Contacts of the helix formed by residues 47 - 62 (chain D) in PDB entry 7CE1
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 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ASP 3.7 2.6 + - - -
46D ILE* 1.3 71.4 - - - +
48D ALA* 1.3 56.0 + - - -
49D GLU 3.1 2.9 - - - -
50D THR* 2.3 45.6 + - - -
51D LYS* 2.8 7.6 + - - -
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Residues in contact with ALA 48 (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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46D ILE 3.7 2.8 + - - -
47D GLY* 1.3 69.6 - - - -
49D GLU* 1.3 56.6 + - - +
51D LYS* 3.9 19.1 - - - +
52D GLU* 3.0 30.3 + - - +
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Residues in contact with GLU 49 (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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47D GLY 3.1 1.0 - - - -
48D ALA* 1.3 79.1 - - - +
50D THR* 1.3 64.5 + - + +
52D GLU* 3.7 5.0 + - - +
53D ARG* 3.2 21.1 + - - +
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Residues in contact with THR 50 (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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31D LEU* 4.8 20.2 - - + -
46D ILE* 3.4 10.0 - - - +
47D GLY* 2.3 48.4 + - - -
49D GLU* 1.3 73.4 - - + +
51D LYS* 1.3 61.7 + - - -
53D ARG* 3.2 9.5 + - + +
54D VAL* 3.1 29.1 + - - +
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Residues in contact with LYS 51 (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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39D ALA* 4.6 6.7 - - - +
42D ASP* 4.3 18.7 + - - +
43D ALA 3.8 17.8 + - - +
44D PRO* 6.1 0.2 - - - +
46D ILE* 3.2 39.0 + - + +
47D GLY 2.8 23.2 + - - +
48D ALA* 4.0 16.2 - - - +
50D THR* 1.3 69.1 - - - +
52D GLU* 1.3 64.3 + - - +
54D VAL* 3.2 12.4 - - - +
55D ARG* 2.9 46.8 - - - +
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Residues in contact with GLU 52 (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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48D ALA 3.0 18.0 + - - +
49D GLU* 4.1 5.4 - - - +
51D LYS* 1.3 76.4 - - - +
53D ARG* 1.3 61.5 + - - +
55D ARG* 3.6 7.6 + - - +
56D LEU* 2.9 37.1 + - + +
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Residues in contact with ARG 53 (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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29D THR* 5.9 3.1 - - + -
49D GLU 3.2 16.5 + - - +
50D THR* 3.2 14.4 - - + +
51D LYS 3.1 0.4 - - - -
52D GLU* 1.3 78.2 - - - +
54D VAL* 1.3 62.4 + - + +
56D LEU* 3.5 4.7 + - - +
57D ILE* 3.2 23.6 + - - +
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Residues in contact with VAL 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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25D ILE* 4.9 3.1 - - + +
29D THR* 5.5 7.0 - - + -
31D LEU* 5.1 14.4 - - + -
35D THR 5.2 0.2 - - - +
36D VAL* 5.0 16.4 - - + +
39D ALA* 3.4 35.2 - - + -
40D LEU* 4.1 14.1 - - + -
50D THR* 3.1 15.1 + - - +
51D LYS* 3.2 12.6 - - - +
53D ARG* 1.3 77.9 - - + +
55D ARG* 1.3 64.5 + - + +
57D ILE* 3.0 12.3 - - + +
58D ALA* 2.7 38.0 + - - +
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Residues in contact with ARG 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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39D ALA 3.0 22.8 + - - -
40D LEU* 3.3 27.6 + - + +
41D LYS 4.5 0.8 + - - -
42D ASP* 4.3 26.0 + - - +
51D LYS* 2.9 37.6 + - - +
52D GLU* 4.1 7.2 - - - +
53D ARG 3.3 0.6 - - - -
54D VAL* 1.3 81.7 - - + +
56D LEU* 1.3 61.0 + - + +
58D ALA* 4.0 6.1 - - - +
59D GLN* 3.1 27.2 + - - +
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Residues in contact with LEU 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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52D GLU* 2.9 33.7 + - + +
53D ARG* 3.5 6.9 + - - +
54D VAL 3.3 0.4 - - - -
55D ARG* 1.3 80.9 - - + +
57D ILE* 1.3 60.4 + - - +
59D GLN* 3.8 5.5 - - - +
60D GLN* 2.9 38.5 + - - +
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Residues in contact with ILE 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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25D ILE* 4.1 16.2 - - + -
28D MET* 4.1 32.8 - - + -
29D THR* 3.8 28.5 - - + -
53D ARG 3.2 14.5 + - - +
54D VAL* 3.0 28.9 - - - +
56D LEU* 1.3 75.8 - - - +
58D ALA* 1.3 64.1 + - - +
60D GLN* 3.2 22.6 + - + +
61D ILE* 3.3 16.6 + - + +
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Residues in contact with ALA 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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25D ILE* 3.9 24.5 - - + -
40D LEU* 4.0 19.7 - - + -
54D VAL 2.7 23.2 + - - +
55D ARG* 4.0 4.3 - - - +
57D ILE* 1.3 72.9 - - - +
59D GLN* 1.3 62.3 + - - +
61D ILE* 3.6 4.1 - - - +
62D GLY 3.2 3.5 + - - -
63D TYR* 3.0 35.6 + - + +
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Residues in contact with GLN 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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55D ARG 3.1 20.9 + - - +
56D LEU* 3.8 6.7 - - - +
58D ALA* 1.3 76.2 - - - +
60D GLN* 1.3 62.3 + - - +
62D GLY* 3.4 11.7 + - - +
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Residues in contact with GLN 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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56D LEU* 2.9 25.2 + - - +
57D ILE* 3.3 20.2 - - + +
58D ALA 3.1 0.4 - - - -
59D GLN* 1.3 75.8 - - - +
61D ILE* 1.3 61.9 + - - +
62D GLY 3.1 1.7 + - - -
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Residues in contact with ILE 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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18D GLU* 5.3 14.6 - - - +
20D PRO* 3.6 29.8 - - + +
24D THR* 5.7 3.8 - - - +
25D ILE* 5.0 8.1 - - + -
28D MET* 4.8 27.8 - - + -
57D ILE* 3.3 10.9 + - + +
58D ALA* 3.6 12.6 - - - +
60D GLN* 1.3 79.2 - - - +
62D GLY* 1.3 62.9 + - - +
63D TYR* 3.7 13.5 - - + +
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Residues in contact with GLY 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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132C GLU* 4.9 2.8 - - - +
20D PRO* 3.4 11.2 - - - +
58D ALA 3.2 5.8 + - - -
59D GLN* 3.4 9.1 + - - -
60D GLN 3.1 4.6 - - - -
61D ILE* 1.3 79.3 - - - +
63D TYR* 1.3 65.1 + - - +
64D GLN* 3.4 17.1 + - - +
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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