Contacts of the helix formed by residues 45 - 53 (chain C) 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 GLY 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLY 3.4 15.6 - - - +
19C ARG* 5.2 0.9 - - - -
42C ASP 5.0 0.8 + - - -
43C GLU 3.6 2.8 + - - -
44C SER* 1.3 77.5 - - - +
46C GLY* 1.3 64.2 + - - +
47C ARG* 3.3 2.7 - - - +
48C ALA* 3.2 13.3 + - - +
49C LEU* 3.0 20.8 + - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLY* 3.5 12.6 - - - -
38C ILE* 4.0 8.5 - - - +
44C SER* 3.1 12.6 + - - -
45C GLY* 1.3 77.9 - - - +
47C ARG* 1.3 61.8 + - - +
49C LEU* 3.2 7.2 + - - +
50C GLU 3.0 18.5 + - - -
58C PHE* 3.5 29.4 - - - +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP* 2.8 48.5 + - - +
45C GLY 3.3 0.8 - - - +
46C GLY* 1.3 75.6 - - - +
48C ALA* 1.3 61.7 + - - +
50C GLU* 3.3 11.7 + - - +
51C GLN* 3.1 19.6 + - - +
58C PHE* 3.7 40.3 - - + -
60C LEU* 4.3 16.2 - - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY* 3.2 13.9 + - - +
47C ARG* 1.3 76.0 - - - +
49C LEU* 1.3 66.6 + - - +
51C GLN* 3.2 17.6 + - - +
52C GLU* 3.0 24.5 + - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLY 3.2 26.9 - - - +
18C GLY* 3.8 13.9 - - - +
23C ALA* 3.8 13.9 - - + -
26C VAL* 4.3 7.9 - - + -
27C ARG* 3.5 37.2 - - + +
38C ILE* 3.8 19.1 - - + -
45C GLY 3.0 13.5 + - - +
46C GLY 3.5 8.5 - - - +
48C ALA* 1.3 74.4 - - - +
50C GLU* 1.3 59.9 + - - +
52C GLU* 3.2 3.9 + - - +
53C LEU* 2.9 49.8 + - + +
56C ALA* 4.6 2.5 - - + -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.8 0.4 - - - +
46C GLY 3.0 12.0 + - - +
47C ARG* 3.5 14.1 - - - +
49C LEU* 1.3 76.8 - - - +
51C GLN* 1.3 64.7 + - - +
53C LEU 3.5 12.5 - - - +
54C PRO* 5.1 0.9 - - - +
56C ALA* 3.4 23.9 - - - +
57C VAL* 3.5 9.8 - - - +
58C PHE* 2.9 40.1 + - + +
79C ARG* 5.6 0.7 + - - -
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Residues in contact with GLN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ARG 3.1 12.9 + - - +
48C ALA* 3.3 18.1 - - - +
49C LEU 3.2 0.2 - - - -
50C GLU* 1.3 77.7 - - - +
52C GLU* 1.3 63.5 + - - +
53C LEU 5.1 0.3 - - - -
54C PRO* 5.4 0.7 - - - +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG* 2.9 46.0 + - - -
48C ALA 3.0 16.0 + - - +
49C LEU* 3.2 7.2 + - - +
51C GLN* 1.3 83.5 - - + +
53C LEU* 1.3 68.0 + - + +
54C PRO* 3.5 10.4 - - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.3 16.4 - - + -
27C ARG* 4.1 35.4 - - + +
30C VAL* 4.4 22.7 - - + -
31C ASN* 6.0 1.6 - - - +
49C LEU* 2.9 29.5 + - + +
50C GLU 3.5 8.1 - - - +
51C GLN 3.5 0.6 - - - -
52C GLU* 1.3 97.7 - - + +
54C PRO* 1.3 70.5 - - + +
55C GLY 3.1 1.8 - - - +
56C ALA* 3.0 27.3 + - + +
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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