Contacts of the helix formed by residues 52 - 59 (chain A) in PDB entry 4CE3
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.2 20.1 + - + +
49A SER* 3.3 14.4 - - - -
51A SER* 1.3 79.7 - - - +
53A PRO* 1.4 68.1 - - - +
54A LYS* 3.3 15.3 + - - +
55A GLN* 3.2 41.2 + - + +
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Residues in contact with PRO 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 SER* 3.2 16.8 - - - +
50A LEU 4.6 5.2 - - - +
51A SER 3.8 5.4 - - - +
52A ASP* 1.4 87.2 - - - +
54A LYS* 1.4 57.2 + - - +
55A GLN 3.1 5.5 + - - -
56A LEU* 3.3 22.7 + - + +
57A GLU* 4.3 8.0 + - - +
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Residues in contact with LYS 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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52A ASP* 3.2 10.4 + - - +
53A PRO* 1.4 74.1 - - - +
55A GLN* 1.3 64.7 + - - +
56A LEU 3.3 0.7 - - - -
57A GLU* 3.3 45.7 + - + +
58A THR* 4.6 3.6 + - - +
141A ASN* 5.0 0.3 + - - -
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Residues in contact with GLN 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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45A ILE* 4.0 16.8 - - + +
48A LYS* 3.6 34.0 + - + +
49A SER* 4.7 6.7 - - - -
52A ASP* 3.4 44.3 + - + +
53A PRO 3.1 0.6 - - - -
54A LYS* 1.3 78.1 - - - +
56A LEU* 1.4 59.8 + - - +
58A THR* 3.3 9.2 + - - -
82A ILE* 6.0 0.2 - - - +
141A ASN* 2.8 45.7 + - - +
142A ASP* 5.1 6.5 + - - +
169A ARG* 3.5 6.1 + - - -
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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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45A ILE* 4.1 22.0 - - + +
46A ARG* 5.7 1.8 - - + -
49A SER* 3.6 30.1 - - - +
53A PRO* 3.3 9.5 + - + +
54A LYS 3.3 1.0 - - - -
55A GLN* 1.4 75.9 - - - +
57A GLU* 1.3 58.2 + - + +
58A THR 3.3 1.3 - - - -
59A GLU 3.0 29.7 - - - +
60A PRO* 3.0 13.9 - - + +
62A LEU* 3.9 35.7 - - + -
169A ARG* 3.7 5.8 - - - +
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Residues in contact with GLU 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 PRO* 4.5 5.1 - - - +
54A LYS* 3.3 46.5 + - + +
56A LEU* 1.3 78.1 - - + +
58A THR* 1.4 60.5 + - - +
59A GLU 3.2 0.7 + - - -
60A PRO* 3.9 16.3 - - + +
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Residues in contact with THR 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 LYS 4.6 2.8 + - - +
55A GLN 3.3 10.1 + - - +
57A GLU* 1.4 74.3 - - - +
59A GLU* 1.3 59.7 + - - +
60A PRO* 4.3 1.0 - - - +
139A LYS* 5.9 2.2 - - - +
141A ASN* 2.6 35.2 + - + +
168A GLY* 3.5 29.7 - - - +
169A ARG* 3.4 8.1 + - - +
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Residues in contact with GLU 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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56A LEU* 3.0 4.6 + - - +
57A GLU 3.2 0.4 - - - -
58A THR* 1.3 79.1 - - - +
60A PRO* 1.4 72.7 - - - +
61A ASP* 3.3 18.0 + - - +
62A LEU* 4.6 0.5 - - - +
63A PHE* 4.1 14.7 - - - -
78A ARG* 3.7 21.1 + - - -
80A SER* 3.4 26.5 - - - -
168A GLY* 4.5 7.6 + - - -
169A ARG* 2.8 55.7 + - + +
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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