Contacts of the helix formed by residues 28 - 40 (chain D) 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 GLY 28 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D GLY* 3.5 4.2 - - - -
27D VAL* 1.3 78.2 - - - +
29D ASP* 1.3 56.2 - - - -
30D VAL* 2.4 20.6 + - - -
31D GLY 2.5 15.2 + - - -
32D MET 3.2 0.2 + - - -
51D ASP* 5.1 0.4 + - - -
56D LYS* 4.8 3.4 - - - -
98D ARG* 3.7 20.3 - - - +
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TRP* 5.6 0.9 - - - -
27D VAL 3.3 3.4 + - - -
28D GLY* 1.3 69.7 - - - -
30D VAL* 1.3 52.4 - - + +
32D MET* 3.2 9.9 - - - +
33D ALA* 2.8 34.6 + - - +
56D LYS* 4.4 9.9 + - - +
99D MET* 4.5 5.5 - - - +
246D TYR* 2.8 66.3 - - + +
248D SER* 4.4 3.3 - - - -
249D TRP* 5.1 2.9 - - + -
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLY 2.4 7.2 + - - -
29D ASP* 1.3 67.2 - - + +
31D GLY* 1.3 66.6 + - - +
32D MET 2.7 6.6 + - - -
33D ALA* 3.0 5.3 + - - +
34D CYS* 2.9 30.7 + - + +
94D THR* 4.8 3.4 - - + -
98D ARG* 3.9 18.6 - - + +
99D MET* 4.2 17.7 - - + -
135D VAL* 4.2 12.8 - - + -
247D THR* 2.9 31.6 - - + +
248D SER* 4.2 2.9 - - - +
251D ILE* 3.2 33.7 - - + -
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Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 3.5 19.9 - - - +
26D GLY 3.2 15.9 - - - -
27D VAL* 4.0 2.0 - - - -
28D GLY 2.5 11.5 + - - -
30D VAL* 1.3 75.9 - - - +
32D MET* 1.3 54.2 + - - -
34D CYS* 3.7 4.1 - - - +
35D ALA* 3.3 14.9 + - - +
92D ILE* 5.0 0.2 - - - -
94D THR* 2.8 31.6 + - - -
98D ARG* 3.4 4.0 - - - +
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Residues in contact with MET 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TRP* 3.2 38.6 - - + +
27D VAL* 3.1 44.1 - - + +
28D GLY 3.2 2.0 + - - -
29D ASP* 3.2 14.8 - - - +
30D VAL 2.7 0.2 - - - -
31D GLY* 1.3 74.1 - - - +
33D ALA* 1.3 55.4 + - - +
34D CYS 3.0 6.3 - - - -
35D ALA* 2.9 27.8 + - + +
36D ILE* 3.1 10.0 + - - +
49D LEU* 5.1 3.4 - - + -
60D GLU* 3.2 53.2 - - + +
61D ALA 4.8 0.2 - - - +
64D LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TRP* 5.0 1.5 - - - -
29D ASP 2.8 18.9 + - - +
30D VAL 3.0 2.5 + - - +
32D MET* 1.3 68.9 - - - +
34D CYS* 1.3 60.5 + - - +
35D ALA 2.9 6.2 + - - -
36D ILE* 3.6 14.9 - - + +
37D SER* 3.5 22.0 - - - -
248D SER 3.8 18.2 - - - +
249D TRP* 3.6 37.6 - - + +
252D GLY* 4.1 4.8 - - - -
253D LEU 4.9 0.2 + - - -
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Residues in contact with CYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 5.0 3.1 - - - +
30D VAL* 2.9 18.2 + - + +
31D GLY 3.7 3.1 - - - +
33D ALA* 1.3 77.7 - - - +
35D ALA* 1.3 62.2 + - - +
37D SER* 5.0 1.1 - - - -
38D ILE* 3.5 30.0 + - - +
92D ILE* 3.2 36.1 - - - -
94D THR* 4.7 2.2 - - - -
135D VAL* 4.7 3.6 - - - -
252D GLY* 3.6 21.1 - - - -
255D VAL* 3.7 33.2 - - - -
256D THR* 5.1 1.0 - - - -
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 4.5 12.6 - - + -
31D GLY 3.3 9.6 + - - +
32D MET* 2.9 27.7 + - - +
33D ALA 2.9 0.6 - - - -
34D CYS* 1.3 76.0 - - - +
36D ILE* 1.3 57.8 + - - +
37D SER 3.1 1.6 - - - -
38D ILE* 2.6 33.2 + - - +
39D LEU* 3.2 13.0 + - + +
47D LEU* 5.0 6.5 - - + -
49D LEU* 5.2 5.4 - - + -
64D LEU* 4.7 12.3 - - + -
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 5.1 24.2 - - + -
37B SER* 5.9 2.5 - - - +
249B TRP* 4.8 26.7 - - + +
253B LEU* 4.0 23.1 - - + -
32D MET 3.1 9.2 + - - +
33D ALA* 3.6 19.5 - - + +
35D ALA* 1.3 74.9 - - - +
37D SER* 1.3 62.1 + - - +
39D LEU* 2.8 25.9 - - + +
40D LEU* 2.8 64.9 + - + +
64D LEU* 4.3 10.7 - - + +
71D LEU* 5.4 1.6 - - + -
249D TRP* 5.9 2.5 - - + -
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Residues in contact with SER 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 6.0 2.9 - - - -
40B LEU* 3.1 27.8 - - - +
70B PHE* 4.6 1.6 - - - -
33D ALA 3.5 15.7 - - - -
34D CYS 5.0 0.2 - - - -
35D ALA 2.8 4.2 + - - -
36D ILE* 1.3 77.1 - - - +
38D ILE* 1.3 64.0 + - - +
39D LEU 2.8 5.9 + - - -
40D LEU* 3.1 23.5 + - - +
41D LYS* 3.8 5.9 + - - +
253D LEU* 4.0 11.3 - - - +
256D THR* 3.7 26.9 + - - +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.0 29.8 - - + -
24D VAL* 5.0 1.6 - - + -
34D CYS* 3.5 17.7 + - - +
35D ALA 2.6 17.8 + - - +
37D SER* 1.3 74.1 - - - +
39D LEU* 1.3 57.8 + - + -
41D LYS* 3.3 16.8 - - - +
43D LEU* 3.9 27.3 + - + +
44D ALA* 4.6 6.4 + - + +
47D LEU* 3.4 25.4 - - + -
73D THR* 5.5 1.2 - - - +
90D LEU* 4.9 0.7 - - + -
92D ILE* 4.9 13.0 - - + -
255D VAL* 5.3 5.2 - - + -
256D THR* 3.8 23.8 - - - +
259D ALA* 4.5 16.2 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 3.6 5.8 - - + +
36D ILE* 2.8 37.9 + - + +
37D SER 2.8 1.0 - - - -
38D ILE* 1.3 76.7 - - - +
40D LEU* 1.3 57.0 + - + +
41D LYS 2.4 30.1 + - - +
47D LEU* 4.3 19.1 - - + -
64D LEU* 3.7 31.6 - - + -
70D PHE* 5.8 1.4 - - - -
71D LEU* 3.7 21.2 - - + -
72D SER 5.2 3.8 + - - -
73D THR* 3.9 21.0 - - + +
76D ILE* 3.6 29.4 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 3.1 28.5 - - - +
40B LEU* 3.7 50.1 - - + +
253B LEU* 3.9 8.5 - - + -
36D ILE* 2.8 50.6 + - + +
37D SER* 3.1 7.7 + - - +
39D LEU* 1.3 73.7 - - + +
41D LYS* 1.3 67.1 + - - +
70D PHE* 3.6 30.1 - - + -
71D LEU* 4.9 3.4 - - + -
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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