Contacts of the strand formed by residues 43 - 45 (chain A) in PDB entry 1F3H
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 PHE 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.7 9.7 - - - +
22A PHE* 3.5 23.8 - - + -
38A MET* 3.5 33.8 + - + +
39A ALA* 4.0 2.4 - - - -
41A ALA* 3.6 12.3 - - + -
42A GLY* 1.3 80.7 - - - +
44A ILE* 1.3 68.8 + - - +
55A ALA* 3.7 27.1 - - + -
56A GLN* 3.5 5.6 - - - -
57A CYS* 3.5 24.0 - - + -
62A LYS* 4.8 3.6 - - + -
64A LEU* 4.1 26.7 - - + -
67A TRP* 4.7 3.6 - + - -
73A PRO* 3.3 26.0 - - + -
77A HIS* 3.4 34.8 - + + -
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Residues in contact with ILE 44 (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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12A PRO* 5.0 3.8 - - + -
17A HIS* 4.4 9.0 - - + -
18A ARG* 3.2 47.6 - - + +
21A THR* 3.6 23.8 - - + +
22A PHE* 4.0 4.0 - - - -
43A PHE* 1.3 75.5 - - - +
45A HIS* 1.3 70.8 + - - +
46A CYS* 3.6 9.3 + - - -
55A ALA* 3.2 6.5 - - - -
56A GLN* 3.0 32.2 + - + +
58A PHE* 4.2 22.0 - - + -
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Residues in contact with HIS 45 (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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21A THR* 3.3 30.4 + - - +
22A PHE* 3.8 13.4 - + + +
23A LYS 3.6 32.3 + - - -
24A ASN* 4.7 2.0 - - + -
25A TRP* 3.3 41.2 - + - -
44A ILE* 1.3 79.9 - - - +
46A CYS* 1.3 60.7 + - - +
47A PRO* 3.4 32.1 - - + +
52A PRO 3.3 21.6 + - - -
54A MET 3.7 14.4 - - - -
55A ALA* 4.6 1.8 - - + -
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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