Contacts of the helix formed by residues 49 - 63 (chain F) in PDB entry 4BMJ
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 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F ASP 3.1 7.2 + - - -
48F TYR* 1.3 79.5 - - + +
50F GLN* 1.3 71.3 + - - +
51F GLN* 3.6 19.2 + - - +
52F VAL* 2.6 35.5 + - + +
53F PHE* 3.1 19.6 + - - +
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Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LYS* 2.6 30.0 + - - +
48F TYR 3.1 3.0 + - - +
49F ASP* 1.3 76.4 + - - +
51F GLN* 1.3 69.8 + - - +
53F PHE* 3.3 15.6 + - - +
54F GLU* 2.8 62.6 + - - +
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Residues in contact with GLN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ASP* 3.5 15.0 + - - +
50F GLN* 1.3 89.0 - - - +
52F VAL* 1.3 61.7 + - - +
54F GLU* 3.3 15.6 + - - +
55F ARG* 2.9 43.2 + - - +
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 6.1 0.2 - - - +
31E GLU* 3.4 29.6 - - + +
32E SER* 5.1 4.0 - - - -
48F TYR* 3.8 26.5 - - + +
49F ASP* 2.6 43.7 - - + +
50F GLN 3.2 0.2 - - - -
51F GLN* 1.3 76.0 - - + +
53F PHE* 1.3 64.1 + - - +
55F ARG* 3.1 29.7 + - - +
56F HIS* 3.1 12.3 + - - +
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Residues in contact with PHE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LYS* 3.4 37.2 - - + -
36F VAL 3.5 33.9 - - - -
37F CYS* 4.2 2.2 - - - -
38F PRO* 4.8 1.6 - - + -
44F PHE* 3.9 31.2 - + - -
48F TYR* 3.9 13.8 - - + -
49F ASP 3.1 14.8 + - - +
50F GLN* 3.5 18.8 - - - +
52F VAL* 1.3 78.0 - - - +
54F GLU* 1.3 73.8 + - + +
56F HIS* 3.0 16.9 + - - +
57F VAL* 3.2 27.2 + - + +
42G GLU* 4.1 8.7 - - - -
43G GLN* 6.3 0.7 - - - -
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLN* 2.8 56.7 + - - +
51F GLN* 3.8 16.5 + - - +
53F PHE* 1.3 78.2 - - + +
55F ARG* 1.3 57.1 + - - +
57F VAL* 3.4 7.2 + - - +
58F GLN* 2.8 30.9 + - - +
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Residues in contact with ARG 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 3.4 65.5 + - - +
29E HIS* 4.4 4.5 - - - +
31E GLU* 4.0 12.3 + - - -
32E SER* 3.9 8.2 - - - +
51F GLN* 2.9 29.9 + - - +
52F VAL* 3.3 30.6 - - - +
53F PHE 3.0 0.2 - - - -
54F GLU* 1.3 74.4 - - - +
56F HIS* 1.3 64.9 + - - +
58F GLN* 3.8 6.6 - - + +
59F THR* 2.9 32.6 + - - +
103F CL 3.5 28.2 - - + +
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Residues in contact with HIS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E SER* 3.1 35.9 + - - +
33E HIS* 5.0 4.0 - - - -
34E TRP 4.4 9.5 + - - -
37F CYS* 3.4 16.5 - - + +
40F CYS* 3.4 7.5 - - - -
42F GLU* 4.0 16.0 - - + +
44F PHE* 3.8 20.4 - + + -
48F TYR* 6.2 0.2 - - + -
52F VAL 3.1 10.1 + - - +
53F PHE* 3.0 11.2 + - - +
55F ARG* 1.3 80.1 - - - +
57F VAL* 1.3 70.4 + - + +
59F THR* 3.2 13.2 + - - -
60F HIS* 3.5 15.4 - + - -
102F ZN 2.0 37.5 - - - -
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Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F CYS* 3.7 9.9 - - - -
38F PRO* 3.3 30.7 - - + -
39F MET* 4.7 2.4 - - + +
53F PHE* 3.2 25.9 + - + +
54F GLU* 3.6 9.9 - - - +
56F HIS* 1.3 80.3 - - + +
58F GLN* 1.3 68.0 + - - +
60F HIS* 2.8 30.5 + - - +
61F PHE* 3.9 10.4 + - + -
34G TRP* 4.2 25.1 - - + -
43G GLN* 6.1 0.7 - - - +
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Residues in contact with GLN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLU 2.8 22.1 + - - +
55F ARG* 3.8 8.3 - - + +
57F VAL* 1.3 76.2 - - - +
59F THR* 1.3 57.7 + - - +
61F PHE* 2.8 30.5 + - - +
62F ASP* 2.8 43.9 + - - +
27G GLU* 3.1 37.2 + - - +
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Residues in contact with THR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E HIS* 4.4 14.3 + - + -
32E SER* 2.7 27.7 + - - +
33E HIS* 3.6 33.4 - - + +
55F ARG* 2.9 16.2 + - - +
56F HIS 3.4 10.1 - - - -
57F VAL 3.1 0.2 + - - -
58F GLN* 1.3 76.4 - - - +
60F HIS* 1.3 64.3 + - - +
62F ASP* 4.1 10.9 + - + +
63F GLN* 2.9 32.3 + - + +
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Residues in contact with HIS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F CYS* 3.7 4.5 - - - -
39F MET* 3.6 35.7 - - + +
40F CYS* 3.4 20.2 - - + -
56F HIS* 3.0 26.4 + + - -
57F VAL* 2.8 13.7 + - - +
59F THR* 1.3 78.6 - - + +
61F PHE* 1.3 61.2 + - - +
63F GLN* 3.7 18.3 + - - +
64F ASN* 3.3 16.8 + - - -
102F ZN 1.9 37.2 - - - -
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Residues in contact with PHE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F MET* 3.1 33.2 - - + -
57F VAL* 4.2 14.1 - - + -
58F GLN* 2.8 20.9 + - - +
60F HIS* 1.3 75.5 - - - +
62F ASP* 1.3 53.8 + - - +
63F GLN 2.9 1.8 - - - -
64F ASN* 2.4 37.5 + - - +
65F VAL 3.2 6.5 + - - -
8G LYS* 6.3 0.9 - - - +
11G PRO* 5.8 0.4 - - + -
23G GLN* 4.1 7.2 + - - +
26G PHE* 4.8 11.9 - + - -
27G GLU* 3.6 50.5 - - + +
30G VAL* 4.1 24.2 - - + -
34G TRP* 4.0 28.7 - + - -
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Residues in contact with ASP 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 3.7 25.0 - - + +
29E HIS* 5.9 1.3 - - + +
58F GLN* 2.8 45.6 + - - +
59F THR* 4.0 9.3 + - + +
61F PHE* 1.3 71.7 - - - +
63F GLN* 1.3 54.4 + - - +
64F ASN 2.7 10.6 + - - -
65F VAL* 3.1 33.1 + - + +
27G GLU* 4.5 1.2 - - - +
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Residues in contact with GLN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU 4.9 1.6 - - - +
13E CYS* 3.5 24.8 - - + +
14E GLU* 5.5 5.2 + - - +
15E LEU* 4.3 18.0 - - + +
33E HIS* 3.9 20.2 + - + -
59F THR* 2.9 34.8 + - + +
60F HIS* 3.7 20.7 + - - +
61F PHE 2.6 3.4 + - - -
62F ASP* 1.3 72.1 - - - +
64F ASN* 1.3 71.3 + - - +
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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