Contacts of the helix formed by residues 40 - 55 (chain D) in PDB entry 2BHT
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 VAL 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D GLU* 3.2 40.8 - - + +
35D ASN* 4.2 1.3 - - - +
39D SER* 1.3 72.1 + - - +
41D LYS* 1.3 63.4 + - + +
42D ASP 3.0 7.0 + - - -
43D ARG* 3.5 14.9 + - - +
44D ALA 4.0 0.3 + - - -
150D HIS* 3.3 28.4 + - + -
154D THR* 6.0 0.2 - - + -
178D THR* 4.0 6.7 - - + +
278D ILE* 5.1 5.8 - - + -
280D CYS* 3.2 16.4 + - + +
320D PLP 3.5 41.7 - - + +
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D SER* 2.9 11.5 + - - +
40D VAL* 1.3 76.5 - - + +
42D ASP* 1.3 61.3 + - - +
43D ARG 3.3 0.2 - - - -
44D ALA* 3.9 9.4 - - + +
45D ALA* 2.8 36.9 + - + +
69D SER* 4.1 9.6 + - - -
71D ASN* 4.1 11.0 - - + +
72D THR* 3.4 31.2 - - + +
75D ALA* 3.5 18.8 - - + +
175D THR* 4.4 14.0 + - + +
208D GLY 4.6 3.8 + - - -
320D PLP 1.5 93.0 + - + +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.6 25.5 - - + +
35D ASN* 3.4 5.3 - - + +
36D PRO* 3.4 9.5 - - - +
37D ALA* 2.6 42.5 + - - +
38D GLY 4.3 0.7 - - - -
39D SER* 3.6 27.2 + - - +
40D VAL 3.0 0.2 - - - -
41D LYS* 1.3 76.1 - - - +
43D ARG* 1.3 68.7 + - - +
45D ALA* 3.8 4.2 - - - +
46D LEU* 2.9 24.4 + - - +
75D ALA* 3.9 8.5 - - - +
78D MET* 3.2 14.5 - - - +
79D ILE* 4.5 1.2 - - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.5 16.5 - - + +
9D GLY* 3.1 18.0 - - - -
10D ASN 3.2 1.4 - - - +
11D THR* 3.3 13.1 + - - +
30D LYS* 3.7 0.8 - - - +
32D GLU* 2.5 43.8 + - - -
35D ASN* 3.4 14.7 - - - +
40D VAL* 3.5 8.7 + - - +
42D ASP* 1.3 75.5 - - - +
44D ALA* 1.3 58.8 + - - +
46D LEU* 2.9 26.9 - - - +
47D SER* 3.2 3.6 + - - -
149D ALA* 3.7 12.2 - - + +
150D HIS* 3.7 12.1 - - + +
153D THR* 3.9 14.0 + - - +
154D THR* 3.1 31.2 + - - +
157D GLU* 2.5 39.8 + - - -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL 4.0 0.6 + - - -
41D LYS* 3.7 14.0 + - + +
42D ASP 3.4 0.2 - - - -
43D ARG* 1.3 75.3 - - - +
45D ALA* 1.3 61.3 + - - +
47D SER* 2.6 24.8 + - - -
48D MET* 3.0 28.7 + - + +
146D ASN* 3.4 29.6 - - + +
149D ALA* 3.6 12.1 - - - +
150D HIS* 4.3 8.5 - - - +
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 2.8 26.0 + - + +
42D ASP* 3.9 2.7 - - - +
44D ALA* 1.3 72.5 - - - +
46D LEU* 1.3 64.2 + - - +
48D MET* 4.0 7.8 - - + +
49D ILE* 3.4 26.0 + - - +
72D THR* 6.1 0.9 - - + -
75D ALA* 3.9 12.6 - - + -
76D LEU* 3.4 30.3 - - + -
79D ILE* 3.9 15.7 - - + +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 4.5 28.9 - - + +
8D ILE* 4.0 21.3 - - + -
42D ASP 2.9 10.3 + - - +
43D ARG* 2.9 17.7 - - - +
45D ALA* 1.3 80.0 - - - +
47D SER* 1.3 63.6 + - - +
48D MET 3.1 0.3 + - - -
49D ILE* 3.7 0.5 - - - +
50D VAL* 3.1 42.7 + - + +
79D ILE* 4.1 20.0 - - + +
83D LYS* 5.5 1.8 - - - -
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ARG 3.2 0.8 + - - -
44D ALA 2.6 12.5 + - - -
46D LEU* 1.3 75.8 - - - +
48D MET* 1.3 56.4 - - - -
50D VAL* 3.8 4.2 - - - +
51D GLU* 2.9 39.2 + - - +
145D ASP* 3.1 27.5 + - - -
148D LYS* 4.1 8.5 - - - +
149D ALA* 3.3 28.0 + - - +
152D THR* 5.3 0.7 + - - -
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Residues in contact with MET 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA* 3.0 32.2 + - + +
45D ALA* 4.0 9.0 - - - +
47D SER* 1.3 75.6 - - - +
49D ILE* 1.3 60.4 + - + +
50D VAL 3.0 4.9 + - - -
51D GLU* 4.0 0.5 - - - +
52D ALA* 3.3 27.9 + - - +
66D GLU* 6.4 0.4 - - + -
72D THR* 5.8 3.1 - - + -
76D LEU* 5.3 7.2 - - + -
138D LEU* 4.4 18.6 - - + +
140D GLN* 3.9 25.4 - - + -
143D ASN* 3.5 42.2 + - - +
145D ASP* 3.7 15.9 - - + +
146D ASN* 3.7 28.0 - - + +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA 3.4 13.0 + - - +
46D LEU 3.2 3.5 + - - +
48D MET* 1.3 74.6 - - + +
50D VAL* 1.3 61.1 + - - +
53D GLU* 3.3 21.4 - - - +
58D ILE* 3.4 26.5 - - + -
64D LEU* 3.5 27.6 - - + -
76D LEU* 3.8 26.5 - - + +
79D ILE* 3.9 30.1 - - + -
80D ALA 5.0 1.3 - - - +
83D LYS* 6.5 0.2 - - + -
85D TYR* 4.1 13.2 - - + -
87D MET* 4.3 5.8 - - + -
138D LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.1 38.2 + - + +
47D SER* 4.0 4.7 - - - +
48D MET 3.0 0.8 - - - -
49D ILE* 1.3 84.2 - - - +
51D GLU* 1.3 62.3 + - + +
53D GLU* 3.9 7.2 - - - +
54D LYS* 3.0 44.3 + - + +
79D ILE* 5.9 1.6 - - + -
83D LYS* 4.2 21.3 - - - +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D SER* 2.9 21.4 + - - +
50D VAL* 1.3 76.0 - - + +
52D ALA* 1.3 50.9 + - - +
54D LYS* 2.6 46.5 + - - +
55D ARG* 2.7 39.3 + - - +
145D ASP* 2.8 39.5 - - + +
148D LYS* 3.1 31.3 + - - -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D MET 3.3 13.6 + - - +
49D ILE* 5.1 0.2 - - - -
51D GLU* 1.3 77.6 - - - +
53D GLU* 1.3 59.8 + - - +
54D LYS 3.1 0.9 + - - -
55D ARG* 3.2 13.1 + - - +
57D ARG* 2.5 65.4 + - + +
58D ILE* 3.5 19.7 - - + -
138D LEU* 5.9 3.1 - - + -
145D ASP* 4.1 0.4 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 3.3 20.1 - - - +
50D VAL* 3.9 8.3 - - - +
51D GLU 3.2 0.4 - - - -
52D ALA* 1.3 74.6 - - - +
54D LYS* 1.3 60.0 + - - +
56D GLY* 3.8 7.5 + - - -
58D ILE* 3.0 24.2 - - + +
60D PRO* 3.1 28.5 - - + +
83D LYS* 4.5 21.6 + - - +
85D TYR* 2.3 49.1 + - - +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 3.0 30.0 + - + +
51D GLU* 2.6 43.0 + - - +
53D GLU* 1.3 70.7 - - - +
55D ARG* 1.3 57.9 + - + +
56D GLY 3.2 6.5 + - - -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 2.7 34.4 + - - +
52D ALA* 3.2 14.6 + - - +
54D LYS* 1.3 74.5 - - + +
56D GLY* 1.3 56.1 + - - +
57D ARG* 3.0 43.8 + - + +
145D ASP* 2.7 32.9 + - - -
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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