Contacts of the strand formed by residues 91 - 97 (chain F) in PDB entry 2CFX
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 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E THR* 2.7 58.7 + - + +
140E LYS* 5.6 1.2 - - - +
85F ILE* 4.6 11.4 - - + +
88F LEU* 3.8 46.2 + - + +
89F PRO 3.9 3.6 - - - +
90F ASN* 1.3 76.3 - - - +
92F GLU* 1.3 57.6 + - - +
93F PHE 3.6 17.7 - - - +
94F CYS* 4.5 4.3 - - + -
105F LEU* 4.6 9.4 - - + -
106F LYS 3.4 3.8 - - - +
107F ILE* 3.2 32.8 - - + -
118F PHE* 4.3 6.1 - - + -
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Residues in contact with GLU 92 (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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95E TYR* 3.9 7.3 + - - -
139E THR* 3.9 3.6 + - - -
140E LYS* 5.6 3.3 - - - +
58F GLN* 4.5 10.5 + - - +
90F ASN 3.5 4.0 + - - -
91F ILE* 1.3 74.5 - - - +
93F PHE* 1.3 67.4 + - + +
106F LYS* 2.9 51.5 + - + +
108F ASN* 3.2 20.4 + - - +
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Residues in contact with PHE 93 (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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68E ILE* 5.1 0.7 - - + -
93E PHE* 3.5 40.4 - + - -
95E TYR* 4.5 2.2 - + - -
136E GLU* 4.7 7.6 - - - +
137E ILE 5.5 0.2 - - - -
139E THR* 4.4 4.0 - - - -
68F ILE* 4.1 10.8 - - + -
91F ILE* 3.5 8.1 - - - +
92F GLU* 1.3 88.4 - - + +
94F CYS* 1.3 61.7 + - - +
95F TYR* 3.3 42.2 - + + +
104F MET* 3.5 23.6 - - + -
105F LEU* 3.0 28.2 - - - +
106F LYS* 3.2 41.7 + - + -
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Residues in contact with CYS 94 (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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136E GLU* 3.3 6.5 - - - +
137E ILE* 2.9 51.5 + - + +
139E THR* 4.1 19.1 - - + -
81F PHE* 4.2 3.1 - - - -
85F ILE* 4.1 9.2 - - + -
91F ILE* 4.5 0.2 - - + -
93F PHE* 1.3 77.4 - - - +
95F TYR* 1.3 61.4 + - - +
96F ARG 4.0 0.2 + - - -
103F TYR* 3.6 28.9 - - - -
104F MET 3.5 4.5 - - - -
105F LEU* 3.8 24.5 - - + -
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Residues in contact with TYR 95 (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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68E ILE* 4.0 15.0 - - + -
92E GLU* 3.9 8.1 + - - -
93E PHE* 4.9 0.9 - - - -
106E LYS* 2.7 42.5 + - + +
133E ILE* 3.9 32.3 - - + -
135E SER 3.6 1.1 - - - +
136E GLU* 3.6 40.6 + - + -
93F PHE* 3.3 54.5 - + + +
94F CYS* 1.3 73.2 - - - +
96F ARG* 1.3 60.5 + - - +
97F ILE* 3.6 7.4 + - + +
103F TYR* 3.0 9.9 - - - +
104F MET* 2.9 35.8 + - + +
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Residues in contact with ARG 96 (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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116D GLU* 3.9 30.1 + - - +
119D ILE* 3.8 22.1 - - - +
120D ASN* 2.7 28.7 + - - +
133E ILE* 3.4 5.9 - - - -
134E PHE* 2.7 40.6 + - + -
135E SER* 2.8 28.5 + - - +
136E GLU* 4.4 1.1 - - - +
137E ILE* 6.2 0.2 - - + -
78F TYR* 3.4 22.2 + - - -
94F CYS 4.0 0.8 + - - -
95F TYR* 1.3 71.0 - - - +
97F ILE* 1.3 65.7 + - - +
101F ALA 4.9 0.4 + - - -
102F CYS* 3.1 37.3 + - - +
103F TYR* 3.6 34.5 + - + -
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Residues in contact with ILE 97 (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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68E ILE* 4.0 16.6 - - + -
131E HIS* 4.0 22.2 - - + +
132E VAL 3.4 10.1 - - - +
133E ILE* 4.0 18.2 - - + -
134E PHE* 3.6 12.9 - - - -
95F TYR* 4.2 8.7 - - + +
96F ARG* 1.3 85.6 + - - +
98F ALA* 1.3 62.1 + - - +
99F GLY* 4.0 0.4 + - - -
101F ALA* 3.8 24.3 - - + +
102F CYS 2.9 30.3 + - - +
103F TYR* 4.1 12.8 - - - +
104F MET* 3.3 31.4 - - + -
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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