Contacts of the helix formed by residues 90 - 95 (chain D) in PDB entry 2XLR
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 THR 90 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D GLU* 3.4 13.7 - - - +
86D PHE 4.3 3.8 - - - +
87D ALA 4.6 7.9 - - - +
88D ASP 5.5 0.7 - - - -
89D TYR* 1.3 81.1 - - - +
91D PHE* 1.3 65.2 + - - +
92D ASP* 3.5 5.6 + - - +
93D GLU* 3.1 31.7 + - - +
94D HIS* 3.2 17.0 + - - +
111D TYR* 3.7 8.1 - - - -
425D MET* 4.2 18.4 - - + +
426D THR* 4.5 11.7 - - + +
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LYS* 3.5 59.0 - - + -
82D GLU* 5.3 0.9 - - - -
84D LEU* 4.1 8.5 - - + -
85D GLU* 2.9 55.6 + - + +
90D THR* 1.3 70.8 - - - +
92D ASP* 1.3 64.5 + - - +
94D HIS* 3.2 1.2 + - - -
95D PHE* 2.9 55.5 + + + +
97D LYS 5.0 1.6 - - - +
99D ILE* 5.1 2.0 - - + -
103D PRO* 5.4 0.2 - - + -
108D LEU* 4.2 8.7 - - + -
111D TYR* 3.5 45.5 - + + -
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Residues in contact with ASP 92 (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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85D GLU* 5.2 0.2 - - - +
90D THR* 3.3 4.0 + - - +
91D PHE* 1.3 81.1 - - - +
93D GLU* 1.3 67.6 + - - +
95D PHE 2.9 21.3 - - - +
96D GLY* 3.6 12.8 - - - +
97D LYS 4.3 14.2 - - - +
98D PRO* 4.8 7.5 - - - +
423D SER* 6.0 0.3 - - - -
426D THR* 3.6 27.8 + - + +
428D THR* 3.6 17.2 + - - +
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Residues in contact with GLU 93 (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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88D ASP 4.3 3.6 - - - +
89D TYR* 3.6 29.0 - - + -
90D THR* 3.1 32.8 + - - +
92D ASP* 1.3 80.7 - - - +
94D HIS* 1.3 62.1 + - - +
95D PHE 4.6 0.7 - - - -
96D GLY* 4.7 1.6 + - - -
118D LYS* 3.1 29.3 + - - +
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Residues in contact with HIS 94 (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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89D TYR* 2.7 45.0 + + + +
90D THR 3.2 12.4 + - - +
91D PHE 3.2 1.5 + - - +
93D GLU* 1.3 78.6 - - - +
95D PHE* 1.3 89.5 + + - +
96D GLY 3.8 1.6 + - - -
110D ASP* 2.7 50.1 + - - -
111D TYR* 3.7 14.2 - + + -
114D GLY* 4.0 8.7 - - - -
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Residues in contact with PHE 95 (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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91D PHE* 2.9 46.7 + + - +
92D ASP 2.9 6.8 - - - +
94D HIS* 1.3 99.4 - + - +
96D GLY* 1.3 51.2 + - - +
97D LYS* 2.4 37.1 + - + +
99D ILE* 3.9 24.2 - - + -
107D VAL* 3.5 39.0 - - + -
110D ASP* 4.1 8.3 - - + -
111D TYR* 4.0 5.8 - - + -
445D LEU* 5.1 1.1 - - + -
449D LEU* 4.3 31.0 - - + -
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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