Contacts of the helix formed by residues 53 - 67 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLY* 5.0 2.5 - - - +
50B ARG 5.1 0.4 + - - -
51B ARG 3.9 3.4 + - - -
52B MET* 1.3 70.4 - - - +
54B ALA* 1.3 63.9 + - - +
55B PRO* 3.4 16.8 - - + +
56B ALA* 3.0 23.2 + - - +
57B SER* 2.8 23.1 + - - -
86B ILE* 4.5 2.2 - - - -
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Residues in contact with ALA 54 (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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53B ASP* 1.3 76.8 - - - +
55B PRO* 1.3 63.8 - - + +
57B SER* 3.3 4.0 + - - -
58B ALA* 2.9 30.0 + - - +
86B ILE* 4.1 32.3 - - + +
90B LEU* 4.9 2.2 - - + +
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Residues in contact with PRO 55 (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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53B ASP* 3.4 19.5 - - + +
54B ALA* 1.3 94.3 - - + +
56B ALA* 1.3 62.0 + - - +
58B ALA* 3.3 6.5 + - + +
59B ALA* 3.0 24.0 + - - +
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Residues in contact with ALA 56 (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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52B MET* 3.6 25.5 - - + +
53B ASP* 3.0 21.6 + - - +
55B PRO* 1.3 75.4 - - - +
57B SER* 1.3 58.5 + - - +
59B ALA* 3.3 7.6 + - - +
60B ALA* 2.9 28.6 + - - +
321B LEU* 4.7 8.8 - - + +
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Residues in contact with SER 57 (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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48B MET* 3.5 33.8 - - - +
52B MET* 3.4 22.8 + - - +
53B ASP 2.8 22.0 + - - -
54B ALA 3.5 4.5 - - - -
56B ALA* 1.3 76.1 - - - +
58B ALA* 1.3 56.2 + - - +
60B ALA* 3.1 5.1 + - - +
61B VAL* 3.0 33.6 + - - +
86B ILE* 3.8 17.2 - - - +
90B LEU* 5.3 0.2 - - - -
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Residues in contact with ALA 58 (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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54B ALA 2.9 17.4 + - - +
55B PRO* 3.7 7.2 - - + +
57B SER* 1.3 72.5 - - - +
59B ALA* 1.3 65.9 + - - +
61B VAL* 3.4 2.8 + - - +
62B ARG* 3.0 39.5 + - - +
90B LEU* 3.6 32.2 - - + +
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Residues in contact with ALA 59 (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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55B PRO 3.0 14.0 + - - +
56B ALA* 3.7 9.6 - - - +
58B ALA* 1.3 75.8 - - - +
60B ALA* 1.3 58.0 + - - +
62B ARG* 3.3 23.5 + - - +
63B ALA* 2.9 29.5 + - - +
321B LEU* 3.7 25.4 - - + +
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Residues in contact with ALA 60 (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 LEU* 4.3 1.6 - - - -
48B MET* 4.4 2.2 - - + -
52B MET* 3.8 18.8 - - + -
56B ALA 2.9 14.0 + - - +
57B SER* 3.1 10.3 + - - +
59B ALA* 1.3 73.1 - - - +
61B VAL* 1.3 65.3 + - - +
63B ALA 3.3 1.4 + - - -
64B PHE* 3.0 20.4 + - - +
318B MET* 3.9 11.9 - - + -
321B LEU* 3.5 13.4 - - + +
324B LEU* 3.3 24.9 - - + +
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Residues in contact with VAL 61 (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 LEU* 4.0 12.5 - - + +
48B MET* 4.0 17.7 - - + -
57B SER 3.0 17.6 + - - +
58B ALA 3.8 7.0 - - - +
59B ALA 3.4 0.2 - - - -
60B ALA* 1.3 73.2 - - - +
62B ARG* 1.3 58.3 + - - +
64B PHE* 3.3 2.4 + - - +
65B LEU* 2.9 49.5 + - + +
72B LEU* 4.4 11.4 - - + -
87B LEU* 4.1 10.3 - - + -
90B LEU* 3.8 29.2 - - + -
92B LEU* 4.3 13.5 - - + -
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Residues in contact with ARG 62 (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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55B PRO 5.7 0.2 + - - -
58B ALA* 3.0 33.8 + - - +
59B ALA* 3.4 28.9 - - - +
61B VAL* 1.3 77.4 - - - +
63B ALA* 1.3 54.6 + - - +
65B LEU* 3.2 7.5 + - - +
66B GLU* 2.8 57.3 + - + +
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Residues in contact with ALA 63 (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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59B ALA 2.9 16.5 + - - +
60B ALA 3.6 4.5 - - - +
62B ARG* 1.3 74.7 - - - +
64B PHE* 1.3 65.1 + - - +
66B GLU* 3.5 14.6 + - - +
67B ARG* 3.3 25.3 + - - +
321B LEU* 4.3 14.1 - - + -
324B LEU* 4.5 1.8 - - + -
325B GLU* 4.6 11.9 - - + +
328B LEU* 4.0 15.7 - - + +
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Residues in contact with PHE 64 (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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41B SER* 3.3 20.9 - - - -
42B VAL 3.9 3.6 - - - -
43B LEU* 3.5 34.8 - - + -
60B ALA 3.0 12.9 + - - +
61B VAL 3.4 7.0 - - - +
63B ALA* 1.3 77.1 - - - +
65B LEU* 1.3 70.5 + - + +
67B ARG* 3.1 17.3 + - - +
69B HIS* 3.2 49.3 + + + -
70B THR 3.8 2.7 - - - -
71B GLU 3.1 39.3 - - - -
72B LEU* 3.7 20.2 - - + -
316B LEU* 5.1 2.5 - - + -
324B LEU* 4.7 1.6 - - + -
328B LEU* 4.2 17.2 - - + +
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Residues in contact with LEU 65 (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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61B VAL* 2.9 37.4 + - + +
62B ARG* 3.8 5.8 - - - +
64B PHE* 1.3 85.7 - - + +
66B GLU* 1.3 61.4 + - - +
68B GLY* 2.8 23.0 + - - -
69B HIS 3.2 22.3 - - - +
70B THR* 4.2 6.7 - - - -
72B LEU* 5.0 1.3 - - + -
92B LEU* 4.5 10.3 - - + -
100B ARG* 4.1 14.9 + - - +
101B VAL* 3.8 35.2 - - + -
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Residues in contact with GLU 66 (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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62B ARG* 2.8 42.1 + - + +
63B ALA* 3.6 15.2 + - - +
64B PHE 3.3 0.2 - - - -
65B LEU* 1.3 71.7 - - - +
67B ARG* 1.3 59.9 + - + +
68B GLY 3.2 1.2 + - - -
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Residues in contact with ARG 67 (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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63B ALA 3.3 14.3 + - - +
64B PHE 3.1 9.7 + - - +
65B LEU 3.1 1.8 - - - -
66B GLU* 1.3 77.7 - - + +
68B GLY* 1.3 58.7 + - - +
69B HIS* 3.4 23.3 + - + +
325B GLU* 4.4 4.4 + - - +
328B LEU* 4.0 27.1 - - + +
329B ALA* 3.9 26.1 - - - +
332B GLU* 3.3 44.9 + - - +
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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