Contacts of the helix formed by residues 53 - 67 (chain C) in PDB entry 2LDX
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C ASP* 2.6 33.8 - - - +
52C ALA* 1.3 78.4 + - - +
54C THR* 1.3 52.7 + - - +
55C ASP* 2.5 23.3 + - - +
56C LYS* 3.1 19.3 + - + +
57C LEU* 3.5 9.4 + - - -
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Residues in contact with THR 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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51C ASP 4.7 1.5 + - - -
52C ALA 3.1 3.0 - - - +
53C ASP* 1.3 73.8 - - - +
55C ASP* 1.3 91.6 + - - +
57C LEU* 4.1 2.0 - - - +
58C ARG* 3.3 29.9 + - - +
78C PHE* 3.8 16.0 - - - -
80C LYS* 3.7 40.3 - - - +
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Residues in contact with ASP 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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243A MET* 4.3 18.8 - - + +
53C ASP* 2.5 10.1 + - - +
54C THR* 1.3 95.5 - - - +
56C LYS* 1.3 65.5 + - - +
57C LEU 3.0 0.3 + - - -
58C ARG* 3.2 9.0 + - - +
59C GLY* 3.4 6.9 + - - -
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Residues in contact with LYS 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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243A MET 3.7 18.9 + - - +
244A LYS* 4.2 11.9 - - + +
246A TYR* 5.1 6.9 + - - -
27C VAL* 3.2 33.9 + - + -
28C GLY* 4.8 2.1 - - - -
29C ASP* 4.4 14.1 + - - +
51C ASP* 5.1 2.0 - - - +
53C ASP* 3.1 11.7 + - + +
55C ASP* 1.3 75.8 - - - +
57C LEU* 1.3 59.1 + - - +
59C GLY* 3.2 1.6 + - - -
60C GLU* 2.6 63.7 + - + +
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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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27C VAL* 3.1 43.7 - - + -
32C MET* 6.2 0.2 - - + -
49C LEU* 3.4 23.8 - - + +
50C VAL 5.0 0.2 - - - -
51C ASP* 3.1 27.1 + - + +
53C ASP 3.5 5.9 + - - +
54C THR* 4.1 2.5 - - - +
55C ASP 3.0 2.2 + - - -
56C LYS* 1.3 74.9 - - - +
58C ARG* 1.3 48.5 + - - +
59C GLY 2.6 9.6 + - - -
60C GLU* 2.8 2.9 + - + -
61C ALA* 2.6 35.7 + - + +
78C PHE* 3.1 56.5 - - + -
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Residues in contact with ARG 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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243A MET* 2.9 26.5 - - + +
54C THR* 3.3 15.4 + - - +
55C ASP* 3.2 5.2 + - - +
57C LEU* 1.3 70.5 - - - +
59C GLY* 1.3 57.1 + - - +
61C ALA* 4.2 2.2 - - - -
62C LEU* 3.0 32.7 - - + +
78C PHE* 2.9 40.7 - - + -
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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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240A VAL* 4.1 9.0 - - - +
243A MET* 3.4 28.5 - - - -
244A LYS* 4.4 9.6 - - - -
55C ASP 3.4 4.2 + - - -
56C LYS 3.2 5.2 + - - -
57C LEU 2.6 7.1 + - - -
58C ARG* 1.3 75.3 - - - +
60C GLU* 1.3 56.2 + - - -
62C LEU* 3.2 6.4 + - - +
63C ASP* 3.0 27.2 + - - +
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Residues in contact with GLU 60 (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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244A LYS* 2.3 49.0 + - + +
246A TYR* 4.5 4.9 + - - -
249A TRP* 3.6 6.8 + - - -
27C VAL* 4.4 2.9 - - + -
32C MET* 3.2 41.8 - - + +
56C LYS* 2.6 64.4 + - + +
57C LEU* 3.6 4.3 - - + +
59C GLY* 1.3 68.8 - - - -
61C ALA* 1.3 66.3 + - - +
63C ASP* 3.1 12.6 + - - +
64C LEU* 3.1 17.5 + - - +
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Residues in contact with ALA 61 (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 MET* 4.8 0.4 - - - +
49C LEU* 3.4 32.8 - - + -
57C LEU* 2.6 26.9 + - + +
58C ARG* 4.2 2.0 - - - -
60C GLU* 1.3 71.9 - - - +
62C LEU* 1.3 50.4 + - + +
64C LEU* 2.9 13.9 + - - +
65C GLN* 2.8 38.0 + - - +
76C ILE* 4.6 5.0 - - + +
77C VAL 5.8 0.2 - - - -
78C PHE* 3.9 14.8 - - + -
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Residues in contact with LEU 62 (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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171A TYR* 4.9 5.6 - - + +
172A LEU* 6.5 0.2 - - + -
239A GLU* 5.7 5.8 - - + -
240A VAL* 5.5 4.5 - - + -
243A MET* 4.1 11.7 - - + -
58C ARG* 3.0 35.1 + - + +
59C GLY* 3.2 7.2 + - - +
61C ALA* 1.3 75.0 - - + +
63C ASP* 1.3 61.5 + - - +
65C GLN* 3.5 25.7 - - + +
66C HIS* 2.8 56.0 + - + +
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Residues in contact with ASP 63 (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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168A ARG* 5.5 1.4 + - - -
240A VAL* 4.1 18.4 - - + +
244A LYS* 2.8 15.6 + - - +
247A THR* 5.3 1.9 + - - -
248A SER* 2.7 36.5 + - - -
249A TRP* 4.2 11.2 + - + -
250A ALA* 3.5 23.4 + - - +
59C GLY 3.0 12.9 + - - +
60C GLU 3.1 12.3 - - - +
62C LEU* 1.3 77.4 - - - +
64C LEU* 1.3 66.7 + - - +
65C GLN 3.2 0.2 + - - -
66C HIS* 3.3 7.8 + - - +
67C GLY* 3.1 16.8 + - - -
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Residues in contact with LEU 64 (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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249A TRP* 2.8 40.4 - - + +
253A LEU* 5.6 3.1 - - + -
32C MET* 4.2 13.5 - - + -
35C ALA* 4.7 6.5 - - + -
36C ILE* 4.3 9.2 - - + -
39C LEU* 3.7 32.3 - - + -
47C LEU* 5.1 1.1 - - + -
49C LEU* 4.1 26.0 - - + -
60C GLU 3.1 9.7 + - - +
61C ALA* 2.9 8.5 + - - +
63C ASP* 1.3 76.1 - - - +
65C GLN* 1.3 53.5 + - - +
67C GLY* 2.8 27.6 + - - -
68C SER 3.2 4.2 + - - -
71C LEU* 4.2 11.7 - - + +
76C ILE* 4.6 17.0 - - + +
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Residues in contact with GLN 65 (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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171A TYR* 3.2 35.2 + - + +
175A GLU* 5.3 0.6 + - - -
61C ALA* 2.8 17.2 + - - +
62C LEU* 3.8 22.6 - - + +
63C ASP 3.1 0.2 - - - -
64C LEU* 1.3 72.4 - - - +
66C HIS* 1.3 54.6 + - - +
67C GLY 2.7 4.6 + - - -
68C SER* 2.7 40.3 + - - +
76C ILE* 2.5 45.0 - - + +
77C VAL* 4.7 1.7 - - - +
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Residues in contact with HIS 66 (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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167A ALA* 4.3 11.8 - - - +
168A ARG* 2.8 48.2 + - + +
171A TYR* 4.0 37.0 - + - +
172A LEU* 5.1 7.7 - - + +
232A GLN 5.6 0.4 + - - -
236A GLY* 3.1 37.0 - - - -
240A VAL* 3.9 10.9 - - + +
250A ALA* 4.5 7.0 - - + +
62C LEU* 2.8 38.8 + - + +
63C ASP* 3.6 8.2 + - - +
65C GLN* 1.3 72.7 - - - +
67C GLY* 1.3 58.4 + - - +
68C SER 3.3 0.8 + - - -
69C LEU* 4.9 1.7 + - - +
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Residues in contact with GLY 67 (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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250A ALA* 4.4 14.1 - - - -
253A LEU* 5.1 9.7 - - - +
63C ASP 3.1 8.4 + - - -
64C LEU* 2.8 15.2 + - - -
65C GLN 2.7 1.2 + - - -
66C HIS* 1.3 78.0 - - - +
68C SER* 1.3 67.6 + - - +
69C LEU* 3.0 10.7 + - - -
70C PHE* 3.7 6.8 + - - +
71C LEU* 3.9 9.8 - - - +
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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