Contacts of the helix formed by residues 47 - 59 (chain C) in PDB entry 1DXX
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 GLY 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LEU 3.4 9.3 + - - -
45C GLN 3.3 4.2 + - - -
46C ASP* 1.3 80.2 + - - +
48C ARG* 1.3 62.5 + - - -
49C ARG 3.4 1.6 - - - -
50C LEU* 3.5 8.5 + - - +
51C LEU* 3.2 25.6 + - - +
76C ASN* 3.6 16.9 - - - +
77C VAL* 3.7 17.9 - - - -
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Residues in contact with ARG 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASP* 2.7 38.5 + - - +
47C GLY* 1.3 71.5 - - - -
49C ARG* 1.3 65.9 + - - +
51C LEU* 3.1 9.3 + - - +
52C ASP* 3.0 27.8 + - - +
64C LYS* 3.5 44.8 + - + +
65C GLU 3.6 13.9 + - - +
66C LYS* 4.1 13.6 + - - +
67C GLY 5.5 1.6 - - - -
76C ASN* 3.6 17.0 - - - +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.5 28.5 - - + -
34C LYS* 4.6 6.1 - - - +
35C GLN* 2.4 59.1 + - - +
36C HIS 4.2 3.2 + - - -
37C ILE* 4.2 11.9 - - + +
43C ASP* 3.6 17.0 - - + +
44C LEU* 3.8 21.3 - - + +
46C ASP* 4.4 2.7 + - - +
48C ARG* 1.3 81.1 - - + +
50C LEU* 1.3 67.0 + - - +
52C ASP* 2.5 51.8 + - - +
53C LEU* 2.7 21.9 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.3 23.7 + - + +
47C GLY* 3.5 9.1 + - - +
48C ARG 3.4 0.6 - - - -
49C ARG* 1.3 74.8 - - - +
51C LEU* 1.3 64.9 + - - +
53C LEU* 2.9 20.8 + - + +
54C LEU* 3.0 23.6 + - + +
77C VAL* 4.5 16.2 - - + -
80C ALA* 4.2 15.7 - - + -
84C LEU* 5.4 0.7 - - + -
99C ILE* 4.0 22.2 - - + -
110C LEU* 3.7 33.2 - - + -
111C ILE* 4.5 11.9 - - + -
114C ILE* 4.2 19.1 - - + -
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLY 3.2 14.6 + - - +
48C ARG 3.1 7.2 + - - +
50C LEU* 1.3 75.7 - - - +
52C ASP* 1.3 62.8 + - - +
54C LEU* 3.0 8.4 + - - +
55C GLU* 2.9 25.8 + - - +
62C LEU* 3.9 24.9 - - + +
63C PRO 4.0 5.6 - - - +
64C LYS* 3.4 38.6 - - + -
76C ASN* 3.5 28.9 - - + +
79C LYS* 3.6 27.4 - - + -
80C ALA* 4.0 13.2 - - + +
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Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.6 7.1 - - + -
32C PHE* 5.7 0.9 - - - -
34C LYS* 2.8 40.3 + - - +
48C ARG* 3.0 12.0 + - - +
49C ARG* 2.5 43.3 + - - +
51C LEU* 1.3 74.4 - - - +
53C LEU* 1.3 65.4 + - - +
55C GLU* 3.3 15.3 + - - +
56C GLY* 3.4 1.6 + - - -
64C LYS* 2.6 31.8 + - - -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TRP* 4.3 7.9 - - + -
25C VAL* 4.5 21.3 - - + +
28C GLN* 3.6 34.8 - - + -
29C PHE* 3.6 20.6 - - + -
32C PHE* 5.3 2.5 - - + -
44C LEU* 6.5 0.4 - - + -
49C ARG 2.7 17.2 + - - +
50C LEU* 2.9 13.0 + - + +
52C ASP* 1.3 75.9 - - - +
54C LEU* 1.3 57.8 + - + +
56C GLY* 3.4 1.7 + - - -
57C LEU* 3.0 59.6 + - + +
111C ILE* 4.9 2.7 - - + -
114C ILE* 4.2 26.0 - - + -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.0 17.3 + - + +
51C LEU* 3.0 10.5 + - - +
53C LEU* 1.3 76.1 - - + +
55C GLU* 1.3 51.5 + - - +
57C LEU* 4.1 5.8 - - + -
58C THR* 2.5 64.4 + - + +
62C LEU* 3.7 13.9 - - + -
80C ALA* 3.6 35.9 - - + +
83C VAL* 3.9 12.3 - - + -
84C LEU* 3.8 36.8 - - + -
114C ILE* 5.4 2.7 - - + -
118C TRP* 4.2 11.9 - - + -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.3 18.8 + - - +
51C LEU 2.9 15.8 + - - +
52C ASP* 3.7 17.6 - - - +
53C LEU 3.3 0.2 - - - -
54C LEU* 1.3 77.6 - - - +
56C GLY* 1.3 63.0 + - - +
58C THR* 3.8 1.1 - - - -
59C GLY* 2.9 22.9 + - - -
60C GLN 3.3 20.9 - - - +
61C LYS* 3.4 6.2 - - - +
62C LEU* 2.5 44.0 + - + +
64C LYS* 4.8 3.9 + - - -
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Residues in contact with GLY 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 2.9 57.3 - - - -
34C LYS* 3.6 3.7 - - - +
52C ASP 3.4 5.3 + - - -
53C LEU 3.4 5.0 + - - -
55C GLU* 1.3 75.8 - - - +
57C LEU* 1.3 63.1 + - - +
59C GLY* 4.5 1.8 + - - -
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TRP* 4.6 9.4 - - + -
28C GLN* 4.7 9.9 - - - +
32C PHE* 4.9 5.8 - - + -
53C LEU* 3.0 53.5 + - + +
54C LEU* 3.6 10.1 - - + +
55C GLU 3.1 0.2 - - - -
56C GLY* 1.3 83.9 - - - +
58C THR* 1.3 60.8 + - + +
59C GLY 3.9 0.2 + - - -
114C ILE* 4.0 22.0 - - + -
118C TRP* 3.9 56.3 + - + -
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Residues in contact with THR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 2.5 43.7 + - + +
55C GLU* 3.4 1.6 + - - -
57C LEU* 1.3 78.4 - - + +
59C GLY* 1.3 57.9 + - - +
60C GLN* 3.3 32.3 + - - +
62C LEU* 4.3 1.4 - - - +
83C VAL* 3.7 28.0 - - + -
87C ASN* 4.3 14.1 - - - +
118C TRP* 4.5 6.3 - - + -
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLU 2.9 17.9 + - - -
56C GLY 4.5 1.4 + - - -
57C LEU 3.7 1.0 - - - -
58C THR* 1.3 70.8 - - - +
60C GLN* 1.3 60.1 + - - +
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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