Contacts of the strand formed by residues 118 - 122 (chain A) in PDB entry 1XBT
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 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG 4.6 6.9 + - - -
20A GLN* 3.6 20.5 + - + +
22A GLN* 4.3 11.9 - - - +
43A PHE* 4.2 26.6 - - + -
92A ALA 3.1 12.3 + - - -
93A VAL* 3.4 13.4 - - + +
94A ILE* 2.8 27.9 + - - +
116A GLY 4.1 0.9 + - - -
117A LYS* 1.3 71.5 - - - +
119A VAL* 1.3 60.7 + - - +
120A ILE* 4.1 20.6 - - + -
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Residues in contact with VAL 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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20A GLN 2.8 16.7 + - - +
21A ILE* 3.3 8.1 - - + +
22A GLN* 2.8 32.7 + - - +
94A ILE* 3.3 17.3 - - + +
96A ILE* 4.1 11.4 - - + -
108A PHE* 5.0 1.6 - - + -
109A CYS* 3.7 39.0 - - - +
112A MET* 3.8 28.3 - - + -
113A ALA* 4.1 1.3 - - + +
117A LYS* 4.1 9.4 - - + +
118A THR* 1.3 77.1 - - - +
120A ILE* 1.3 60.3 + - - +
121A VAL* 4.1 7.6 - - + -
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Residues in contact with ILE 120 (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 GLN* 3.4 24.2 - - - +
24A ILE* 3.8 21.5 - - + -
36A LEU* 3.4 23.3 - - + +
39A ARG* 3.8 36.3 - - + +
40A VAL* 4.5 3.4 - - + -
43A PHE* 4.2 21.5 - - + -
93A VAL* 4.5 8.5 - - + -
94A ILE 2.8 12.6 + - - +
95A GLY* 3.3 3.0 - - - -
96A ILE* 2.7 32.2 + - - +
118A THR* 4.1 13.5 - - + +
119A VAL* 1.3 78.3 - - - +
121A VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.8 4.0 - - + -
22A GLN 2.8 15.3 + - - +
23A VAL* 3.5 5.7 - - + +
24A ILE* 2.7 36.6 + - - +
96A ILE* 3.5 12.6 - - + +
99A GLY* 4.1 7.9 - - - -
105A ILE* 4.0 18.2 - - + -
109A CYS* 3.7 29.4 - - - -
119A VAL* 4.1 8.3 - - + -
120A ILE* 1.3 79.5 - - - +
122A ALA* 1.3 68.3 + - - +
123A ALA* 4.4 6.3 - - + -
136A ILE* 4.8 2.2 - - + -
139A LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 122 (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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24A ILE* 3.4 7.4 - - + -
32A LYS* 3.8 33.9 - - + +
36A LEU* 4.0 12.9 - - + +
96A ILE 2.8 9.5 + - - +
97A ASP* 3.8 19.1 - - - +
98A GLU 3.0 9.7 + - - -
99A GLY* 2.9 22.2 + - - -
120A ILE 4.2 0.4 + - - -
121A VAL* 1.3 71.4 - - - +
123A ALA* 1.3 61.7 + - - +
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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