Contacts of the strand formed by residues 16 - 21 (chain X) in PDB entry 2FSO
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 16 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12X GLU* 3.5 4.0 - - - -
13X LEU 2.6 35.0 + - - +
14X ASN* 3.7 8.3 - - + +
15X LYS* 1.3 82.0 - - + +
17X ILE* 1.3 63.6 + - - +
18X TRP* 3.4 15.8 + - - -
54X LYS* 3.1 27.3 + - + +
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Residues in contact with ILE 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ARG* 3.2 65.3 + - + +
11X GLN 3.6 7.4 - - - +
12X GLU* 4.4 12.1 - - + +
16X THR* 1.3 74.6 - - - +
18X TRP* 1.3 63.4 + - - +
19X GLU* 3.8 2.4 + - - +
54X LYS* 3.2 15.3 + - - -
101X ASP* 5.5 0.7 - - - +
103X TYR* 3.9 1.4 + - - -
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Residues in contact with TRP 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X TYR 3.7 0.5 - - - +
10X ARG* 3.1 5.2 - - - +
11X GLN* 2.9 37.7 + - + +
13X LEU* 3.4 37.9 + - + +
14X ASN* 3.7 11.8 - - - +
16X THR* 3.4 19.8 + - - -
17X ILE* 1.3 73.2 - - - +
19X GLU* 1.3 60.5 + - - +
20X VAL* 4.1 6.3 - - + -
27X LEU* 3.5 17.5 - - + -
37X SER* 3.2 44.3 + - - -
39X CYS* 3.6 20.9 - - + -
52X VAL* 3.3 36.3 - - + -
54X LYS* 3.6 19.4 - - + +
103X TYR* 3.4 20.6 - + + +
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Residues in contact with GLU 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ARG* 5.1 3.3 + - - -
8X PHE* 3.5 36.8 - - + +
9X TYR 3.2 7.6 - - - +
10X ARG* 2.9 44.4 + - - +
17X ILE 4.8 1.6 - - - +
18X TRP* 1.3 76.0 - - - +
20X VAL* 1.3 61.1 + - - +
90X PHE* 3.5 10.0 - - - -
92X PRO* 3.8 26.1 - - + +
94X ARG* 5.8 1.9 + - - -
103X TYR* 3.0 17.6 + - - +
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Residues in contact with VAL 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X PHE* 3.5 5.6 - - - -
9X TYR* 3.0 56.9 + - + +
18X TRP* 4.4 3.8 - - + -
19X GLU* 1.3 81.8 - - - +
21X PRO* 1.3 85.2 - - + +
24X TYR* 4.0 12.3 - - + +
27X LEU* 4.2 24.2 - - + -
52X VAL* 4.6 2.5 - - + -
90X PHE* 3.6 16.6 - - + -
103X TYR* 4.0 14.6 - - + -
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Residues in contact with PRO 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X PRO* 4.0 30.3 - - + -
7X THR 3.5 8.7 - - - +
8X PHE* 3.6 11.6 - - + -
20X VAL* 1.3 96.1 - - + +
22X GLU* 1.3 60.3 + - - +
23X ARG* 3.9 20.2 - - + +
24X TYR* 3.0 29.0 + - + +
88X ASP* 5.0 2.2 - - - +
90X PHE* 3.4 37.9 - - + -
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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