Contacts of the helix formed by residues 49 - 65 (chain X) in PDB entry 2BOD
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 GLN 49 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46X ASN* 3.0 37.7 + - + +
48X GLY* 1.3 88.6 - - - +
50X ILE* 1.3 63.7 + - - +
51X THR 3.4 2.7 - - - -
52X GLY* 3.3 6.0 + - - -
53X GLN* 3.2 28.3 + - + +
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Residues in contact with ILE 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X PHE* 3.5 32.1 - - + -
46X ASN* 3.0 30.3 + - - +
47X PRO 3.8 7.4 - - - +
48X GLY 3.8 0.2 - - - -
49X GLN* 1.3 74.5 - - - +
51X THR* 1.3 69.9 + - - +
53X GLN* 3.2 8.1 + - - +
54X VAL* 3.0 23.5 + - + +
97X TRP* 3.7 24.9 - - + +
100X GLU* 3.5 28.7 - - + -
101X PHE* 3.7 33.9 - - + +
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Residues in contact with THR 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X PRO 4.9 1.7 + - - -
48X GLY 5.3 1.3 - - - -
49X GLN 3.4 0.6 - - - -
50X ILE* 1.3 80.9 - - - +
52X GLY* 1.3 57.3 + - - +
54X VAL* 4.8 0.4 - - - -
55X ASP* 2.9 33.6 + - + +
100X GLU* 2.7 34.7 + - - +
103X ALA* 3.9 12.6 - - + +
104X GLY* 3.7 26.6 - - - +
106X LYS* 6.0 2.5 - - - -
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Residues in contact with GLY 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X GLN 3.3 7.0 + - - -
50X ILE 3.3 0.4 - - - -
51X THR* 1.3 80.5 - - - +
53X GLN* 1.3 57.4 + - - +
55X ASP* 3.7 5.9 - - - +
56X ALA* 2.9 30.3 + - - +
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Residues in contact with GLN 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X PHE* 4.1 21.3 - - + -
46X ASN* 2.9 30.4 + - - +
49X GLN* 3.2 16.9 + - + +
50X ILE* 3.2 15.2 + - - +
52X GLY* 1.3 77.7 - - - +
54X VAL* 1.3 61.2 + - - +
56X ALA* 3.4 6.0 + - - +
57X LEU* 3.2 22.7 + - - +
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Residues in contact with VAL 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X PHE* 4.3 8.3 - - + -
50X ILE* 3.0 21.6 + - + +
51X THR 3.8 2.9 - - - +
53X GLN* 1.3 73.5 - - - +
55X ASP* 1.3 60.8 + - - +
57X LEU* 3.3 7.4 + - - +
58X MET* 2.9 36.4 + - + +
70X LEU* 4.9 3.1 - - + -
101X PHE* 3.6 55.4 - - + +
104X GLY 3.7 9.0 - - - -
105X LEU* 3.6 31.2 - - + -
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Residues in contact with ASP 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X THR* 2.9 22.0 + - + +
52X GLY* 3.7 7.8 - - - +
54X VAL* 1.3 77.5 - - - +
56X ALA* 1.3 57.1 + - - +
58X MET* 3.8 0.3 - - - +
59X SER* 2.9 43.3 + - - -
104X GLY* 3.4 13.9 - - - +
106X LYS* 2.9 34.2 + - - +
108X ARG* 2.9 21.3 + - - +
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Residues in contact with ALA 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X GLY 2.9 19.0 + - - +
53X GLN* 3.6 7.4 - - - +
54X VAL 3.3 0.2 - - - -
55X ASP* 1.3 76.6 - - - +
57X LEU* 1.3 61.9 + - - +
59X SER* 3.7 5.0 - - - -
60X ALA* 3.1 23.4 + - - +
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Residues in contact with LEU 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X TYR* 3.3 39.7 - - + +
8X ASN* 3.9 12.6 - - - +
40X THR* 3.7 20.0 - - + +
42X PHE* 3.7 20.0 - - + -
53X GLN 3.2 10.4 + - - +
54X VAL* 3.7 7.6 - - - +
56X ALA* 1.3 77.9 - - - +
58X MET* 1.3 64.3 + - + +
60X ALA* 3.3 5.2 + - - +
61X ALA* 3.0 20.6 + - - +
68X PRO* 4.5 5.4 - - + -
70X LEU* 3.3 33.4 - - + -
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Residues in contact with MET 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X VAL* 2.9 34.7 + - + +
57X LEU* 1.3 75.7 - - + +
59X SER* 1.3 57.1 + - - +
61X ALA* 3.4 4.4 + - - +
62X GLN* 2.9 30.8 + - - +
68X PRO* 3.7 22.4 - - + -
70X LEU* 4.1 8.7 - - - -
104X GLY 4.2 3.6 - - - +
105X LEU* 3.9 20.2 - - + +
108X ARG* 3.5 51.9 - - + +
109X PRO 3.2 22.7 - - - +
110X ALA* 3.8 10.5 - - + -
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Residues in contact with SER 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ASP* 2.9 25.8 + - - -
56X ALA* 3.7 6.2 - - - -
58X MET* 1.3 75.2 - - - +
60X ALA* 1.3 64.9 + - - +
62X GLN* 3.4 3.4 + - - +
63X ALA* 3.0 23.7 + - - +
108X ARG* 2.9 23.8 + - - +
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Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X TYR* 3.4 23.6 - - - +
56X ALA 3.1 16.7 + - - +
57X LEU* 3.7 4.5 - - - +
59X SER* 1.3 76.9 - - - +
61X ALA* 1.3 63.2 + - - +
63X ALA* 3.4 7.3 + - - +
64X ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X TYR* 3.7 32.2 - - + -
57X LEU 3.0 16.4 + - - +
58X MET 3.8 3.8 - - - +
59X SER 3.3 0.2 - - - -
60X ALA* 1.3 75.3 - - - +
62X GLN* 1.3 58.2 + - - +
64X ALA* 3.2 2.9 + - - +
65X GLY 3.0 7.6 + - - -
66X LYS 3.0 40.2 + - - +
68X PRO* 3.8 19.3 - - + -
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Residues in contact with GLN 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X MET 2.9 18.1 + - - +
59X SER* 3.9 4.9 - - - +
60X ALA 3.3 0.2 - - - -
61X ALA* 1.3 77.0 - - - +
63X ALA* 1.3 60.9 + - - +
65X GLY* 3.0 15.1 + - - +
66X LYS 4.3 4.0 + - - +
108X ARG* 4.2 23.4 - - - +
109X PRO* 3.3 35.9 - - - +
150X GLN* 5.5 4.9 + - - +
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Residues in contact with ALA 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X SER 3.0 16.8 + - - +
60X ALA* 3.5 7.9 - - - +
61X ALA 3.3 0.2 - - - -
62X GLN* 1.3 76.9 - - - +
64X ALA* 1.3 58.2 + - - +
65X GLY 3.5 0.5 + - - -
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Residues in contact with ALA 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X TYR* 4.4 9.4 - - + -
60X ALA 3.1 13.5 + - - +
61X ALA* 3.2 10.7 + - - +
63X ALA* 1.3 75.1 - - - +
65X GLY* 1.3 61.1 + - - +
66X LYS* 3.6 26.9 - - + +
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Residues in contact with GLY 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X PRO* 4.5 2.8 - - - +
61X ALA 3.0 3.4 + - - -
62X GLN* 3.0 15.2 + - - -
63X ALA 3.3 0.8 + - - -
64X ALA* 1.3 79.4 - - - +
66X LYS* 1.3 67.6 + - - +
67X ILE* 4.7 5.6 - - - +
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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