Contacts of the helix formed by residues 53 - 67 (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 ASP 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D ASP* 2.6 33.7 - - - +
52D ALA* 1.3 78.5 + - - +
54D THR* 1.3 52.9 + - - +
55D ASP* 2.5 23.2 + - - +
56D LYS* 3.1 19.9 + - + +
57D LEU* 3.5 10.2 + - - -
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Residues in contact with THR 54 (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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51D ASP 4.7 1.5 + - - -
52D ALA 3.1 3.2 - - - +
53D ASP* 1.3 73.2 - - - +
55D ASP* 1.3 89.1 + - - +
57D LEU* 4.1 2.0 - - - +
58D ARG* 3.3 30.0 + - - +
78D PHE* 3.8 15.7 - - - -
80D LYS* 3.7 41.2 - - - +
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Residues in contact with ASP 55 (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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243B MET* 4.3 18.8 - - + +
53D ASP* 2.5 9.1 + - - +
54D THR* 1.3 96.7 - - - +
56D LYS* 1.3 66.6 + - - +
57D LEU 3.0 0.2 + - - -
58D ARG* 3.2 9.2 + - - +
59D GLY* 3.4 6.9 + - - -
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Residues in contact with LYS 56 (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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243B MET 3.7 18.7 + - - +
244B LYS* 4.2 11.7 - - + +
246B TYR* 5.1 7.3 + - - -
27D VAL* 3.2 33.8 + - + -
28D GLY* 4.8 2.3 - - - -
29D ASP* 4.4 13.7 + - - +
51D ASP* 5.1 2.0 - - - +
53D ASP* 3.1 11.9 + - + +
55D ASP* 1.3 76.6 - - - +
57D LEU* 1.3 59.6 + - - +
59D GLY* 3.2 1.2 + - - -
60D GLU* 2.6 62.8 + - + +
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Residues in contact with LEU 57 (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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27D VAL* 3.1 42.6 - - + -
32D MET* 6.2 0.2 - - + -
49D LEU* 3.4 23.6 - - + +
50D VAL 5.0 0.2 - - - -
51D ASP* 3.1 27.1 + - + +
53D ASP 3.5 6.4 + - - +
54D THR* 4.1 2.2 - - - +
55D ASP 3.0 2.2 + - - -
56D LYS* 1.3 74.6 - - - +
58D ARG* 1.3 49.3 + - - +
59D GLY 2.6 10.1 + - - -
60D GLU* 2.8 2.9 + - + -
61D ALA* 2.6 35.3 + - + +
78D PHE* 3.1 57.4 - - + -
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Residues in contact with ARG 58 (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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243B MET* 2.9 25.7 - - + +
54D THR* 3.3 15.2 + - - +
55D ASP* 3.2 5.6 + - - +
57D LEU* 1.3 71.5 - - - +
59D GLY* 1.3 56.4 + - - +
61D ALA* 4.2 2.5 - - - -
62D LEU* 3.0 33.0 - - + +
78D PHE* 2.9 40.9 - - + -
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Residues in contact with GLY 59 (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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240B VAL* 4.1 9.2 - - - +
243B MET* 3.4 28.9 - - - -
244B LYS* 4.4 9.9 - - - -
55D ASP 3.4 4.2 + - - -
56D LYS 3.2 5.2 + - - -
57D LEU 2.6 7.7 + - - -
58D ARG* 1.3 75.4 - - - +
60D GLU* 1.3 57.7 + - - -
62D LEU* 3.2 6.2 + - - +
63D ASP* 3.0 26.7 + - - +
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Residues in contact with GLU 60 (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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244B LYS* 2.3 47.9 + - + +
246B TYR* 4.5 4.7 + - - -
249B TRP* 3.6 6.8 + - - -
27D VAL* 4.4 2.5 - - + -
32D MET* 3.2 40.7 - - + +
56D LYS* 2.6 65.4 + - + +
57D LEU* 3.6 4.5 - - + +
59D GLY* 1.3 68.6 - - - -
61D ALA* 1.3 67.2 - - - +
63D ASP* 3.1 13.0 + - - +
64D LEU* 3.1 17.0 + - - +
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Residues in contact with ALA 61 (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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32D MET* 5.4 0.2 - - - -
49D LEU* 3.4 33.7 - - + -
57D LEU* 2.6 25.9 + - + +
58D ARG* 4.2 2.5 - - - -
60D GLU* 1.3 71.3 - - - +
62D LEU* 1.3 50.2 + - + +
64D LEU* 2.9 13.4 + - - +
65D GLN* 2.8 38.6 + - - +
76D ILE* 4.6 4.3 - - + +
77D VAL 5.8 0.2 - - - -
78D PHE* 3.9 14.6 - - + -
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Residues in contact with LEU 62 (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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171B TYR* 4.9 5.8 - - + +
239B GLU* 5.7 5.6 - - + -
240B VAL* 5.5 4.7 - - + -
243B MET* 4.2 11.7 - - + -
58D ARG* 3.0 35.4 + - + +
59D GLY* 3.2 7.0 + - - +
61D ALA* 1.3 74.8 - - + +
63D ASP* 1.3 59.7 + - - +
65D GLN* 3.5 24.6 - - + +
66D HIS* 2.8 56.1 + - + +
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Residues in contact with ASP 63 (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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168B ARG* 5.5 1.6 + - - -
240B VAL* 4.1 18.4 - - + +
244B LYS* 2.8 16.1 + - - +
247B THR* 5.3 1.9 + - - -
248B SER* 2.7 35.8 + - - -
249B TRP* 3.5 11.3 + - + -
250B ALA* 3.5 23.5 + - - +
59D GLY 3.0 12.6 + - - +
60D GLU 3.1 11.2 - - - +
61D ALA 3.1 0.2 - - - -
62D LEU* 1.3 76.5 - - - +
64D LEU* 1.3 66.3 - - - +
65D GLN 3.2 0.2 + - - -
66D HIS* 3.3 7.7 + - - +
67D GLY* 3.1 17.0 + - - -
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Residues in contact with LEU 64 (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* 2.8 40.8 - - + +
253B LEU* 5.6 2.9 - - + -
32D MET* 4.2 13.0 - - + -
35D ALA* 4.7 6.7 - - + -
36D ILE* 4.3 9.9 - - + -
39D LEU* 3.7 32.1 - - + -
47D LEU* 5.1 1.3 - - + -
49D LEU* 4.1 25.6 - - + -
60D GLU 3.1 6.7 + - - +
61D ALA* 2.9 8.1 + - - +
63D ASP* 1.3 78.6 - - - +
65D GLN* 1.3 52.7 - - - +
67D GLY* 2.8 27.9 + - - -
68D SER 3.2 4.0 + - - -
71D LEU* 4.2 10.4 - - + +
76D ILE* 4.6 18.6 - - + -
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Residues in contact with GLN 65 (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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171B TYR* 3.2 36.2 + - + +
175B GLU* 5.3 0.4 + - - -
61D ALA* 2.8 17.1 + - - +
62D LEU* 3.8 23.9 - - + +
63D ASP 3.1 0.2 - - - -
64D LEU* 1.3 72.2 - - - +
66D HIS* 1.3 54.7 + - - +
67D GLY 2.8 3.8 - - - -
68D SER* 2.7 40.5 + - - +
76D ILE* 2.5 44.2 - - + +
77D VAL* 4.7 1.9 - - - +
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Residues in contact with HIS 66 (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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167B ALA* 4.3 7.3 - - - +
168B ARG* 2.8 53.6 + - + +
171B TYR* 4.0 37.7 - + - +
172B LEU* 5.1 7.5 - - + +
232B GLN 5.6 0.4 + - - -
236B GLY* 3.1 37.2 - - - -
240B VAL* 3.9 9.9 - - + +
250B ALA* 4.6 7.3 - - + +
62D LEU* 2.8 39.3 + - + +
63D ASP* 3.6 8.2 + - - +
65D GLN* 1.3 72.3 - - - +
67D GLY* 1.3 59.2 + - - +
68D SER 3.3 0.6 + - - -
69D LEU* 4.9 1.7 + - - +
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Residues in contact with GLY 67 (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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250B ALA* 4.4 13.9 - - - -
253B LEU* 5.1 9.1 - - - +
63D ASP 3.1 8.6 + - - -
64D LEU* 2.8 14.8 + - - -
65D GLN 2.7 1.4 + - - -
66D HIS* 1.3 77.8 - - - +
68D SER* 1.3 67.6 + - - +
69D LEU 3.0 10.8 + - - +
70D PHE* 3.7 6.4 + - - +
71D LEU* 3.9 10.4 - - - +
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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