Contacts of the helix formed by residues 91 - 99 (chain F) in PDB entry 2J3W
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 VAL 91 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F LEU* 2.9 22.0 + - + +
90F LYS* 1.3 86.8 - - + +
92F ASN* 1.3 78.7 + - - +
93F VAL 3.5 0.9 - - - -
94F TRP 3.5 0.5 + - - -
95F LYS* 3.0 50.6 + - + +
101F GLU* 3.7 30.1 - - - +
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Residues in contact with ASN 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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69F LEU* 4.6 4.3 - - + -
73F GLU* 3.5 36.8 - - + +
74F LYS* 3.9 19.7 - - - +
87F LEU 4.1 0.6 + - - -
88F PHE* 3.2 54.6 + - + +
91F VAL* 1.3 84.5 - - - +
93F VAL* 1.3 64.8 + - - +
95F LYS* 3.6 4.8 + - - +
96F ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 5.3 0.4 - - + -
69F LEU* 4.1 12.3 - - + -
88F PHE* 3.0 31.3 + - + +
89F ILE* 3.6 36.1 - - + +
92F ASN* 1.3 71.8 - - - +
94F TRP* 1.3 65.2 - - + +
96F ALA* 3.1 3.8 + - - +
97F LEU* 3.1 43.0 + - + +
146F ILE* 4.6 4.5 - - + -
147F VAL* 4.9 4.7 - - + -
150F ILE* 3.6 28.7 - - + -
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Residues in contact with TRP 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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89F ILE* 3.1 30.9 + - + +
90F LYS 3.6 13.7 - - - +
92F ASN 3.4 0.6 - - - -
93F VAL* 1.3 75.6 - - + +
95F LYS* 1.3 53.6 + - - +
97F LEU* 3.2 3.0 + - + -
98F PHE* 2.7 65.1 + + + -
100F LYS* 3.1 26.0 - - - +
101F GLU 3.8 1.8 - - - -
102F ALA* 3.4 21.1 - - + +
117F ILE* 3.8 21.1 - - + -
119F GLU* 3.4 41.8 + - + +
123F LEU* 3.5 16.3 - - + +
143F THR* 3.9 16.8 - - + -
147F VAL* 4.5 7.2 - - + -
168F THR* 6.4 0.2 - - + -
170F LEU* 3.7 36.3 - - + -
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Residues in contact with LYS 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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73F GLU* 4.6 14.7 + - - +
91F VAL* 3.0 47.3 + - + +
92F ASN* 3.6 4.7 - - - +
94F TRP* 1.3 76.9 - - - +
96F ALA* 1.3 58.9 + - - +
99F GLY* 2.7 29.5 + - - -
100F LYS* 3.4 27.1 - - - +
101F GLU* 3.8 8.3 - - + +
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Residues in contact with ALA 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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14D MET* 4.8 6.9 - - - +
18D LEU* 4.4 8.7 - - - +
65F LEU* 5.3 3.4 - - + -
69F LEU* 3.8 31.6 - - + -
73F GLU* 4.9 3.1 + - - +
92F ASN 3.0 14.5 + - - +
93F VAL 3.1 9.2 + - - +
95F LYS* 1.3 75.8 - - - +
97F LEU* 1.3 67.7 + - + +
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Residues in contact with LEU 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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14D MET* 4.3 3.5 - - - +
18D LEU* 3.9 22.3 - - + +
65F LEU* 3.8 28.0 - - + -
93F VAL* 3.1 34.5 + - + +
94F TRP* 4.9 1.6 - - + -
96F ALA* 1.3 85.5 - - + +
98F PHE* 1.3 85.3 + - + +
99F GLY 3.7 0.7 - - - -
127F TYR* 2.5 33.7 + - - +
143F THR* 4.2 17.0 - - + +
146F ILE* 4.3 20.2 - - + -
147F VAL* 5.7 0.2 - - + -
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Residues in contact with PHE 98 (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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94F TRP* 2.7 64.4 + + + +
97F LEU* 1.3 92.1 - - + +
99F GLY* 1.3 61.3 + - - +
100F LYS* 2.9 16.8 + - + +
119F GLU* 5.9 0.9 - - - +
123F LEU* 3.7 42.0 - - + -
126F ALA* 3.9 23.6 - - + +
127F TYR* 3.8 21.8 - + - -
139F CYS* 4.2 2.9 - - - -
143F THR* 3.3 33.4 - - + -
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Residues in contact with GLY 99 (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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95F LYS* 2.7 31.2 + - - -
96F ALA 5.0 0.2 + - - -
97F LEU 3.7 0.6 - - - -
98F PHE* 1.3 71.8 - - - +
100F LYS* 1.3 56.2 + - - +
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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