Contacts of the helix formed by residues 52 - 58 (chain A) in PDB entry 3NYN
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 2.9 34.2 + - + +
51A ARG* 1.3 74.3 - - - +
53A TYR* 1.3 57.2 + - - +
54A HIS* 3.6 14.6 + - - +
55A SER* 2.7 58.8 + - - -
56A LEU* 2.9 16.4 + - - +
158A PHE* 3.7 3.4 - - - -
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Residues in contact with TYR 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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51A ARG 4.1 0.2 + - - -
52A ASP* 1.3 68.9 + - - +
54A HIS* 1.3 61.0 + - + +
57A CYS* 2.8 40.6 + - + +
58A GLU* 3.7 16.2 + - - +
67A PHE* 3.8 22.4 - + - -
150A HIS* 3.5 28.8 + - + -
153A LEU* 3.6 18.8 - - - +
154A SER* 3.5 47.6 - - - +
158A PHE* 3.1 38.0 - + + -
583A BU3 3.5 23.2 - - + +
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Residues in contact with HIS 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* 3.0 14.6 + - - +
53A TYR* 1.3 82.9 - - + +
55A SER* 1.3 58.3 + - - +
58A GLU* 2.9 29.0 + - + +
59A ARG* 3.0 54.7 + - + +
539B TRP* 3.4 48.1 - + - -
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Residues in contact with SER 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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50A GLU 5.6 0.7 - - - -
52A ASP* 2.7 35.1 + - - -
54A HIS* 1.3 74.2 - - - +
56A LEU* 1.3 63.9 + - - +
59A ARG* 4.5 8.5 - - - +
60A GLN* 3.2 50.9 + - - +
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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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49A LEU* 4.6 13.5 - - + -
50A GLU 3.6 24.0 - - - +
51A ARG* 4.1 3.1 - - - -
52A ASP 2.9 20.6 + - - +
55A SER* 1.3 82.1 - - - +
57A CYS* 1.3 69.6 + - - +
58A GLU 3.8 0.2 - - - -
60A GLN* 4.1 11.7 - - - +
63A GLY* 3.3 29.1 - - - +
158A PHE* 4.2 3.6 - - + -
161A TYR* 4.8 5.4 + - + -
162A LEU* 4.0 25.1 - - + -
167A PHE* 4.2 11.9 - - + -
170A PHE* 3.6 34.8 - - + -
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Residues in contact with CYS 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 TYR* 2.8 24.2 + - + +
56A LEU* 1.3 84.6 - - - +
58A GLU* 1.3 60.3 + - - +
60A GLN 5.2 0.2 - - - -
63A GLY 4.5 0.7 - - - -
64A ARG* 3.3 32.5 - - - +
67A PHE* 3.6 35.5 - - + -
158A PHE* 3.6 36.8 - - - -
161A TYR* 4.5 6.3 - - - -
583A BU3 3.5 10.2 - - + +
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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 TYR* 4.1 24.0 - - + +
54A HIS* 2.9 41.8 + - - +
56A LEU 3.8 0.4 - - - -
57A CYS* 1.3 87.3 - - - +
59A ARG* 1.3 66.1 + - - +
60A GLN 3.4 1.2 - - - -
61A PRO* 5.4 0.7 - - - +
64A ARG* 3.8 11.8 - - - +
150A HIS* 3.3 24.3 + - - -
583A BU3 3.8 17.7 + - + +
539B TRP* 3.4 48.8 + - + +
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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