Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 1XTR
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 ILE 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.9 17.0 - - + +
83A LEU* 4.6 7.6 - - + -
100A HIS* 4.2 28.3 - - + +
103A LEU* 3.7 25.4 - - + -
104A LEU* 4.2 12.8 - - + -
112A ILE* 3.4 25.4 + - + +
113A PRO* 1.3 79.6 - - - +
115A MET* 1.3 68.4 + - - +
141A TRP* 4.5 4.9 - - + -
143A ALA* 2.9 36.1 - - + +
144A ALA* 3.5 5.0 + - - +
163A ILE* 4.5 1.1 - - - +
166A GLU* 5.3 5.3 - - - +
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Residues in contact with MET 115 (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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81A TYR 3.2 15.2 + - - +
82A ILE* 4.3 11.4 - - + -
83A LEU* 3.0 27.6 + - - +
114A ILE* 1.3 81.1 - - - +
116A LEU* 1.3 63.9 + - - +
117A VAL* 3.8 22.9 - - + -
144A ALA* 3.5 21.8 - - + +
146A LEU* 3.9 36.1 - - + +
159A VAL* 3.5 25.6 - - - +
162A ARG* 4.1 9.0 - - + -
163A ILE* 4.0 25.6 - - + -
166A GLU* 5.4 1.3 - - + -
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Residues in contact with LEU 116 (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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83A LEU* 3.2 24.0 - - - +
85A TYR* 3.4 34.8 - - + -
96A ILE* 4.1 10.8 - - + -
115A MET* 1.3 72.8 - - - +
117A VAL* 1.3 61.0 + - - +
134A GLY 3.4 25.4 - - - +
137A LEU* 4.0 15.5 - - + -
138A ALA* 3.7 20.0 - - + +
141A TRP* 4.0 27.6 - - + -
143A ALA* 4.8 0.8 - - + +
144A ALA 2.7 14.1 + - - +
145A PHE* 3.3 10.0 - - + -
146A LEU 3.2 22.3 + - - -
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Residues in contact with VAL 117 (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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22A LEU* 4.1 5.6 - - + -
82A ILE* 3.7 25.1 - - + -
83A LEU 3.0 6.9 + - - -
84A VAL* 3.2 23.4 - - + -
85A TYR* 2.8 35.8 + - - -
115A MET* 3.8 21.3 - - + -
116A LEU* 1.3 76.3 - - - +
118A GLY* 1.3 61.5 + - - +
146A LEU 3.3 8.7 - - - +
148A SER* 3.2 29.8 - - - +
159A VAL* 4.1 12.8 - - + -
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Residues in contact with GLY 118 (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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85A TYR* 3.4 31.9 - - - -
87A VAL* 3.8 7.9 - - - +
117A VAL* 1.3 73.0 - - - +
119A ASN* 1.3 62.2 + - - -
121A LYS 4.8 0.5 + - - -
145A PHE* 4.3 1.2 - - - -
146A LEU 3.0 11.0 + - - -
147A GLU* 3.1 12.4 - - - +
148A SER 2.8 23.8 + - - -
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Residues in contact with ASN 119 (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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17A VAL 2.7 25.4 + - - +
18A GLY* 3.8 5.1 + - - -
22A LEU* 3.8 10.4 - - - +
84A VAL* 3.6 16.8 - - + -
85A TYR 2.6 18.8 + - - +
86A SER* 3.6 0.3 - - - -
87A VAL* 3.0 23.0 + - - +
117A VAL 3.7 1.0 - - - -
118A GLY* 1.3 73.2 - - - +
120A LYS* 1.3 78.6 + - - +
148A SER* 2.8 35.9 + - - +
150A ALA* 3.6 6.7 + - - +
179A GNP 2.9 30.5 + - - +
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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