Contacts of the helix formed by residues 55 - 63 (chain A) in PDB entry 1CDZ
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 PRO 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TRP* 4.2 7.6 - - + +
54A ASP* 1.3 92.2 - - - +
56A SER* 1.3 61.2 + - - +
58A GLU* 3.1 36.0 + - - +
59A GLU* 3.1 17.6 - - - +
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Residues in contact with SER 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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14A TYR* 3.4 20.3 + - - -
54A ASP* 2.5 29.7 + - - -
55A PRO* 1.3 76.7 - - - +
57A PHE* 1.3 68.8 + - - +
59A GLU* 3.1 23.5 + - - +
60A ALA* 2.9 23.3 + - - +
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Residues in contact with PHE 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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14A TYR* 3.7 44.2 - + - -
40A MET* 6.2 2.9 - - - -
47A VAL* 4.5 3.4 - - + -
49A THR* 4.0 19.3 - - + -
52A GLU 4.1 3.6 - - - -
53A TRP* 3.3 41.7 - + + -
54A ASP* 2.6 40.9 + - + +
56A SER* 1.3 72.0 - - - +
58A GLU* 1.3 51.6 + - - +
60A ALA* 2.8 9.0 + - + +
61A LEU* 2.5 39.2 + - - +
69A PHE* 3.3 41.2 - + + -
92A VAL* 4.4 2.7 - - + -
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Residues in contact with GLU 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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53A TRP* 3.5 33.0 + - + +
55A PRO* 3.1 23.8 + - - +
57A PHE* 1.3 73.9 - - - +
59A GLU* 1.3 51.9 + - - +
61A LEU* 2.7 12.8 + - - +
62A MET* 2.6 39.8 + - + +
94A PRO* 5.3 2.6 - - - +
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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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55A PRO* 3.1 21.5 + - - +
56A SER* 3.1 32.9 + - - +
58A GLU* 1.3 77.9 - - - +
60A ALA* 1.3 62.6 + - - +
62A MET* 3.4 27.9 + - + +
63A ASP* 3.3 19.4 - - - +
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Residues in contact with ALA 60 (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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40A MET* 4.4 21.1 - - + -
56A SER 2.9 13.4 + - - +
57A PHE* 2.8 16.5 + - + +
59A GLU* 1.3 80.3 - - + +
61A LEU* 1.3 56.8 + - - +
63A ASP* 3.5 5.4 - - - +
64A ASN* 3.0 30.5 + - - +
67A LEU* 4.3 16.3 - - + +
69A PHE* 5.4 0.4 - - + -
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Residues in contact with LEU 61 (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 TRP* 4.2 17.0 - - + -
57A PHE 2.5 12.2 + - - +
58A GLU* 2.7 16.1 + - - +
60A ALA* 1.3 70.4 - - - +
62A MET* 1.3 49.7 + - - +
63A ASP 2.7 16.4 + - - -
64A ASN 3.0 23.5 + - - +
65A PRO* 3.1 37.3 - - + +
67A LEU* 3.9 12.1 - - + +
69A PHE* 3.6 27.8 - - + -
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Residues in contact with MET 62 (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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58A GLU* 2.6 21.8 + - + +
59A GLU* 3.5 24.2 - - + +
60A ALA 3.4 0.2 - - - -
61A LEU* 1.3 69.8 - - + +
63A ASP* 1.3 65.3 + - - +
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Residues in contact with ASP 63 (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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42A ASP* 4.4 13.9 - - - +
59A GLU 3.3 15.2 - - - +
60A ALA* 3.5 6.5 - - - +
61A LEU 2.7 1.8 + - - -
62A MET* 1.3 82.4 - - - +
64A ASN* 1.3 65.9 + - + +
65A PRO* 3.9 5.8 - - - +
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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