Contacts of the helix formed by residues 37 - 54 (chain A) in PDB entry 2BOO
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 ALA 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO 3.3 20.3 + - - +
34A GLU* 3.2 11.0 + - - +
36A SER* 1.3 77.4 - - - +
38A PRO* 1.3 75.2 - - + +
39A TYR* 3.8 23.3 - - + -
40A PHE* 3.2 12.6 + - - +
41A HIS* 3.2 16.0 + - - -
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Residues in contact with PRO 38 (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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36A SER 4.1 3.8 - - - +
37A ALA* 1.3 82.9 - - + +
39A TYR* 1.3 66.1 + - - +
41A HIS* 3.3 8.7 + - + +
42A GLU* 3.1 36.6 + - + +
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Residues in contact with TYR 39 (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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34A GLU* 2.7 42.7 + - - +
37A ALA* 3.4 21.7 - - + -
38A PRO* 1.3 77.9 - - - +
40A PHE* 1.3 68.6 + + + +
42A GLU* 3.4 14.2 + - - +
43A LEU* 3.0 27.7 + - + +
158A LYS 4.9 2.6 - - - +
159A GLY* 3.5 32.5 - - - -
162A HIS* 3.7 27.8 - + + -
163A PHE* 3.4 25.7 + - + +
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Residues in contact with PHE 40 (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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18A ILE 5.0 4.5 - - - -
20A PRO* 5.6 2.0 - - + -
34A GLU 3.1 26.7 - - - +
35A PHE* 3.6 35.0 - + - +
37A ALA 3.2 4.6 + - - +
38A PRO 3.1 1.0 - - - -
39A TYR* 1.3 92.6 - + + +
41A HIS* 1.3 59.3 + - - +
43A LEU* 3.2 10.5 + - + +
44A THR* 3.0 56.9 + - + +
64A PHE* 3.8 21.5 - + - -
160A TRP* 4.4 12.3 - + - -
163A PHE* 3.7 37.2 - + - -
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Residues in contact with HIS 41 (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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18A ILE* 4.5 20.4 - - + +
35A PHE 3.6 20.1 + - - -
36A SER* 3.8 20.2 - - - -
37A ALA 3.2 11.9 + - - -
38A PRO* 3.3 9.1 + - + +
40A PHE* 1.3 77.1 - - - +
42A GLU* 1.3 61.4 + - + +
44A THR* 3.3 9.6 + - - -
45A ASP* 3.1 31.0 + - - +
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Residues in contact with GLU 42 (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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38A PRO* 3.1 31.9 + - - +
39A TYR* 3.7 12.5 + - - +
41A HIS* 1.3 72.0 - - + +
43A LEU* 1.3 60.5 + - - +
45A ASP* 3.4 9.2 + - - +
46A PHE* 2.9 29.3 + - - +
158A LYS 5.4 0.4 - - - -
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Residues in contact with LEU 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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39A TYR* 3.0 16.2 + - + +
40A PHE* 3.2 23.3 + - + +
42A GLU* 1.3 77.2 - - - +
44A THR* 1.3 65.0 + - + +
46A PHE* 3.2 11.4 + - + +
47A LEU* 3.0 38.6 + - + +
158A LYS* 3.6 35.1 + - + +
159A GLY* 4.0 14.8 - - - +
160A TRP* 3.6 56.5 - - + +
163A PHE* 5.4 0.2 - - + -
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Residues in contact with THR 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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40A PHE* 3.0 45.9 + - + +
41A HIS* 3.3 14.4 + - - -
42A GLU 3.4 0.2 - - - -
43A LEU* 1.3 79.6 - - + +
45A ASP* 1.3 65.3 + - - +
47A LEU* 3.3 12.3 + - + +
48A ARG* 3.0 28.1 + - - +
160A TRP* 6.1 0.9 - - + -
1249A NO3 5.1 7.1 + - - +
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Residues in contact with ASP 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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41A HIS* 3.1 24.1 + - - +
42A GLU* 3.7 8.0 - - - +
43A LEU 3.2 0.2 - - - -
44A THR* 1.3 75.7 + - - +
46A PHE* 1.3 67.7 + - - +
47A LEU 3.3 0.2 + - - -
48A ARG* 3.3 16.5 + - - +
49A GLN* 3.1 22.9 + - - +
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Residues in contact with PHE 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 GLU 2.9 15.0 + - - +
43A LEU* 3.2 13.7 - - + +
45A ASP* 1.3 75.8 - - - +
47A LEU* 1.3 61.1 + - + +
49A GLN* 3.2 10.1 + - + +
50A GLU* 2.8 73.7 + - + +
148A ARG* 5.4 2.5 - - - -
154A SER 5.0 0.7 - - - -
155A HIS* 3.6 25.4 - + + -
158A LYS* 3.6 53.2 - - + +
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Residues in contact with LEU 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 LEU* 3.0 28.7 + - + +
44A THR* 3.7 10.5 - - + +
46A PHE* 1.3 83.6 - - + +
48A ARG* 1.3 66.7 + - - +
50A GLU* 3.7 2.1 - - + +
51A ARG* 2.8 29.5 + - - +
56A ILE* 5.1 3.4 - - + -
146A THR* 3.8 12.6 - - + +
155A HIS* 3.7 30.7 - - + +
160A TRP* 3.5 31.6 - - + -
1249A NO3 3.4 37.0 - - - +
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Residues in contact with ARG 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 THR 3.0 15.3 + - - +
45A ASP* 3.4 19.3 - - - +
47A LEU* 1.3 76.4 - - - +
49A GLN* 1.3 61.7 + - - +
51A ARG* 3.4 11.0 + - - +
52A LYS* 3.5 18.1 + - - +
1249A NO3 4.3 3.9 + - - +
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Residues in contact with GLN 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 ASP 3.1 9.9 + - - +
46A PHE* 3.4 11.2 - - + +
48A ARG* 1.3 78.8 - - - +
50A GLU* 1.3 65.1 + - + +
52A LYS* 3.1 45.6 + - - +
53A GLU* 2.9 40.1 + - - +
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Residues in contact with GLU 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 PHE* 2.8 61.7 + - + +
47A LEU* 3.1 7.8 + - - +
49A GLN* 1.3 74.3 - - + +
51A ARG* 1.3 58.2 + - - +
53A GLU* 3.3 3.4 + - - +
54A TYR* 2.9 45.6 + - - +
56A ILE* 3.9 12.9 - - + +
148A ARG* 2.9 41.7 + - - +
155A HIS* 2.8 20.9 + - + +
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Residues in contact with ARG 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 LEU* 2.8 17.6 + - - +
48A ARG* 3.9 7.2 - - - +
49A GLN 3.2 0.6 - - - -
50A GLU* 1.3 77.0 - - - +
52A LYS* 1.3 58.0 + - - +
53A GLU 3.4 0.2 - - - -
54A TYR 3.1 18.4 - - - +
56A ILE* 3.3 47.8 + - + +
58A PRO 2.9 22.8 + - - -
59A PRO* 4.1 3.0 - - - +
60A ALA* 3.5 27.8 - - - +
63A VAL* 3.9 4.8 - - - +
146A THR* 4.3 1.6 - - - +
1249A NO3 2.3 44.4 + - - -
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Residues in contact with LYS 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 ARG 3.5 12.8 + - - +
49A GLN* 3.1 45.5 - - - +
51A ARG* 1.3 78.2 - - - +
53A GLU* 1.3 60.3 + - + +
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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 GLN* 2.9 41.6 + - - +
50A GLU* 3.3 3.8 + - - +
52A LYS* 1.3 78.4 - - + +
54A TYR* 1.3 97.5 + - + +
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Residues in contact with TYR 54 (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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50A GLU* 2.9 35.9 + - - +
51A ARG* 3.1 23.2 - - - +
53A GLU* 1.3 112.0 + - + +
55A THR* 1.3 65.4 + - - +
56A ILE* 3.8 13.4 + - + -
148A ARG* 3.5 48.8 + - + -
151A GLN* 4.8 3.4 - - - -
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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