Contacts of the strand formed by residues 45 - 48 (chain F) in PDB entry 3SF4
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 CYS 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C PHE* 3.9 30.1 - - + -
103C ASN* 3.4 9.4 - - - +
106C LYS* 3.9 14.1 - - - -
107C VAL* 4.1 6.5 - - - -
43F CYS* 3.4 6.1 - - - -
44F MET* 1.3 88.9 - - - +
46F VAL* 1.3 61.0 + - - +
47F LEU* 3.7 1.5 + - - +
65F ALA* 3.0 37.1 + - - +
67F GLY* 3.5 30.3 - - - -
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Residues in contact with VAL 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY 5.4 0.5 - - - -
100C ASN* 4.6 1.4 - - - +
103C ASN* 3.1 25.7 - - - +
136C ARG* 5.5 9.9 - - + +
139C TYR* 3.6 33.7 - - + -
140C ASN* 3.6 18.9 + - - +
143C ASN* 4.8 0.4 - - - +
196C ARG* 5.4 1.6 - - - +
43F CYS* 3.9 15.0 - - - +
44F MET 4.0 0.6 - - - -
45F CYS* 1.3 73.5 - - - +
47F LEU* 1.3 64.4 + - - +
48F GLN* 4.3 3.1 + - + +
62F LEU* 3.9 31.4 - - + -
63F ILE 3.4 8.1 - - - +
64F LEU* 4.0 10.1 - - + -
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Residues in contact with LEU 47 (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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63C ASN* 3.5 45.1 - - + +
66C PHE* 3.8 39.7 - - + -
67C TYR* 5.3 1.1 - - + +
78C HIS* 4.6 0.9 - - - +
100C ASN* 3.5 15.5 - - - +
103C ASN* 4.1 24.7 - - + -
45F CYS 4.5 6.7 - - - +
46F VAL* 1.3 77.1 - - - +
48F GLN* 1.3 63.6 + - - +
61F ASP 3.6 0.3 - - - +
62F LEU* 3.7 2.3 - - - -
63F ILE* 2.8 49.9 + - + +
65F ALA* 4.3 10.8 - - + -
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Residues in contact with GLN 48 (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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59C SER* 4.1 1.9 + - - -
63C ASN* 2.9 15.6 - - - +
96C LYS* 3.6 44.9 - - + +
100C ASN* 3.0 25.0 + - - +
121C HIS* 3.1 31.7 + - + -
130C ASP* 5.8 0.6 + - - -
132C VAL* 5.7 1.2 - - - +
133C GLY* 5.0 5.7 - - - -
136C ARG* 2.6 50.2 - - + +
46F VAL* 4.3 3.8 + - + +
47F LEU* 1.3 76.6 - - - +
49F ALA* 1.3 60.6 + - - +
61F ASP 3.1 3.8 - - - +
62F LEU* 5.2 0.7 - - - -
63F ILE* 5.0 0.2 - - - -
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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