Contacts of the strand formed by residues 20 - 24 (chain B) in PDB entry 2FHO
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 ILE 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU* 3.7 20.0 - - + -
407A MET* 3.4 33.7 - - + -
408A PHE* 4.0 23.3 - - + -
18B ASN* 3.1 10.7 - - + +
19B ARG* 1.3 80.5 - - + +
21B LEU* 1.3 62.5 + - - +
61B TYR* 4.1 13.7 - - + -
62B VAL 3.3 9.6 - - - +
63B VAL* 4.2 13.9 - - + -
91B TYR* 4.1 1.6 - - - +
92B TYR* 3.5 52.6 + - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.9 2.9 - - + -
18B ASN 4.2 11.9 - - - +
19B ARG 4.2 7.0 - - - +
20B ILE* 1.3 79.7 - - - +
22B TYR* 1.3 59.5 + - - +
23B ILE* 3.9 17.3 + - + +
39B PHE* 6.4 1.1 - - + -
60B ALA 4.1 0.2 - - - +
61B TYR* 3.2 4.1 - - - -
62B VAL* 2.8 39.7 + - + +
64B TYR* 3.8 32.1 - - + -
70B ALA* 4.0 19.7 - - + +
73B ALA* 5.8 0.9 - - + -
74B CYS* 4.0 33.2 - - + +
89B VAL* 4.6 4.0 - - + -
90B LEU 3.6 4.5 - - - +
91B TYR* 4.4 12.3 - - + -
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A TYR* 4.2 1.9 + - - -
20B ILE 4.3 0.6 - - - -
21B LEU* 1.3 71.5 - - - +
23B ILE* 1.3 71.1 + - - +
24B ARG* 3.5 40.7 + - + +
59B THR* 3.0 35.0 + - - +
60B ALA 3.3 13.5 - - - -
61B TYR* 3.2 56.4 + + + -
88B VAL 3.8 0.2 - - - +
89B VAL* 3.4 5.7 - - - -
90B LEU* 2.8 58.4 + - + +
91B TYR* 4.9 6.6 - - - +
92B TYR* 5.4 0.4 - - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.1 17.5 - - + +
22B TYR* 1.3 83.7 - - - +
24B ARG* 1.3 68.7 + - - +
26B LEU* 3.6 29.4 - - + -
39B PHE* 4.0 31.4 - - + -
59B THR* 3.5 7.3 - - - -
60B ALA 2.8 40.4 + - - +
62B VAL* 4.4 5.2 - - + -
77B LEU* 5.2 6.3 - - + -
87B LEU* 4.6 13.0 - - + -
88B VAL 3.3 9.0 - - - +
89B VAL* 4.1 26.5 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.5 45.9 + - + +
23B ILE* 1.3 74.4 - - - +
25B ASN* 1.3 70.4 + - + +
26B LEU 3.3 4.1 + - - +
59B THR* 4.0 13.4 - - + +
87B LEU* 3.8 7.3 - - - +
88B VAL* 3.1 47.8 + - + +
90B LEU* 5.6 8.2 - - - +
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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