Contacts of the helix formed by residues 41 - 51 (chain B) 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 SER 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B HIS* 5.2 0.2 - - - -
40B LEU* 1.3 77.0 - - - +
42B THR* 1.3 64.7 + - - +
43B GLY* 3.8 3.0 + - - -
44B GLU* 3.4 25.9 + - - +
45B LEU* 3.0 29.2 + - - +
79B LEU* 5.9 0.7 - - - -
95B ILE* 5.2 3.4 - - - -
96B ASP* 3.4 26.5 - - - +
1201B AMP 3.8 20.6 + - - -
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU 2.5 25.8 + - - -
66A ARG* 3.7 10.8 - - - +
41B SER* 1.3 75.4 - - - +
43B GLY* 1.3 52.8 + - - +
45B LEU* 3.6 7.2 - - - +
46B LEU* 2.8 45.9 + - - +
75B VAL* 3.5 32.1 - - + -
79B LEU* 4.8 7.2 - - + -
95B ILE* 6.0 0.7 - - + -
96B ASP 4.6 2.9 + - - -
97B GLY 5.2 5.0 + - - +
98B TYR* 3.6 28.5 - - + +
104B GLN* 5.2 1.1 - - - +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 3.1 39.8 + - - +
41B SER* 3.2 4.7 + - - -
42B THR* 1.3 77.5 + - - +
44B GLU* 1.3 55.9 - - - +
46B LEU* 3.8 5.0 - - - +
47B ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS 6.1 0.9 - - - +
40B LEU* 6.4 0.4 - - - -
41B SER* 3.4 24.2 + - - +
42B THR 3.3 0.4 - - - -
43B GLY* 1.3 74.3 - - - +
45B LEU* 1.3 61.5 + - + +
47B ARG* 3.0 40.8 + - - -
48B GLU* 2.9 34.1 + - + +
1201B AMP 4.1 43.1 + - + +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.7 9.6 - - + -
41B SER 3.0 29.6 + - - +
42B THR* 3.2 8.5 + - + +
44B GLU* 1.3 76.8 - - + +
46B LEU* 1.3 58.7 + - + +
48B GLU* 3.6 19.0 + - - +
49B GLU* 3.1 29.3 + - - +
75B VAL* 5.1 0.9 - - + +
78B LEU* 3.9 23.6 - - + +
79B LEU* 3.7 45.1 - - + +
82B ALA* 3.6 26.5 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET 4.0 20.9 - - - +
65A GLU 4.2 5.2 - - - +
66A ARG 4.7 1.1 - - - -
67A GLY* 4.1 20.0 - - - +
42B THR* 2.8 28.7 + - - +
43B GLY* 3.8 5.8 - - - +
45B LEU* 1.3 71.4 - - - +
47B ARG* 1.3 63.3 + - - +
49B GLU* 3.5 1.5 + - - +
50B LEU* 3.0 37.3 + - + +
60B ILE* 4.1 28.0 - - + -
64B MET* 4.5 8.7 - - + -
70B VAL* 4.5 12.6 - - + -
75B VAL* 5.0 10.3 - - + -
78B LEU* 3.9 21.5 - - + -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLY 3.0 18.8 + - - +
44B GLU* 3.0 38.5 + - - +
46B LEU* 1.3 76.5 - - - +
48B GLU* 1.3 76.2 + - - +
50B LEU* 3.3 9.7 + - + +
51B ALA* 3.1 35.2 + - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 2.9 20.4 + - - +
45B LEU* 3.9 23.3 - - - +
47B ARG* 1.3 91.8 - - - +
49B GLU* 1.3 64.3 + - - +
51B ALA* 3.3 14.7 + - - +
52B SER* 3.4 12.6 + - - -
82B ALA* 5.7 1.0 - - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 3.1 18.9 + - - +
46B LEU* 3.8 4.3 - - - +
48B GLU* 1.3 75.5 - - - +
50B LEU* 1.3 64.0 + - - +
52B SER* 2.8 29.6 + - - -
54B SER* 2.7 24.9 + - - -
56B ARG* 3.0 39.9 + - - -
57B SER* 3.0 15.8 + - - -
60B ILE* 3.6 26.9 - - + -
78B LEU* 3.7 15.6 - - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.0 29.9 + - + +
47B ARG* 3.6 7.9 - - - +
49B GLU* 1.3 77.7 - - + +
51B ALA* 1.3 59.3 + - - +
52B SER 3.2 0.7 + - - -
53B GLU* 4.1 5.7 + - - -
57B SER* 3.6 26.0 - - - +
60B ILE* 4.0 16.2 - - + -
61B ARG* 3.4 49.9 + - + +
64B MET* 4.1 22.4 - - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ARG* 3.1 26.1 + - - +
48B GLU* 3.5 11.7 - - - +
49B GLU 3.2 0.4 - - - -
50B LEU* 1.3 75.4 - - - +
52B SER* 1.3 58.8 + - - +
53B GLU* 3.6 5.2 + - - +
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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