Contacts of the helix formed by residues 42 - 52 (chain C) in PDB entry 2BWJ
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 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C SER* 1.3 73.4 - - - +
43C GLY* 1.3 57.8 + - - +
45C LEU* 3.2 11.3 + - - +
46C LEU* 2.9 44.2 + - + +
75C VAL* 3.6 33.9 - - + +
79C LEU* 5.7 0.3 - - - +
95C ILE* 6.1 0.6 - - - +
96C ASP 4.5 3.4 + - - -
97C GLY 6.1 0.4 - - - -
98C TYR* 3.8 20.2 - - - +
104C GLN* 5.0 1.4 + - - +
65F GLU 3.5 17.0 - - - +
66F ARG* 3.8 21.8 + - - +
67F GLY 4.0 0.2 - - - +
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Residues in contact with GLY 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 SER* 3.3 4.5 + - - -
42C THR* 1.3 78.0 - - - +
44C GLU* 1.3 57.6 + - - +
46C LEU* 3.7 7.6 - - - +
47C ARG* 2.9 29.3 + - - +
65F GLU* 3.2 34.8 + - - +
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Residues in contact with GLU 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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39C HIS 6.1 0.9 - - - +
40C LEU* 6.1 0.9 - - - -
41C SER* 3.3 24.1 + - - +
42C THR 3.3 0.2 - - - -
43C GLY* 1.3 74.6 - - - +
45C LEU* 1.3 59.0 + - + +
47C ARG* 2.6 42.5 + - - +
48C GLU* 3.0 31.9 + - + +
1199C AMP 3.8 51.8 + - + +
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Residues in contact with LEU 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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40C LEU* 4.7 9.0 - - + -
41C SER 3.0 26.2 + - - +
42C THR* 3.2 12.1 + - - +
44C GLU* 1.3 75.8 - - - +
46C LEU* 1.3 58.6 + - - +
48C GLU* 3.5 17.8 + - - +
49C GLU* 2.9 28.4 + - - +
75C VAL* 4.8 4.0 - - + +
78C LEU* 3.8 23.4 - - + +
79C LEU* 3.6 44.0 - - + +
82C ALA* 3.6 28.7 - - + -
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Residues in contact with LEU 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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42C THR* 2.9 38.2 + - + +
43C GLY* 3.7 5.8 - - - +
45C LEU* 1.3 73.8 - - - +
47C ARG* 1.3 59.7 + - - +
49C GLU* 3.3 1.8 + - - +
50C LEU* 2.9 36.7 + - - +
60C ILE* 3.9 25.1 - - + +
64C MET* 4.1 24.7 - - + -
70C VAL* 4.2 26.5 - - + -
75C VAL* 4.9 2.9 - - + -
78C LEU* 3.8 22.2 - - + -
64F MET 4.1 17.5 - - - +
67F GLY* 4.5 2.7 - - - -
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Residues in contact with ARG 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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43C GLY 2.9 18.6 + - - +
44C GLU* 2.6 48.6 + - - +
46C LEU* 1.3 75.4 - - - +
48C GLU* 1.3 97.8 + - - +
50C LEU* 3.5 11.8 + - - +
51C ALA* 3.2 30.1 + - - +
64C MET* 5.7 0.4 - - - +
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Residues in contact with GLU 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 GLU* 3.0 18.6 + - + +
45C LEU* 3.6 22.8 - - - +
47C ARG* 1.3 94.4 - - - +
49C GLU* 1.3 65.0 + - - +
51C ALA* 3.2 12.3 + - - +
52C SER* 3.3 11.4 + - - -
82C ALA* 5.3 3.1 - - - +
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Residues in contact with GLU 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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45C LEU 2.9 18.2 + - - +
46C LEU* 3.7 4.7 - - - +
48C GLU* 1.3 75.3 - - - +
50C LEU* 1.3 58.2 + - + +
52C SER* 2.5 39.6 + - - -
54C SER* 2.6 28.1 + - - -
56C ARG* 2.9 38.8 + - - -
57C SER* 3.1 14.1 + - - -
60C ILE* 3.7 26.0 - - + -
78C LEU* 3.8 16.1 - - + +
81C GLU* 5.1 0.2 - - - +
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Residues in contact with LEU 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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46C LEU 2.9 23.6 + - - +
47C ARG* 3.7 9.0 - - - +
49C GLU* 1.3 76.2 - - - +
51C ALA* 1.3 58.5 + - - +
53C GLU* 4.3 5.2 + - - +
57C SER* 3.6 27.9 + - - +
60C ILE* 4.0 10.8 - - + -
61C ARG* 2.8 65.7 + - + +
64C MET* 3.8 30.5 - - + -
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Residues in contact with ALA 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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47C ARG* 3.2 24.5 + - - +
48C GLU* 3.7 7.4 - - - +
49C GLU 3.1 1.2 - - - -
50C LEU* 1.3 77.5 - - - +
52C SER* 1.3 60.1 + - - +
53C GLU* 3.3 12.2 + - - +
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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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48C GLU 3.3 9.5 + - - -
49C GLU* 2.5 32.1 + - - -
51C ALA* 1.3 76.7 - - - +
53C GLU* 1.3 71.1 + - - +
54C SER* 3.1 25.4 + - - -
137F ARG 5.2 1.4 - - - +
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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