Contacts of the helix formed by residues 49 - 63 (chain B) in PDB entry 2B4M
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.6 8.3 - - - +
22B ASP* 3.4 18.2 - - - +
48B ALA* 1.3 79.0 - - - +
50B SER* 1.3 66.5 + - - +
51B ALA* 4.1 5.3 + - - +
52B ALA* 3.4 21.0 + - - +
53B MET* 3.0 23.7 + - - +
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Residues in contact with SER 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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21B ILE* 3.8 8.1 - - - +
22B ASP* 3.7 6.9 + - - -
49B SER* 1.3 74.1 - - - +
51B ALA* 1.3 65.4 + - - +
53B MET* 3.7 0.3 - - - +
54B THR* 3.0 33.7 + - - +
72B TRP* 3.4 28.8 - - - -
75B HIS* 4.4 7.1 + - - -
178B TRP* 3.9 18.2 - - - -
179B ASP* 5.5 4.6 + - - -
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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
----------------------------------------------------------
49B SER* 4.1 6.1 + - - +
50B SER* 1.3 78.0 - - - +
52B ALA* 1.3 60.6 + - - +
54B THR* 3.2 17.0 + - - -
55B ALA* 3.3 15.2 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.0 18.8 - - + -
49B SER* 3.4 17.9 + - - +
50B SER 3.2 1.0 - - - -
51B ALA* 1.3 77.1 - - - +
53B MET* 1.3 60.5 + - - +
55B ALA* 3.6 6.4 + - - +
56B THR* 3.1 31.3 + - - -
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Residues in contact with MET 53 (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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19B ILE* 3.8 25.1 - - + +
20B GLY 3.6 21.8 - - - +
21B ILE* 3.6 17.5 - - + -
48B ALA* 4.6 2.0 - - + +
49B SER 3.0 19.2 + - - +
50B SER 3.8 0.4 - - - +
52B ALA* 1.3 75.0 - - - +
54B THR* 1.3 74.6 + - + +
56B THR* 3.3 7.3 + - - -
57B LEU* 2.8 30.7 + - - +
69B ILE* 3.7 29.9 - - + +
70B THR 3.4 25.8 - - - +
72B TRP* 3.8 12.1 - - + -
77B MET* 4.5 4.7 - - + +
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Residues in contact with THR 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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50B SER* 3.0 24.2 + - - +
51B ALA* 3.2 13.0 + - - -
53B MET* 1.3 90.3 - - + +
55B ALA* 1.3 56.5 + - - +
57B LEU* 3.6 12.7 - - + +
58B LYS* 3.0 25.3 + - - +
75B HIS* 4.4 14.4 - - + +
76B TRP* 3.8 36.1 - - + -
77B MET* 5.6 5.8 - - + -
81B TYR* 4.3 5.1 + - - -
136B GLU* 5.2 1.6 + - - -
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Residues in contact with ALA 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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51B ALA 3.3 14.9 + - - +
52B ALA* 3.6 7.9 - - - +
54B THR* 1.3 78.8 + - - +
56B THR* 1.3 64.7 + - - +
58B LYS* 3.2 8.6 + - - +
59B LYS* 3.1 34.3 + - - +
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Residues in contact with THR 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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19B ILE* 4.5 22.9 - - + +
52B ALA 3.1 16.4 + - - -
53B MET* 3.6 10.5 - - - -
55B ALA* 1.3 72.1 - - - +
57B LEU* 1.3 65.1 + - - +
59B LYS* 3.5 19.0 + - - +
60B SER* 3.2 27.1 + - - +
67B ILE* 4.0 14.3 - - + +
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Residues in contact with LEU 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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53B MET* 2.8 18.5 + - - +
54B THR* 3.6 12.6 - - + +
56B THR* 1.3 74.0 - - - +
58B LYS* 1.3 58.9 + - - +
60B SER* 3.4 1.0 + - - -
61B TYR* 2.9 40.9 + - + +
67B ILE* 3.9 28.6 - - + +
69B ILE* 4.2 32.3 - - + -
76B TRP* 6.4 0.2 - - + -
77B MET* 4.6 9.0 - - + -
81B TYR* 4.0 30.3 - - + -
83B LEU* 4.1 27.4 - - + -
258B PRO* 4.9 0.4 - - + -
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Residues in contact with LYS 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 THR 3.0 12.4 + - - +
55B ALA* 3.2 11.8 + - - +
57B LEU* 1.3 77.1 - - - +
59B LYS* 1.3 63.5 + - - +
61B TYR* 3.3 0.7 + - - +
62B ASP* 3.0 52.0 + - - +
80B ARG* 3.8 17.3 - - - +
81B TYR* 3.2 29.2 - - + +
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Residues in contact with LYS 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 ALA* 3.1 28.5 + - - +
56B THR* 3.7 20.0 + - + +
57B LEU 3.4 0.2 - - - -
58B LYS* 1.3 77.6 - - + +
60B SER* 1.3 62.5 + - - +
62B ASP* 3.5 0.8 + - - -
63B ARG* 2.8 59.8 + - - +
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Residues in contact with SER 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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56B THR* 3.2 20.0 + - - +
57B LEU 4.0 0.9 - - - -
59B LYS* 1.3 75.3 - - - +
61B TYR* 1.3 64.3 + - - +
63B ARG* 3.5 0.6 + - - -
64B LYS 3.1 2.1 + - - -
65B LYS* 2.7 64.9 + - - +
66B PRO 5.2 0.2 + - - -
67B ILE* 4.0 26.5 - - - +
260B TYR* 3.0 3.9 + - - -
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Residues in contact with TYR 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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57B LEU* 2.9 24.6 + - + +
58B LYS 3.6 4.0 - - - +
60B SER* 1.3 75.6 - - - +
62B ASP* 1.3 64.7 + - - +
64B LYS* 2.9 25.1 + - - +
67B ILE* 5.3 0.8 - - - +
80B ARG 5.3 1.6 - - - -
81B TYR* 3.5 44.1 - + + -
82B LYS* 2.9 44.4 + - - +
83B LEU* 4.6 1.1 - - + -
258B PRO* 3.8 26.0 - - + -
260B TYR* 3.6 26.6 + + - -
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Residues in contact with ASP 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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58B LYS* 3.0 47.6 + - - +
59B LYS 3.8 4.5 - - - +
61B TYR* 1.3 84.3 - - - +
63B ARG* 1.3 73.3 + - - +
64B LYS* 3.4 6.4 + - - +
81B TYR* 5.3 2.6 - - - -
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Residues in contact with ARG 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 LYS* 2.8 59.0 + - - +
60B SER* 4.1 4.3 - - - +
61B TYR 3.2 0.6 - - - -
62B ASP* 1.3 90.0 + - - +
64B LYS* 1.3 69.8 + - - +
65B LYS* 3.4 17.2 + - + +
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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