Contacts of the helix formed by residues 48 - 59 (chain A) in PDB entry 2CSF
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 SER 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.9 1.8 - - - -
47A LYS* 1.3 81.3 - - - +
49A GLN* 1.3 56.7 + - - +
50A GLY* 4.4 3.8 - - - -
51A TRP* 2.5 37.3 + - - +
52A LEU* 3.4 1.9 + - - +
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Residues in contact with GLN 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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36A SER* 3.6 14.3 + - - -
37A GLN* 3.7 24.1 - - + +
38A ALA* 3.3 49.3 - - + +
47A LYS 4.0 1.4 + - - -
48A SER* 1.3 69.6 - - - +
50A GLY* 1.3 54.9 + - - +
52A LEU* 2.5 26.5 + - - +
53A CYS* 2.7 21.3 + - + -
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Residues in contact with GLY 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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48A SER* 2.9 6.7 + - - -
49A GLN* 1.3 77.1 - - - +
51A TRP* 1.3 55.7 + - - +
53A CYS* 4.1 6.9 - - - +
54A GLU* 2.4 43.6 + - - +
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Residues in contact with TRP 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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41A ALA* 4.7 2.0 - - + -
45A ALA* 4.2 6.7 - - + -
47A LYS* 3.2 53.6 - - + +
48A SER* 2.5 21.4 + - - +
50A GLY* 1.3 73.0 - - - +
52A LEU* 1.3 68.6 + - + +
54A GLU* 3.5 8.7 - - - +
55A LEU* 2.9 64.7 + - + +
68A THR* 4.9 5.5 + - - +
69A LEU* 5.4 6.4 - - + +
72A ASN* 3.1 42.3 - - + +
73A LEU* 4.8 2.2 - - + -
76A ILE* 3.4 30.1 - - + -
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Residues in contact with LEU 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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26A ILE* 4.0 26.7 - - + -
37A GLN* 3.2 44.6 - - + +
40A PHE* 4.2 10.3 - - + -
41A ALA* 3.4 27.4 - - + -
48A SER 3.4 0.8 + - - -
49A GLN 2.5 13.6 + - - +
51A TRP* 1.3 87.0 - - + +
53A CYS* 1.3 66.7 + - - +
54A GLU 3.1 1.3 - - - -
55A LEU* 2.8 26.6 + - + +
56A LEU* 3.3 20.4 + - + -
76A ILE* 4.8 1.1 - - + -
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Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.2 32.9 + - - +
49A GLN* 2.7 26.4 + - + +
50A GLY* 4.1 7.0 - - - +
52A LEU* 1.3 72.6 - - - +
54A GLU* 1.3 64.7 + - + +
56A LEU* 3.0 8.2 + - - +
57A ARG* 2.9 21.3 + - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLY* 2.4 32.6 + - - +
51A TRP* 3.5 10.6 + - - +
52A LEU 3.0 0.8 + - - -
53A CYS* 1.3 77.0 - - + +
55A LEU* 1.3 59.7 + - + +
57A ARG* 2.5 35.5 + - - +
58A TRP* 2.7 37.7 + - + +
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Residues in contact with LEU 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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23A TYR* 3.4 27.8 - - + +
26A ILE* 5.6 1.8 - - + -
51A TRP* 2.9 70.2 - - + +
52A LEU* 2.8 19.1 + - + +
54A GLU* 1.3 77.6 - - + +
56A LEU* 1.3 58.7 + - + +
58A TRP* 5.4 1.1 - - - -
59A LYS* 2.7 35.7 + - - +
60A GLU 5.8 0.4 - - - +
69A LEU* 4.6 15.0 - - + -
73A LEU* 4.4 13.9 - - + -
76A ILE* 4.7 1.1 - - + -
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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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23A TYR* 3.8 30.3 - - + +
26A ILE* 4.1 11.7 - - + -
27A GLN* 4.2 22.2 - - + +
30A MET* 3.8 13.9 - - + -
37A GLN* 2.8 33.9 - - - +
52A LEU* 3.4 25.1 - - + +
53A CYS 3.0 5.1 + - - +
55A LEU* 1.3 80.0 - - + +
57A ARG* 1.3 60.5 + - - +
59A LYS* 3.1 32.4 + - - +
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Residues in contact with ARG 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 CYS* 2.9 13.3 + - - +
54A GLU* 2.5 21.3 + - - +
56A LEU* 1.3 74.1 - - - +
58A TRP* 1.3 102.6 + - + +
59A LYS* 4.5 1.2 - - - +
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Residues in contact with TRP 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 GLU* 2.7 46.2 + - + +
55A LEU* 5.4 0.9 - - - -
57A ARG* 1.3 109.5 - - + +
59A LYS* 1.3 71.6 + - - +
60A GLU* 3.1 12.9 + - + +
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Residues in contact with LYS 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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20A ALA* 5.3 3.1 - - - +
23A TYR* 3.4 40.8 - - + -
24A ASP* 3.9 8.7 - - - +
27A GLN* 3.5 32.5 + - - +
55A LEU* 2.7 27.2 + - - +
56A LEU* 3.1 35.1 + - - +
57A ARG 4.5 0.9 - - - +
58A TRP* 1.3 75.9 - - - +
60A GLU* 1.3 69.6 + - - +
61A ASN* 3.5 1.7 + - - -
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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