Contacts of the helix formed by residues 28 - 40 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLY* 3.5 4.0 - - - -
27B VAL* 1.3 78.1 - - - +
29B ASP* 1.3 55.8 + - - -
30B VAL* 2.4 20.1 + - - -
31B GLY 2.5 14.9 + - - -
32B MET 3.2 0.2 + - - -
56B LYS* 4.8 3.4 - - - -
98B ARG* 3.7 19.9 - - - +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL 3.3 3.6 + - - -
28B GLY* 1.3 68.2 - - - -
30B VAL* 1.3 51.5 + - + +
32B MET* 3.2 8.7 - - - +
33B ALA* 2.8 34.2 + - - +
56B LYS* 4.4 9.3 + - - +
99B MET* 4.5 5.5 - - - +
246B TYR* 2.8 66.6 - - + +
248B SER* 4.4 3.3 - - - -
249B TRP* 5.1 3.3 - - + -
249D TRP* 5.6 1.3 - - - -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLY 2.4 9.1 + - - -
29B ASP* 1.3 66.8 - - + +
31B GLY* 1.3 64.7 + - - +
32B MET 2.7 6.3 + - - -
33B ALA* 4.0 5.3 - - - +
34B CYS* 2.9 31.0 + - + +
94B THR* 4.8 4.3 - - + -
98B ARG* 3.9 17.9 - - + +
99B MET* 4.2 18.6 - - + -
135B VAL* 4.2 13.0 - - + -
247B THR* 2.9 31.4 - - + +
248B SER* 4.2 2.7 - - - -
251B ILE* 3.2 32.8 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.5 20.0 - - - +
26B GLY 3.2 16.6 - - - -
27B VAL* 4.0 2.2 - - - -
28B GLY 2.5 11.9 + - - -
30B VAL* 1.3 76.1 - - - +
32B MET* 1.3 53.0 + - - -
34B CYS* 3.7 4.1 - - - +
35B ALA* 3.3 14.7 + - - +
92B ILE* 5.0 0.4 - - - -
94B THR* 2.8 30.7 + - - -
98B ARG* 3.4 3.6 - - - +
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Residues in contact with MET 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.1 43.3 - - + +
28B GLY 3.2 1.8 + - - -
29B ASP* 3.2 14.4 - - - +
30B VAL 2.7 0.4 - - - -
31B GLY* 1.3 74.8 - - - +
33B ALA* 1.3 56.2 + - - +
34B CYS 3.0 5.6 - - - -
35B ALA* 2.9 26.5 + - - +
36B ILE* 3.1 10.0 + - - +
49B LEU* 5.1 3.8 - - + -
60B GLU* 3.2 52.7 - - + +
61B ALA 4.8 0.2 - - - +
64B LEU* 4.2 13.2 - - + -
249D TRP* 3.2 39.5 - - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP 2.8 18.8 + - - +
30B VAL 3.0 2.6 + - - +
32B MET* 1.3 67.7 - - - +
34B CYS* 1.3 59.9 + - - +
35B ALA 2.9 5.8 + - - -
36B ILE* 3.6 14.8 - - + +
37B SER* 3.5 22.0 - - - -
248B SER 3.8 18.8 - - - +
249B TRP* 3.6 37.1 - - + +
252B GLY* 4.1 5.4 - - - -
253B LEU 4.9 0.2 + - - -
249D TRP* 5.0 1.3 - - - -
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Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 5.0 2.2 - - - +
30B VAL* 2.9 18.7 + - + +
31B GLY 3.7 2.9 - - - +
33B ALA* 1.3 77.3 - - - +
35B ALA* 1.3 61.5 + - - +
37B SER* 5.1 0.9 - - - -
38B ILE* 3.5 30.3 + - - +
92B ILE* 3.2 35.7 - - - -
94B THR* 4.7 1.8 - - - -
135B VAL* 4.7 3.8 - - - -
252B GLY* 3.6 21.1 - - - -
255B VAL* 3.7 33.2 - - - -
256B THR* 5.1 1.0 - - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 4.5 11.4 - - + -
31B GLY 3.3 9.3 + - - +
32B MET* 2.9 28.3 + - - +
33B ALA 2.9 0.8 - - - -
34B CYS* 1.3 76.4 - - - +
36B ILE* 1.3 59.0 + - - +
37B SER 3.0 1.1 - - - -
38B ILE* 2.6 32.2 + - - +
39B LEU* 3.2 12.6 + - + +
47B LEU* 4.6 7.8 - - + +
49B LEU* 5.2 4.9 - - + -
64B LEU* 4.7 12.6 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B MET 3.1 9.2 + - - +
33B ALA* 3.6 19.3 - - + +
35B ALA* 1.3 74.7 - - - +
37B SER* 1.3 62.1 + - - +
39B LEU* 2.8 26.9 - - + +
40B LEU* 2.8 65.2 + - + +
64B LEU* 4.3 10.7 - - + +
71B LEU* 5.4 1.6 - - + -
249B TRP* 5.9 2.5 - - + -
36D ILE* 5.1 24.7 - - + -
37D SER* 5.9 2.7 - - - +
249D TRP* 4.8 27.1 - - + +
253D LEU* 4.0 22.7 - - + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA 3.5 16.4 - - - -
34B CYS 5.0 0.2 - - - -
35B ALA 2.8 4.4 + - - -
36B ILE* 1.3 78.1 - - - +
38B ILE* 1.3 63.2 + - - +
39B LEU 2.8 5.9 + - - -
40B LEU* 3.1 23.6 + - - +
41B LYS* 3.8 6.2 + - - +
253B LEU* 4.0 11.3 - - - +
256B THR* 3.7 27.0 + - - +
36D ILE* 6.0 2.5 - - - -
40D LEU* 3.1 28.6 - - - +
70D PHE* 4.6 1.2 - - - -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.0 29.4 - - + -
24B VAL* 5.0 1.3 - - + -
34B CYS* 3.5 17.2 + - - +
35B ALA 2.6 16.9 + - - +
37B SER* 1.3 73.9 - - - +
39B LEU* 1.3 58.3 + - + -
41B LYS* 3.3 17.3 - - - +
43B LEU* 3.9 26.7 + - + +
44B ALA* 4.6 6.8 + - + +
47B LEU* 3.4 25.4 - - + -
73B THR* 5.5 1.0 - - - +
90B LEU* 4.9 0.9 - - + -
92B ILE* 4.9 13.2 - - + -
255B VAL* 5.3 5.4 - - + -
256B THR* 3.8 22.9 - - - +
259B ALA* 4.5 16.4 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA* 3.6 5.8 - - + +
36B ILE* 2.8 38.5 + - + +
37B SER 2.8 1.0 - - - -
38B ILE* 1.3 76.5 - - - +
40B LEU* 1.3 57.5 + - + +
41B LYS 2.4 30.3 + - - +
47B LEU* 4.3 18.6 - - + -
64B LEU* 3.7 31.6 - - + -
70B PHE* 5.8 1.2 - - - -
71B LEU* 3.7 20.6 - - + +
72B SER 5.2 4.2 + - - -
73B THR* 3.9 20.6 - - + +
76B ILE* 3.6 30.1 - - + -
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Residues in contact with LEU 40 (chain B).
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* 2.8 52.0 + - + +
37B SER* 3.1 7.9 + - - +
39B LEU* 1.3 74.4 - - + +
41B LYS* 1.3 67.0 + - - +
70B PHE* 3.6 29.6 - - + -
71B LEU* 4.9 3.4 - - + -
37D SER* 3.1 29.2 - - - +
40D LEU* 3.7 50.0 - - + +
41D LYS* 6.1 0.2 - - + -
70D PHE* 5.8 0.2 - - - -
253D LEU* 3.9 8.3 - - + -
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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