Contacts of the strand formed by residues 100 - 106 (chain F) in PDB entry 1XE0
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 VAL 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F TYR 4.1 0.2 - - - +
32F SER* 3.8 1.1 - - - -
33F PHE* 2.9 52.3 + - + +
44F LEU* 3.9 19.1 - - + -
64F ALA* 4.0 18.2 - - + -
65F GLU 3.4 14.4 - - - +
66F GLY* 5.2 0.7 - - - -
96F ILE* 3.8 31.0 - - + -
97F THR 4.9 1.3 - - - +
98F PRO* 4.9 0.4 - - + -
99F PRO* 1.3 74.8 - - - +
101F ILE* 1.3 76.5 + - - +
102F LEU* 4.2 6.4 + - + +
19J LEU* 4.8 2.9 - - + -
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Residues in contact with ILE 101 (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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30F GLU* 4.1 20.9 - - + +
31F TYR 3.4 7.9 - - - +
32F SER* 4.4 16.4 - - - +
63F GLU 3.8 0.3 - - - +
64F ALA* 3.1 5.2 - - - -
65F GLU* 2.8 55.9 + - + +
99F PRO* 6.5 0.2 - - + -
100F VAL* 1.3 76.1 - - - +
102F LEU* 1.3 75.8 - - - +
103F ARG* 3.8 29.5 + - - +
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Residues in contact with LEU 102 (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 PHE* 4.4 5.8 - - + -
22F CYS* 4.0 22.4 - - - -
24F LEU* 3.9 14.0 - - + +
29F LYS 3.8 0.5 - - - +
30F GLU* 3.3 4.3 - - - -
31F TYR* 2.9 41.0 + - + +
33F PHE* 5.9 0.7 - - + -
44F LEU* 4.3 21.3 - - + -
46F LEU* 4.4 10.8 - - + -
62F VAL* 5.1 3.4 - - + -
63F GLU 3.4 2.5 - - - +
64F ALA* 4.0 19.3 - - + -
78F LEU* 4.2 14.6 - - + -
96F ILE* 5.2 0.7 - - + -
100F VAL* 4.4 10.3 - - + +
101F ILE* 1.3 80.8 - - - +
103F ARG* 1.3 59.2 + - - +
113F VAL* 4.3 19.3 - - + -
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Residues in contact with ARG 103 (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 LEU* 4.0 6.6 - - - +
29F LYS* 3.2 12.1 - - + +
30F GLU* 2.8 38.0 + - + -
62F VAL* 3.3 4.2 - - - +
63F GLU* 2.8 73.1 + - + +
65F GLU* 2.9 38.7 + - - +
75F LYS* 4.4 4.8 - - - +
101F ILE* 3.8 16.6 - - + +
102F LEU* 1.3 76.4 - - - +
104F LEU* 1.3 73.1 + - - +
105F LYS* 3.2 9.2 + - - +
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Residues in contact with LEU 104 (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 LEU* 3.9 19.7 - - + +
25F LYS* 3.9 30.5 - - - +
26F ALA* 4.6 0.7 - - - +
29F LYS* 2.8 40.5 + - + +
60F HIS* 4.2 5.4 - - + +
61F VAL 3.8 7.6 - - - +
62F VAL* 4.6 4.0 - - + +
103F ARG* 1.3 75.8 - - - +
105F LYS* 1.3 64.8 + - - +
106F SER* 3.2 24.2 - - - +
107F GLY 3.6 21.1 - - - +
108F SER 4.1 2.0 - - - +
109F GLY* 4.0 9.2 - - - +
111F VAL* 3.7 24.5 - - + -
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Residues in contact with LYS 105 (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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29F LYS* 5.9 1.0 + - - +
61F VAL* 2.9 35.3 + - + +
63F GLU* 3.9 36.3 + - + +
103F ARG* 3.2 8.3 + - - +
104F LEU* 1.3 75.8 - - - +
106F SER* 1.3 63.4 + - - +
112J TYR* 4.4 19.6 + - - -
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Residues in contact with SER 106 (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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59F LEU 4.1 5.2 + - - -
60F HIS* 3.3 0.7 - - - -
61F VAL* 3.0 45.1 + - - +
104F LEU* 3.2 12.6 - - - +
105F LYS* 1.3 83.0 - - - +
107F GLY* 1.3 63.9 - - - +
53J ALA* 4.0 15.8 - - - +
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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