Contacts of the strand formed by residues 66 - 70 (chain F) in PDB entry 5LF4
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 LEU 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F PHE* 3.8 31.2 - - + +
48F GLY* 5.2 0.2 - - - -
49F VAL* 3.4 28.0 - - + +
64F LYS* 3.5 30.1 - - - +
65F ARG* 1.3 81.1 - - - +
67F PHE* 1.3 65.3 + - - +
75F MET 3.3 2.2 - - - +
76F ALA* 3.3 32.1 - - + -
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Residues in contact with PHE 67 (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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64F LYS* 3.6 23.6 - - + -
65F ARG 3.9 13.2 - - - -
66F LEU* 1.3 78.6 - - - +
68F ASN* 1.3 63.6 + - - +
69F VAL* 4.4 7.2 - - + -
74F GLY* 3.4 3.8 - - - -
75F MET* 2.7 54.7 + - + +
77F VAL* 3.8 29.4 - - + -
81F LEU* 4.5 3.6 - - + -
84F ALA* 5.0 2.0 - - + -
85F ARG* 3.9 34.5 - - + -
88F ALA* 4.1 18.2 - - + -
92F ARG* 4.2 19.1 - - - +
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Residues in contact with ASN 68 (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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67F PHE* 1.3 72.9 - - - +
69F VAL* 1.3 62.3 + - - +
70F ASP 4.2 11.8 - - - +
71F ARG* 6.0 0.2 - - - -
73F VAL 3.7 6.4 - - - +
74F GLY* 5.2 2.6 - - - -
92F ARG* 3.0 28.9 + - - +
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Residues in contact with VAL 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 3.8 2.0 + - + -
68F ASN* 1.3 78.6 - - - +
70F ASP* 1.3 60.8 + - - +
73F VAL* 3.0 39.5 + - + +
75F MET* 3.6 41.5 - - + -
88F ALA* 4.0 19.7 - - + +
91F ALA* 4.0 14.4 - - + -
92F ARG* 3.5 29.5 - - + +
95F ALA* 4.1 4.9 - - - +
111F LEU* 4.2 13.2 - - + -
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Residues in contact with ASP 70 (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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68F ASN* 4.2 10.6 - - - +
69F VAL* 1.3 79.7 + - + +
71F ARG* 1.3 82.5 + - - +
72F HIS* 3.1 27.9 - - + +
73F VAL* 3.1 23.5 + - + +
95F ALA* 3.3 27.4 - - + +
99F ARG* 3.0 37.6 + - - -
106F ILE* 4.1 3.5 + - - +
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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