Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 7ODC
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ASP* 3.0 12.2 + - - -
45A LEU* 1.3 79.2 - - - +
47A ASP* 1.3 54.3 + - - +
49A LEU* 3.3 3.2 + - - +
50A LYS* 2.9 29.2 + - - +
409A MET* 3.7 21.7 - - - +
410A SER* 4.8 1.6 - - - -
413A MET* 4.0 22.6 - - - +
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Residues in contact with ASP 47 (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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44A ASP* 3.0 29.8 + - + +
46A GLY* 1.3 76.5 - - - +
48A ILE* 1.3 57.0 + - - +
50A LYS* 3.3 22.7 + - - +
51A LYS* 2.9 41.2 + - - +
279A TYR 5.0 0.9 - - - +
282A SER* 2.6 31.4 + - - -
283A ALA* 3.2 20.3 + - + +
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Residues in contact with ILE 48 (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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44A ASP 4.2 6.1 - - - +
45A LEU* 3.1 25.0 + - + +
47A ASP* 1.3 78.1 - - - +
49A LEU* 1.3 56.4 + - - +
51A LYS* 3.3 4.0 + - - +
52A HIS* 2.9 26.0 + - - +
76A ILE* 3.4 44.6 - - + -
79A THR* 4.3 13.7 - - + -
80A LEU* 3.5 33.2 - - + -
83A ILE* 4.4 2.2 - - + -
279A TYR* 3.7 26.4 - - + +
280A VAL* 4.7 2.7 - - + -
283A ALA* 4.2 10.1 - - + -
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Residues in contact with LEU 49 (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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45A LEU 3.4 7.5 + - - +
46A GLY 3.3 9.1 + - - +
48A ILE* 1.3 74.7 - - - +
50A LYS* 1.3 64.9 + - - +
52A HIS* 3.1 14.0 + - + -
53A LEU* 2.9 35.8 + - + +
79A THR* 5.5 1.5 - - + +
83A ILE* 4.1 25.4 - - + -
409A MET* 4.6 7.0 - - + -
413A MET* 3.6 24.7 - - - +
416A LEU* 3.4 38.4 - - + -
417A MET* 3.6 26.2 - - + +
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Residues in contact with LYS 50 (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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46A GLY 2.9 14.9 + - - +
47A ASP* 3.4 24.3 + - - +
49A LEU* 1.3 77.4 - - - +
51A LYS* 1.3 63.5 + - + +
53A LEU* 3.3 10.7 + - - +
54A ARG* 3.1 27.6 + - + +
413A MET* 4.5 7.9 - - - -
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Residues in contact with LYS 51 (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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47A ASP* 2.9 25.1 + - - +
48A ILE 3.5 8.3 - - - +
50A LYS* 1.3 79.5 - - + +
52A HIS* 1.3 57.2 + - - +
54A ARG* 3.3 23.2 + - - +
55A TRP 2.9 13.5 + - - -
239A PRO 5.6 0.2 - - - -
240A GLY* 2.9 29.3 + - - -
278A TYR* 2.6 75.4 + - + +
279A TYR* 3.8 20.4 - - + +
282A SER* 3.0 22.5 + - - +
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Residues in contact with HIS 52 (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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48A ILE 2.9 15.2 + - - +
49A LEU* 3.1 13.7 + - + +
51A LYS* 1.3 74.5 - - - +
53A LEU* 1.3 63.3 + - + +
55A TRP* 3.1 3.3 + + - +
56A LEU* 2.9 56.3 + - + +
64A PRO* 4.0 12.6 - - + -
83A ILE* 3.6 44.8 + - + -
84A GLY 5.1 2.0 - - - -
85A THR* 3.9 20.2 - - + +
279A TYR* 2.7 34.7 + - + -
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Residues in contact with LEU 53 (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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49A LEU* 2.9 33.5 + - + +
50A LYS* 3.3 9.6 + - - +
52A HIS* 1.3 76.3 - - + +
54A ARG* 1.3 61.9 + - - +
56A LEU* 3.3 19.5 + - + +
57A LYS* 3.0 24.1 + - - +
413A MET* 4.9 17.5 - - + -
416A LEU* 4.9 14.1 - - + -
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Residues in contact with ARG 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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50A LYS* 3.1 20.7 + - + +
51A LYS* 4.2 23.5 - - - +
53A LEU* 1.3 76.2 - - - +
55A TRP* 1.3 57.8 + - - +
57A LYS* 3.5 6.3 + - - +
58A ALA* 3.0 28.1 + - - +
247A LYS* 4.4 11.1 - - - +
248A PHE* 3.9 18.6 - - + +
249A GLU* 2.7 44.0 + - - +
278A TYR* 3.3 19.3 - - - +
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Residues in contact with TRP 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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51A LYS 2.9 14.0 + - - +
52A HIS* 3.1 8.0 + - - +
54A ARG* 1.3 74.4 - - - +
56A LEU* 1.3 74.9 + - + +
59A LEU* 2.9 50.1 + - + -
62A VAL* 3.0 29.5 + - + -
64A PRO* 3.6 28.3 - - + +
238A PHE* 3.9 14.6 - + - -
248A PHE* 3.6 33.0 - + - -
273A ALA* 3.7 31.9 - - + -
275A PRO* 3.8 24.5 - - + -
278A TYR* 3.4 23.3 + + + +
279A TYR* 4.1 9.6 - + - +
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Residues in contact with LEU 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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52A HIS* 2.9 52.4 + - + +
53A LEU* 3.7 19.5 - - + +
55A TRP* 1.3 83.2 - - + +
57A LYS* 1.3 62.4 + - - +
59A LEU 4.8 2.9 - - - +
60A PRO* 3.4 28.7 - - + +
62A VAL 5.8 1.1 - - - +
64A PRO* 5.5 4.5 - - + -
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Residues in contact with LYS 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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53A LEU 3.0 18.0 + - - +
54A ARG* 3.8 6.5 - - - +
55A TRP 3.1 0.2 - - - -
56A LEU* 1.3 80.7 - - - +
58A ALA* 1.3 66.3 + - + +
60A PRO* 3.6 9.9 - - - +
249A GLU* 6.3 1.6 - - + +
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Residues in contact with ALA 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 ARG 3.0 18.7 + - - +
57A LYS* 1.3 85.7 - - + +
59A LEU* 1.3 63.0 + - - +
60A PRO* 3.4 1.1 - - - -
248A PHE* 3.6 24.2 - - + -
249A GLU* 4.5 10.3 - - + +
252A THR* 3.6 21.5 + - + +
256A ASN* 2.8 24.6 + - - -
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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