Contacts of the helix formed by residues 53 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 2.6 33.3 - - - +
52A ALA* 1.3 78.0 + - - +
54A THR* 1.3 52.7 + - - +
55A ASP* 2.5 23.1 + - - +
56A LYS* 3.1 18.8 + - + +
57A LEU* 3.5 9.7 + - - -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP 4.7 1.3 + - - -
52A ALA 3.1 3.2 - - - +
53A ASP* 1.3 74.4 - - - +
55A ASP* 1.3 88.4 + - - +
57A LEU* 4.1 2.2 - - - +
58A ARG* 3.3 30.0 + - - +
78A PHE* 3.8 17.3 - - - -
80A LYS* 3.7 40.7 - - - +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 2.5 8.8 + - + +
54A THR* 1.3 97.6 - - - +
56A LYS* 1.3 66.2 + - - +
57A LEU 3.0 0.2 + - - -
58A ARG* 3.2 9.5 + - - +
59A GLY* 3.4 6.9 + - - -
243C MET* 4.3 18.7 - - + +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.2 34.3 + - + -
28A GLY* 4.8 2.6 - - - -
29A ASP* 4.4 13.7 + - - +
51A ASP* 5.1 1.8 - - - +
53A ASP* 3.1 11.8 + - + +
55A ASP* 1.3 76.8 - - - +
57A LEU* 1.3 58.6 + - - +
59A GLY* 3.2 1.2 + - - -
60A GLU* 2.6 63.5 + - + +
243C MET 3.7 18.7 + - - +
244C LYS* 4.2 12.6 - - + +
246C TYR* 5.1 6.5 + - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.1 43.1 - - + -
49A LEU* 3.4 23.3 - - + +
50A VAL 5.0 0.2 - - - -
51A ASP* 3.1 26.6 + - + +
53A ASP 3.5 5.5 + - - +
54A THR* 4.1 2.7 - - - +
55A ASP 3.0 2.4 + - - -
56A LYS* 1.3 74.8 - - - +
58A ARG* 1.3 48.3 + - - -
59A GLY 2.6 9.5 + - - -
60A GLU* 2.8 2.3 + - + -
61A ALA* 2.6 36.0 + - + +
78A PHE* 3.1 56.3 - - + -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.3 16.1 + - - +
55A ASP* 3.2 5.4 + - - +
57A LEU* 1.3 72.1 - - - +
59A GLY* 1.3 56.8 + - - +
61A ALA* 4.2 2.2 - - - -
62A LEU* 3.0 33.7 - - + +
78A PHE* 2.9 40.7 - - + -
243C MET* 2.9 25.2 - - + +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP 3.4 4.2 + - - -
56A LYS 3.2 4.7 + - - -
57A LEU 2.6 6.9 + - - -
58A ARG* 1.3 74.3 - - - +
60A GLU* 1.3 56.9 + - - -
62A LEU* 3.2 5.8 + - - +
63A ASP* 3.0 27.2 + - - +
240C VAL* 4.1 9.0 - - - +
243C MET* 3.4 29.6 - - - -
244C LYS* 4.4 9.6 - - - -
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.4 2.5 - - + -
32A MET* 3.2 39.9 - - + +
56A LYS* 2.6 65.8 + - + +
57A LEU* 3.6 4.5 - - + +
59A GLY* 1.3 68.6 - - - -
61A ALA* 1.3 66.4 + - - +
63A ASP* 3.1 12.5 + - - +
64A LEU* 3.1 17.3 + - - +
244C LYS* 2.3 47.2 + - + +
246C TYR* 4.5 4.3 + - - -
249C TRP* 3.6 7.4 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 4.8 0.6 - - - +
49A LEU* 3.4 32.8 - - + -
57A LEU* 2.6 26.1 + - + +
58A ARG* 4.2 2.2 - - - -
60A GLU* 1.3 71.5 - - - +
62A LEU* 1.3 50.0 + - - +
64A LEU* 2.9 14.4 + - - +
65A GLN* 2.8 37.2 + - - +
76A ILE* 4.6 4.8 - - + +
77A VAL 5.8 0.4 - - - -
78A PHE* 3.9 14.1 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.0 35.8 + - + +
59A GLY* 3.2 7.0 + - - +
61A ALA* 1.3 74.7 - - - +
63A ASP* 1.3 58.7 + - - +
65A GLN* 3.5 25.2 - - + +
66A HIS* 2.8 55.2 + - + +
171C TYR* 4.9 5.8 - - + +
172C LEU* 6.5 0.2 - - + -
239C GLU* 5.7 5.8 - - + -
240C VAL* 5.5 4.9 - - + -
243C MET* 4.2 11.4 - - + -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 3.0 12.8 + - - +
60A GLU 3.1 11.4 - - - +
61A ALA 3.1 0.4 - - - -
62A LEU* 1.3 76.8 - - - +
64A LEU* 1.3 67.5 + - - +
65A GLN 3.3 0.2 + - - -
66A HIS* 3.3 7.6 + - - +
67A GLY* 3.1 17.2 + - - -
168C ARG* 5.5 1.2 + - - -
240C VAL* 4.1 18.6 - - + +
244C LYS* 2.8 15.5 + - - +
247C THR* 5.3 2.1 + - - -
248C SER* 2.7 35.5 + - - -
249C TRP* 4.2 11.2 + - + -
250C ALA* 3.5 23.1 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 4.2 13.0 - - + -
35A ALA* 4.7 6.5 - - + -
36A ILE* 4.3 9.9 - - + -
39A LEU* 3.7 31.6 - - + -
47A LEU* 5.1 1.1 - - + -
49A LEU* 4.1 26.7 - - + -
60A GLU 3.1 9.3 + - - +
61A ALA 2.9 8.3 + - - +
63A ASP* 1.3 77.1 - - - +
65A GLN* 1.3 54.7 + - - +
67A GLY* 2.8 27.4 + - - -
68A SER* 3.2 4.3 + - - -
71A LEU* 4.2 11.5 - - + +
76A ILE* 4.6 16.2 - - + -
249C TRP* 2.8 40.8 - - + +
253C LEU* 5.6 2.7 - - + -
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 2.8 16.4 + - - +
62A LEU* 3.8 24.1 - - + +
63A ASP 3.1 0.2 - - - -
64A LEU* 1.3 72.2 - - - +
66A HIS* 1.3 53.9 + - - +
67A GLY 2.8 3.4 - - - -
68A SER* 2.7 39.5 + - - +
76A ILE* 2.5 44.7 - - + +
77A VAL* 4.7 1.4 - - - +
171C TYR* 3.2 36.4 + - + +
175C GLU* 5.3 0.4 + - - -
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 2.8 38.2 + - + +
63A ASP* 3.6 8.2 + - - +
65A GLN* 1.3 72.4 - - - +
67A GLY* 1.3 57.9 - - - +
68A SER 3.3 0.4 + - - -
69A LEU* 4.9 1.7 + - - +
167C ALA* 4.3 6.9 - - - +
168C ARG* 2.8 51.9 + - + +
171C TYR* 4.0 37.2 - + - +
172C LEU* 5.1 7.7 - - + +
232C GLN 5.6 0.6 + - - -
236C GLY* 3.1 36.4 - - - -
240C VAL* 3.9 10.7 - - + +
250C ALA* 4.5 7.3 - - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP 3.1 8.6 + - - -
64A LEU* 2.8 14.6 + - - -
65A GLN 2.7 1.2 + - - -
66A HIS* 1.3 78.6 - - - +
68A SER* 1.3 66.5 + - - +
69A LEU* 3.0 10.8 + - - +
70A PHE* 3.7 6.6 + - - +
71A LEU* 3.9 10.6 - - - +
250C ALA* 4.4 14.4 - - - -
253C LEU* 5.1 9.4 - - - +
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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