -
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Residues in contact with LYS 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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73A GLU* 4.3 10.8 + - - +
75A GLU* 5.6 7.3 - - - +
76A ARG* 3.1 39.8 + - - +
45C ASP* 2.8 28.9 + - - +
48C GLN* 1.3 75.8 - - - +
50C PHE* 1.3 83.2 + - + +
51C PHE 4.0 0.2 + - - -
52C SER* 4.8 1.7 + - - -
91C TYR* 3.6 42.6 - - + +
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Residues in contact with PHE 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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23A GLU* 6.1 0.2 - - - -
76A ARG* 4.3 12.1 - - - +
46C VAL* 2.9 26.3 + - + +
49C LYS* 1.3 104.5 - - + +
51C PHE* 1.3 76.3 + - + +
52C SER* 3.7 1.1 - - - -
84C LYS* 2.7 34.5 + - + +
87C MET* 3.9 48.0 - - + -
88C VAL* 4.0 17.3 - - + -
91C TYR* 3.6 46.0 - + + -
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Residues in contact with PHE 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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30C VAL* 3.8 26.7 - - + -
32C LEU* 5.2 1.3 - - + -
46C VAL* 3.8 18.6 - - + -
47C LEU* 3.2 21.4 + - + +
50C PHE* 1.3 84.9 - - + +
52C SER* 1.3 74.6 + - - +
53C TYR* 3.3 23.8 + - + -
73C CYS* 3.6 35.4 - - + +
76C PHE* 4.1 17.9 - + - -
84C LYS* 3.9 22.9 - - + +
88C VAL* 3.8 28.9 - - + -
101C CYS* 4.9 0.9 - - - -
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Residues in contact with SER 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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23A GLU* 5.5 3.1 + - - -
68A VAL 5.4 1.6 + - - -
70A PRO* 4.2 25.8 - - - +
48C GLN 3.2 17.9 + - - -
49C LYS 4.6 1.8 + - - -
50C PHE 3.7 0.5 - - - -
51C PHE* 1.3 82.2 + - - +
53C TYR* 1.3 64.7 + - - +
54C ASP 3.8 0.9 + - - -
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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