Contacts of the strand formed by residues 118 - 122 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG 4.6 6.4 + - - -
20F GLN* 3.6 32.1 + - + +
22F GLN* 4.1 13.0 - - - +
43F PHE* 4.2 21.5 - - + -
92F ALA 3.1 12.5 + - - -
93F VAL* 3.4 13.1 - - + +
94F ILE* 2.8 27.7 + - - +
116F GLY 4.1 1.0 + - - -
117F LYS* 1.3 70.8 - - - +
119F VAL* 1.3 62.1 + - - +
120F ILE* 4.2 15.0 - - + -
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Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLN 2.8 18.6 + - - +
21F ILE* 3.3 5.5 - - + +
22F GLN* 2.8 27.4 + - - +
94F ILE* 3.3 19.3 - - + +
96F ILE* 4.1 14.8 - - + -
108F PHE* 5.1 2.2 - - + -
109F CYS* 3.7 42.4 - - + +
112F MET* 3.9 26.5 - - + -
113F ALA* 4.0 5.8 - - + +
117F LYS* 4.1 4.3 - - + +
118F THR* 1.3 76.4 - - - +
120F ILE* 1.3 64.5 + - - +
121F VAL* 4.2 2.9 - - + -
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 3.4 25.1 - - + +
24F ILE* 3.7 22.0 - - + -
36F LEU* 3.3 21.7 - - + +
39F ARG* 4.0 30.7 - - + -
40F VAL* 4.1 16.6 - - + +
43F PHE* 4.2 15.9 - - + -
93F VAL* 4.2 17.7 - - + -
94F ILE 2.8 11.2 + - - +
95F GLY* 3.3 2.1 - - - -
96F ILE* 2.7 31.9 + - - +
118F THR* 4.2 5.6 - - + -
119F VAL* 1.3 78.1 - - - +
121F VAL* 1.3 58.4 + - - +
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 4.6 4.5 - - + -
22F GLN 2.8 17.2 + - - +
23F VAL* 3.4 4.0 - - + +
24F ILE* 2.7 37.5 + - - +
96F ILE* 3.5 13.9 - - + +
99F GLY* 4.1 8.5 - - - -
105F ILE* 4.0 19.5 - - + -
109F CYS* 3.8 28.0 - - - -
119F VAL* 4.4 4.0 - - + -
120F ILE* 1.3 77.8 - - - +
122F ALA* 1.3 67.7 + - - +
136F ILE* 4.4 8.7 - - + -
139F LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 3.4 7.9 - - + +
32F LYS* 3.8 34.3 - - + +
36F LEU* 4.0 14.1 - - + +
96F ILE 2.9 10.4 + - - +
97F ASP* 3.9 17.5 - - - +
98F GLU 3.0 10.3 + - - -
99F GLY* 3.0 22.2 + - - -
120F ILE 4.2 0.8 + - - -
121F VAL* 1.3 70.5 - - - +
123F ALA* 1.3 61.9 + - - +
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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