Contacts of the strand formed by residues 80 - 86 (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 GLY 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS 3.4 4.2 + - - -
9A ILE* 3.4 12.5 - - - +
10A ALA 3.1 23.9 + - - -
78A ILE* 3.2 6.8 - - - +
79A ASN* 1.3 79.7 - - - +
81A TYR* 1.3 65.3 + - - -
113A PRO* 3.7 9.9 - - - -
163A ILE* 4.1 16.2 - - - -
167A ALA* 5.7 1.1 - - - -
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Residues in contact with TYR 81 (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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10A ALA* 3.5 12.8 - - + -
12A LEU* 3.5 25.1 - - + -
70A PHE* 4.5 0.4 - + - -
74A TYR* 2.6 30.9 + - + -
75A SER* 4.0 4.7 + - - -
78A ILE* 3.5 35.0 + - + +
80A GLY* 1.3 75.6 - - - -
82A ILE* 1.3 64.7 + - - +
83A LEU* 4.0 12.1 - - + -
103A LEU* 3.5 25.1 - - + -
107A VAL* 3.8 12.6 - - + +
112A ILE* 4.2 20.3 - - + +
113A PRO 3.1 16.9 + - - +
114A ILE* 4.1 17.0 - - + -
115A MET 3.2 22.7 + - - -
163A ILE* 3.5 9.3 - - - +
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Residues in contact with ILE 82 (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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9A ILE* 3.7 19.3 - - + -
10A ALA 2.9 8.6 + - - +
11A ILE* 3.5 15.4 - - + +
12A LEU 2.8 33.3 + - - +
22A LEU* 6.0 2.5 - - + -
81A TYR* 1.3 78.9 - - - +
83A LEU* 1.3 59.1 + - - +
84A VAL* 3.6 3.7 + - + +
115A MET* 3.7 10.5 - - + -
117A VAL* 3.7 31.9 - - + -
159A VAL* 3.9 16.6 - - + -
160A PHE* 3.5 37.2 - - + -
163A ILE* 4.2 14.4 - - + -
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Residues in contact with LEU 83 (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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12A LEU* 3.6 36.8 - - + -
81A TYR* 4.1 8.5 - - + -
82A ILE* 1.3 74.1 - - - +
84A VAL* 1.3 59.7 + - - +
96A ILE* 3.4 23.3 - - + -
99A ILE* 4.8 2.9 - - + -
100A HIS* 3.6 49.1 - - + +
103A LEU* 4.1 14.4 - - + -
114A ILE* 4.6 6.7 - - + -
115A MET 3.0 14.0 + - - +
116A LEU* 3.2 15.5 - - + +
117A VAL 3.0 21.1 + - - -
141A TRP* 4.0 7.9 - - + -
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Residues in contact with VAL 84 (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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11A ILE* 4.3 9.4 - - + -
12A LEU 3.1 7.7 + - - +
13A GLY* 3.7 16.8 - - - -
14A TYR 4.4 1.7 + - - -
17A VAL* 3.8 11.9 - - + +
18A GLY 5.5 0.4 - - - -
19A LYS* 3.4 36.1 - - + -
22A LEU* 4.4 9.2 - - + -
82A ILE* 3.6 5.6 + - + -
83A LEU* 1.3 73.6 - - - +
85A TYR* 1.3 66.3 + - - +
96A ILE* 4.0 4.6 - - - +
117A VAL* 3.2 24.0 - - + +
119A ASN* 3.6 30.1 - - + -
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Residues in contact with TYR 85 (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* 4.1 5.8 - - - -
84A VAL* 1.3 74.5 - - - +
86A SER* 1.3 64.8 + - - +
87A VAL* 3.8 16.3 - - + +
92A SER* 3.9 29.2 - - - +
93A PHE* 3.9 34.8 - + + +
96A ILE* 4.5 5.4 - - + -
116A LEU* 3.4 34.5 - - + -
117A VAL 2.8 26.2 + - - -
118A GLY* 3.4 16.3 - - - -
119A ASN* 2.6 36.7 + - - +
129A ILE* 4.4 7.7 - - + +
130A SER 4.7 2.4 + - - -
134A GLY* 3.3 12.8 + - - -
145A PHE* 3.2 23.8 - + - -
147A GLU* 4.4 4.9 + - - -
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Residues in contact with SER 86 (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* 3.8 19.6 - - - +
85A TYR* 1.3 78.7 - - - +
87A VAL* 1.3 56.5 + - - +
88A THR* 2.8 33.6 + - - -
89A SER* 3.0 19.1 + - - +
92A SER* 3.0 24.6 + - - -
119A ASN* 3.6 5.2 - - - -
120A LYS* 3.2 25.5 + - - +
129A ILE* 4.1 0.7 - - - +
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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