Contacts of the strand formed by residues 52 - 57 (chain D) in PDB entry 3TKR
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 GLU 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D TYR* 2.6 39.6 + - + +
51D TRP* 1.3 82.8 - - - +
53D GLY* 1.3 59.3 + - - +
64D LEU 3.2 13.5 - - - +
65D LYS* 3.9 17.0 + - + -
147D ILE* 3.9 14.3 - - - +
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Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 1.3 76.4 - - - +
54D THR* 1.3 62.5 + - - -
55D ALA 3.7 0.2 + - - -
63D GLU* 3.4 15.5 + - - +
64D LEU* 2.9 32.7 + - - +
140D LEU* 3.8 13.2 - - - +
141D SER 4.7 5.4 - - - -
147D ILE* 5.1 0.7 - - - -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY* 1.3 72.3 - - - -
55D ALA* 1.3 61.6 + - - +
61D PHE* 4.1 23.3 - - + -
62D LYS 3.5 7.4 - - - +
63D GLU* 2.7 24.2 + - - +
116D GLN* 4.0 37.3 + - + +
140D LEU* 4.0 0.6 - - - +
141D SER* 2.9 35.0 + - - -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY 3.7 0.4 + - - -
54D THR* 1.3 75.9 - - - +
56D VAL* 1.3 63.6 + - - +
57D ILE* 3.7 12.2 + - + -
60D GLU 3.4 1.2 - - - +
61D PHE* 3.4 3.6 - - - -
62D LYS* 2.7 37.3 + - - +
64D LEU* 3.9 31.9 - - + -
116D GLN* 5.2 0.7 - - - -
138D PRO* 4.4 2.0 - - + -
139D LEU 3.2 13.5 - - - +
140D LEU* 4.0 7.6 - - + -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 1.3 71.2 - - - +
57D ILE* 1.3 64.4 + - - +
59D GLY* 4.0 22.0 - - - +
60D GLU 3.2 8.5 - - - +
61D PHE* 3.8 14.1 - - + -
116D GLN* 3.4 29.8 - - - +
119D HIS* 3.6 18.2 - - + -
120D LEU* 4.1 8.5 - - + +
123D ILE* 3.7 27.6 - - + -
135D ILE* 5.9 1.0 - - - +
137D ILE 4.3 1.9 - - - +
138D PRO* 3.4 2.8 - - - +
139D LEU* 2.9 33.3 + - + +
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Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 4.1 11.0 - - + +
56D VAL* 1.3 79.7 - - - +
58D ASP* 1.3 78.9 + - + +
59D GLY 3.1 0.7 - - - -
60D GLU* 2.8 28.0 + - - +
62D LYS* 4.1 26.8 - - + +
63D GLU 5.4 0.4 - - - +
64D LEU* 4.1 26.7 - - + -
137D ILE 5.7 0.4 - - - -
138D PRO* 3.8 26.7 - - + -
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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