Contacts of the helix formed by residues 42 - 53 (chain D) in PDB entry 5ICS
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 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D GLY* 5.6 4.8 - - - +
19D ARG* 5.5 9.6 - - + +
40D ASP* 3.4 12.5 + - + +
41D LYS* 1.3 74.4 - - - +
43D GLU* 1.3 64.3 + - - +
44D SER* 3.1 10.6 + - - -
45D GLY* 3.0 26.3 + - - -
46D GLY* 2.9 17.4 + - - +
58D PHE* 3.5 9.8 - - - -
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Residues in contact with GLU 43 (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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41D LYS 3.3 6.2 + - - +
42D ASP* 1.3 73.4 + - - +
44D SER* 1.3 58.8 + - - +
46D GLY* 3.8 0.2 - - - -
47D ARG* 2.8 38.1 + - + +
58D PHE* 4.0 19.2 - - + -
60D LEU* 4.0 31.5 - - + +
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Residues in contact with SER 44 (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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42D ASP* 3.1 6.8 + - - -
43D GLU* 1.3 80.6 - - - +
45D GLY* 1.3 58.2 + - - +
47D ARG* 3.8 4.1 - - - +
48D ALA* 2.9 31.6 + - - +
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Residues in contact with GLY 45 (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 GLY 4.2 14.3 - - - +
42D ASP* 3.0 22.6 + - - -
44D SER* 1.3 76.8 - - - +
46D GLY* 1.3 57.4 + - - +
48D ALA* 3.4 6.7 + - - +
49D LEU* 3.0 32.2 + - - +
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Residues in contact with GLY 46 (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 GLY* 4.9 9.3 - - - -
38D ILE* 4.6 2.8 - - - +
42D ASP* 2.9 16.2 + - - +
45D GLY* 1.3 73.1 - - - +
47D ARG* 1.3 64.8 + - - +
49D LEU* 3.3 6.2 + - - +
50D GLU* 3.0 23.2 + - - +
58D PHE* 3.5 32.3 - - - +
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Residues in contact with ARG 47 (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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43D GLU* 2.8 25.8 + - + +
44D SER* 3.9 4.3 - - - +
46D GLY* 1.3 72.1 - - - -
48D ALA* 1.3 57.0 + - - +
50D GLU* 3.3 17.5 + - - +
51D GLN* 2.9 29.5 + - - +
58D PHE* 3.8 6.9 - - + -
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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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44D SER 2.9 19.3 + - - +
45D GLY* 3.7 8.5 - - - +
46D GLY 3.2 0.2 - - - -
47D ARG* 1.3 78.1 - - - +
49D LEU* 1.3 56.9 + - - +
51D GLN* 3.3 7.0 + - - +
52D GLU* 2.9 30.3 + - - +
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Residues in contact with LEU 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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17D GLY 3.2 26.9 - - - +
18D GLY* 4.0 11.4 - - - +
23D ALA* 4.0 15.7 - - + -
26D VAL* 4.3 6.3 - - + -
27D ARG* 3.4 39.9 - - + +
38D ILE* 3.9 21.1 - - + -
45D GLY 3.0 16.4 + - - +
46D GLY 3.8 4.0 - - - +
48D ALA* 1.3 73.4 - - - +
50D GLU* 1.3 61.9 + - - +
52D GLU* 3.0 4.3 + - - +
53D LEU* 2.8 50.8 + - + +
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Residues in contact with GLU 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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38D ILE* 4.5 1.7 - - + +
46D GLY 3.0 12.8 + - - +
47D ARG* 3.5 16.9 - - - +
49D LEU* 1.3 76.3 - - - +
51D GLN* 1.3 62.5 + - - +
53D LEU 3.2 19.6 - - - +
54D PRO* 4.4 1.7 - - - +
56D ALA* 3.5 25.8 - - - +
57D VAL* 3.6 7.8 - - - +
58D PHE* 2.8 42.5 + - + +
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Residues in contact with GLN 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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47D ARG 2.9 16.5 + - - +
48D ALA* 3.6 8.1 - - - +
49D LEU 3.2 0.2 - - - -
50D GLU* 1.3 78.0 - - - +
52D GLU* 1.3 62.0 + - - +
53D LEU 3.6 0.2 + - - -
54D PRO* 4.8 5.4 - - - +
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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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27D ARG* 2.6 48.5 + - - +
48D ALA 2.9 18.4 + - - +
49D LEU* 3.0 8.5 + - - +
51D GLN* 1.3 78.6 - - - +
53D LEU* 1.3 64.1 + - + +
54D PRO* 3.3 10.7 - - - +
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Residues in contact with LEU 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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26D VAL* 3.7 29.4 - - + -
27D ARG* 4.0 32.5 - - + +
30D VAL* 4.1 26.7 - - + -
31D ASN* 5.7 3.4 - - - +
49D LEU* 2.8 33.3 + - + +
50D GLU 3.2 11.9 - - - +
51D GLN 3.4 0.4 - - - -
52D GLU* 1.3 87.2 - - + +
54D PRO* 1.3 68.8 - - - +
55D GLY 3.3 0.2 + - - -
56D ALA* 3.1 22.0 + - + +
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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