Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 3FN3
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ALA 4.5 3.6 - - - +
53A LEU* 1.3 75.6 - - - +
55A VAL* 1.3 70.8 + - - +
56A TYR* 4.5 12.8 - - + -
66A GLN* 6.0 2.2 - - + +
67A PHE 3.2 5.4 - - - +
68A VAL* 3.6 26.0 - - + -
115A MET* 3.2 12.4 - - + +
116A ILE* 2.9 10.0 - - - +
117A SER* 2.7 57.8 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 5.8 0.2 - - + -
53A LEU* 3.7 20.0 - - + -
54A ILE* 1.3 77.7 - - - +
56A TYR* 1.3 63.1 + - - +
57A TRP* 4.0 19.7 - - + +
65A ILE* 4.5 1.1 - - - -
66A GLN* 3.3 1.2 - - - -
67A PHE* 2.3 72.0 + - + +
87A LEU* 4.4 8.1 - - + -
92A LEU* 3.9 12.6 - - + -
97A ALA* 4.0 24.0 - - + -
114A CYS* 6.1 0.7 - - + -
115A MET 3.3 2.5 - - - +
116A ILE* 4.2 10.5 - - + -
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Residues in contact with TYR 56 (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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54A ILE* 4.5 12.1 - - + -
55A VAL* 1.3 76.7 - - - +
57A TRP* 1.3 64.4 + - - +
58A GLU* 3.3 41.3 + - + +
61A ASP 5.0 2.4 + - - -
63A ASN* 3.3 33.5 + - - +
65A ILE 3.2 6.1 - - - -
66A GLN* 3.9 26.2 - - + -
76A VAL* 5.8 3.2 - - + +
113A ARG* 3.9 9.8 - - - +
114A CYS* 3.6 1.0 - - - -
115A MET* 2.7 58.8 + - + +
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Residues in contact with TRP 57 (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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38A ILE* 3.8 31.4 - - + -
40A CYS* 3.7 15.7 - - + -
55A VAL* 4.0 11.6 - - + +
56A TYR* 1.3 76.6 - - - +
58A GLU* 1.3 62.8 + - - +
63A ASN* 3.1 13.2 + - - -
64A ILE* 3.1 20.0 + - + -
65A ILE* 2.8 35.2 + - + +
87A LEU* 3.8 17.3 - - + +
97A ALA* 3.6 22.8 - - + +
99A LEU* 3.6 44.0 - - + +
112A TYR* 4.5 7.0 - - + -
113A ARG 3.5 18.8 - - - -
114A CYS* 3.4 30.3 - - + -
126A ILE* 3.9 13.0 - - + -
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Residues in contact with GLU 58 (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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56A TYR* 3.3 28.9 + - + +
57A TRP* 1.3 78.6 - - - +
59A MET* 1.3 59.9 + - - +
60A GLU 5.4 0.2 + - - -
61A ASP* 3.4 41.5 + - - +
62A LYS 3.3 18.2 - - - +
64A ILE* 3.8 7.2 - - - +
112A TYR* 3.6 1.9 - - - +
113A ARG* 2.8 74.8 + - + +
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Residues in contact with MET 59 (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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58A GLU* 1.3 72.8 - - - +
60A GLU* 1.3 96.5 + - + +
61A ASP 3.1 2.2 - - - -
62A LYS* 2.8 52.1 + - - +
64A ILE* 3.7 8.3 - - + +
81A TYR* 3.7 19.5 - - + +
107A GLN 4.8 5.8 - - - +
108A ASP* 4.9 1.3 - - - +
109A ALA 4.5 10.8 - - - +
111A VAL 3.3 22.2 - - - +
112A TYR* 3.8 36.6 - - + -
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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