Contacts of the helix formed by residues 53 - 67 (chain D) in PDB entry 2BP1
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 ASP 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D GLY* 5.0 1.6 - - - +
50D ARG 5.0 0.6 + - - -
51D ARG 3.9 3.2 + - - -
52D MET* 1.3 72.3 - - - +
54D ALA* 1.3 58.9 + - - +
55D PRO* 3.4 21.5 - - + +
56D ALA* 3.2 20.6 + - - +
57D SER* 2.9 30.2 + - - -
86D ILE* 4.6 2.2 - - - -
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Residues in contact with ALA 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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53D ASP* 1.3 71.5 - - - +
55D PRO* 1.3 65.9 - - + +
57D SER* 3.3 8.0 + - - -
58D ALA* 2.9 30.4 + - - +
86D ILE* 4.2 26.9 - - + +
90D LEU* 4.9 1.7 - - + +
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Residues in contact with PRO 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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53D ASP* 3.4 23.6 - - + +
54D ALA* 1.3 94.3 - - + +
56D ALA* 1.3 61.5 + - - +
58D ALA* 3.2 7.6 + - + +
59D ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 56 (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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52D MET* 3.8 25.5 - - + +
53D ASP* 3.2 21.8 + - - +
55D PRO* 1.3 78.4 - - - +
57D SER* 1.3 57.6 + - - +
59D ALA* 3.3 7.8 + - - +
60D ALA* 2.9 28.9 + - - +
320D SER* 6.3 0.2 - - - -
321D LEU* 4.9 7.7 - - + +
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Residues in contact with SER 57 (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 36.0 - - - +
52D MET* 3.6 12.4 + - - +
53D ASP 2.9 23.2 + - - -
54D ALA 3.4 5.4 - - - -
55D PRO 3.2 0.2 - - - -
56D ALA* 1.3 77.4 - - - +
58D ALA* 1.3 57.0 + - - +
60D ALA* 3.2 8.6 + - - +
61D VAL* 3.0 33.8 + - - +
86D ILE* 3.7 22.2 - - - +
90D LEU* 5.3 0.4 - - - -
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Residues in contact with ALA 58 (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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54D ALA 2.9 15.4 + - - +
55D PRO* 3.2 7.8 + - + +
57D SER* 1.3 72.3 - - - +
59D ALA* 1.3 60.7 + - - +
61D VAL* 3.5 2.8 + - - +
62D ARG* 3.0 43.9 + - - +
90D LEU* 3.5 33.8 - - + +
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Residues in contact with ALA 59 (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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55D PRO 3.0 13.3 + - - +
56D ALA* 3.5 10.8 - - - +
58D ALA* 1.3 73.6 - - - +
60D ALA* 1.3 60.9 + - - +
62D ARG* 3.3 25.1 + - - +
63D ALA* 2.9 30.5 + - - +
321D LEU* 3.8 22.9 - - + +
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Residues in contact with ALA 60 (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 LEU* 4.5 2.0 - - + -
48D MET* 4.5 1.6 - - + -
52D MET* 3.8 9.4 - - + -
56D ALA 2.9 14.2 + - - +
57D SER* 3.3 10.1 - - - +
59D ALA* 1.3 76.7 - - - +
61D VAL* 1.3 63.4 + - - +
63D ALA 3.2 1.7 + - - -
64D PHE* 3.0 21.0 + - - +
318D MET* 3.8 29.4 - - + -
321D LEU* 3.7 13.2 - - + +
324D LEU* 3.3 17.7 - - + +
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Residues in contact with VAL 61 (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 LEU* 4.0 13.5 - - + -
48D MET* 3.8 19.1 - - + -
57D SER 3.0 16.4 + - - +
58D ALA 3.8 4.9 - - - +
60D ALA* 1.3 75.2 - - - +
62D ARG* 1.3 57.0 + - - +
64D PHE* 3.3 2.6 + - - +
65D LEU* 2.9 53.5 + - + +
72D LEU* 4.7 11.9 - - + -
87D LEU* 4.1 8.7 - - + -
90D LEU* 3.8 28.5 - - + -
92D LEU* 4.3 14.1 - - + -
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Residues in contact with ARG 62 (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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58D ALA* 3.0 33.4 + - - +
59D ALA* 3.4 28.6 - - - +
60D ALA 3.2 0.2 - - - -
61D VAL* 1.3 77.2 - - - +
63D ALA* 1.3 53.5 + - - +
65D LEU* 3.2 8.1 + - - +
66D GLU* 2.8 60.6 + - + +
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Residues in contact with ALA 63 (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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59D ALA 2.9 17.2 + - - +
60D ALA 3.7 4.3 - - - +
62D ARG* 1.3 76.4 - - - +
64D PHE* 1.3 61.3 + - - +
66D GLU* 3.7 14.8 + - - +
67D ARG* 3.4 27.0 + - - +
321D LEU* 4.2 14.8 - - + -
324D LEU* 4.5 2.2 - - + -
325D GLU* 4.5 14.4 - - + +
328D LEU* 3.8 14.6 - - + +
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Residues in contact with PHE 64 (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 SER* 3.3 25.6 - - - -
42D VAL 3.8 4.0 - - - -
43D LEU* 3.4 41.3 - - + -
60D ALA 3.0 16.5 + - - +
61D VAL 3.5 4.7 - - - +
63D ALA* 1.3 74.7 - - - +
65D LEU* 1.3 69.7 + - + +
67D ARG 3.2 9.0 + - - -
69D HIS* 3.2 53.3 + + + -
70D THR 3.8 2.9 - - - -
71D GLU 3.2 35.9 - - - -
72D LEU* 4.1 10.5 - - + -
316D LEU* 4.8 3.1 - - + -
324D LEU* 4.5 2.0 - - + -
328D LEU* 4.2 21.5 - - + +
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Residues in contact with LEU 65 (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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61D VAL* 2.9 40.1 + - + +
62D ARG* 3.7 6.3 - - - +
64D PHE* 1.3 82.6 - - + +
66D GLU* 1.3 58.2 + - + +
68D GLY* 2.8 19.2 + - - -
69D HIS 3.3 21.1 - - - +
70D THR* 4.4 6.3 - - - +
72D LEU* 5.6 1.1 - - + -
92D LEU* 4.5 10.3 - - + -
100D ARG* 3.4 29.2 + - - +
101D VAL* 3.8 32.5 - - + -
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Residues in contact with GLU 66 (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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62D ARG* 2.8 43.9 + - + +
63D ALA* 3.7 17.6 + - - +
64D PHE 3.3 0.2 - - - -
65D LEU* 1.3 72.7 - - + +
67D ARG* 1.3 61.5 + - + +
68D GLY 3.2 1.2 + - - -
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Residues in contact with ARG 67 (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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63D ALA 3.4 14.6 - - - +
64D PHE 3.2 3.6 + - - +
65D LEU 3.1 1.6 - - - -
66D GLU* 1.3 79.8 - - + +
68D GLY* 1.3 59.6 + - - +
69D HIS* 3.4 29.6 + - + +
325D GLU* 4.0 8.9 + - - +
328D LEU* 4.0 20.3 - - + +
329D ALA* 3.6 34.4 - - - +
332D GLU* 2.7 43.0 + - - +
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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