Contacts of the helix formed by residues 42 - 53 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 1.3 73.6 - - - +
43A GLY* 1.3 62.9 + - - +
45A LEU* 3.3 9.4 + - - +
46A LEU* 2.9 48.9 + - + +
75A VAL* 3.7 31.1 - - + +
79A LEU* 5.9 0.4 - - - +
96A ASP 4.5 4.0 + - - -
97A GLY 5.3 2.8 + - - -
98A TYR* 3.7 21.4 - - - +
104A GLN* 5.4 0.3 + - - -
65B GLU 3.2 17.0 - - - +
66B ARG* 3.8 18.4 + - - +
67B GLY 4.0 0.2 - - - +
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Residues in contact with GLY 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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41A SER* 3.3 3.8 + - - -
42A THR* 1.3 74.8 - - - +
44A GLU* 1.3 57.5 + - - +
46A LEU* 3.4 4.4 + - - +
47A ARG* 2.9 30.9 + - - +
65B GLU* 3.0 45.3 + - - +
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Residues in contact with GLU 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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39A HIS 5.8 3.8 - - - +
41A SER* 3.3 24.1 + - - +
42A THR 3.3 0.4 - - - -
43A GLY* 1.3 76.9 - - - +
45A LEU* 1.3 57.3 + - + +
47A ARG* 3.1 42.2 + - - +
48A GLU* 2.9 35.3 + - - +
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Residues in contact with LEU 45 (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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40A LEU* 4.5 7.6 - - + -
41A SER 2.9 28.0 + - - +
42A THR* 3.7 8.3 - - - +
44A GLU* 1.3 75.6 - - + +
46A LEU* 1.3 58.1 - - + +
48A GLU* 3.4 17.3 + - - +
49A GLU* 3.0 29.8 + - - +
75A VAL* 4.7 6.1 - - + +
78A LEU* 3.8 25.5 - - + +
79A LEU* 3.5 43.1 - - + +
82A ALA* 3.6 28.5 - - + -
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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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42A THR* 2.9 40.3 + - + +
43A GLY* 3.7 4.5 - - - +
45A LEU* 1.3 73.6 - - + +
47A ARG* 1.3 66.2 + - - +
48A GLU 3.2 0.2 + - - -
49A GLU* 3.3 2.5 + - - +
50A LEU* 3.0 30.2 + - + +
60A ILE* 4.0 24.2 - - + -
64A MET* 4.6 19.1 - - + -
70A VAL* 4.3 18.4 - - + -
74A ILE* 5.3 0.2 - - + -
75A VAL* 4.8 4.9 - - + -
78A LEU* 4.1 19.1 - - + -
64B MET 3.8 20.6 - - - +
65B GLU 4.8 0.2 - - - +
67B GLY* 4.1 10.1 - - - -
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Residues in contact with ARG 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 GLY 2.9 19.1 + - - +
44A GLU* 3.1 37.5 + - - +
46A LEU* 1.3 75.0 - - - +
48A GLU* 1.3 73.7 + - - +
50A LEU* 3.3 10.4 + - - +
51A ALA* 3.0 44.8 + - - +
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Residues in contact with GLU 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 GLU* 2.9 22.0 + - - +
45A LEU* 3.7 20.0 - - - +
46A LEU 3.2 0.2 - - - -
47A ARG* 1.3 92.4 - - - +
49A GLU* 1.3 63.6 + - - +
51A ALA* 3.4 4.8 + - - +
52A SER* 3.1 22.2 + - - -
82A ALA* 5.7 1.2 - - - +
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Residues in contact with GLU 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 LEU 3.0 18.3 + - - +
46A LEU 3.7 4.3 - - - +
48A GLU* 1.3 75.9 - - - +
50A LEU* 1.3 62.0 + - - +
52A SER* 2.6 30.2 + - - -
54A SER* 3.6 8.2 + - - -
56A ARG* 2.8 45.8 + - - +
57A SER* 3.1 31.5 + - - -
60A ILE* 3.6 26.1 - - + +
78A LEU* 3.6 17.5 - - + +
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Residues in contact with LEU 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 3.0 22.9 + - - +
47A ARG* 3.5 8.7 - - - +
49A GLU* 1.3 77.8 - - + +
51A ALA* 1.3 59.9 + - - +
53A GLU* 3.2 24.8 + - - +
57A SER* 3.8 16.0 + - - +
60A ILE* 3.9 12.3 - - + -
61A ARG* 3.7 42.6 - - + +
64A MET* 4.0 26.0 - - + -
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Residues in contact with ALA 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 ARG* 3.0 34.7 + - - +
48A GLU* 3.7 6.3 - - + +
50A LEU* 1.3 74.0 - - - +
52A SER* 1.3 64.3 + - - +
53A GLU* 3.1 12.9 + - - +
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Residues in contact with SER 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 GLU* 3.1 13.1 + - - -
49A GLU* 2.6 25.9 + - - -
51A ALA* 1.3 76.4 - - - +
53A GLU* 1.3 62.2 + - - +
54A SER* 3.1 28.9 + - - -
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Residues in contact with GLU 53 (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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49A GLU 3.7 0.6 + - - -
50A LEU 3.2 19.5 + - - +
51A ALA* 3.1 15.0 - - - +
52A SER* 1.3 78.1 + - - +
54A SER* 1.3 66.5 + - - +
55A GLU* 3.7 1.4 + - - +
57A SER* 3.7 6.7 - - - -
58A LYS* 4.2 19.7 + - - +
61A ARG* 6.0 2.1 - - - -
1200A SO4 4.7 2.2 + - - -
137B ARG* 5.9 3.1 - - - +
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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