Contacts of the helix formed by residues 81 - 91 (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 LYS 81 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ASN* 3.5 22.5 + - - +
79F GLU* 4.7 0.4 - - - +
80F THR* 1.3 94.2 + - - +
82F VAL* 1.3 65.4 + - - +
83F LEU* 3.4 7.6 + - + +
84F ASN* 3.4 27.2 + - - +
85F ILE 3.3 17.3 + - - -
156F PHE* 3.8 9.4 - - - -
182F ASP* 3.8 9.9 - - - +
185F LEU* 6.4 1.8 - - + -
186F ASP* 5.1 9.0 - - - +
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Residues in contact with VAL 82 (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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81F LYS* 1.3 72.5 - - - +
83F LEU* 1.3 65.3 + - - +
85F ILE* 3.1 5.9 - - - +
86F LEU* 3.0 31.5 + - + +
115F TYR* 4.1 15.9 - - + +
156F PHE* 3.9 14.1 - - + -
174F PHE* 3.6 29.6 - - + -
178F VAL* 4.1 22.7 - - + -
179F ILE* 4.4 6.5 - - + -
181F ARG* 5.0 0.2 - - - +
182F ASP* 3.0 39.5 + - + +
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Residues in contact with LEU 83 (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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81F LYS* 3.3 4.1 - - + +
82F VAL* 1.3 80.4 - - - +
84F ASN* 1.3 67.0 + - - +
86F LEU* 3.3 9.2 + - + +
87F LEU* 2.9 52.6 + - + +
105F LEU* 5.0 6.1 - - + -
115F TYR* 6.1 1.6 - - + -
182F ASP* 5.0 0.4 + - - -
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Residues in contact with ASN 84 (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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57C ASN* 5.6 0.7 + - - -
77F LYS* 4.6 6.5 + - - +
79F GLU* 3.3 31.4 - - + +
81F LYS* 3.4 29.4 + - + +
82F VAL 3.3 0.8 - - - -
83F LEU* 1.3 89.9 - - - +
85F ILE* 1.3 61.5 + - - +
87F LEU* 3.1 13.7 + - - +
88F PHE* 2.8 27.9 + - - +
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Residues in contact with ILE 85 (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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79F GLU* 4.0 23.0 - - + +
81F LYS 3.3 9.4 + - - +
82F VAL* 3.1 20.0 - - - +
84F ASN* 1.3 78.5 - - - +
86F LEU* 1.3 68.6 + - + +
88F PHE* 3.3 21.7 + - + +
89F ILE* 3.3 26.6 + - - +
150F ILE* 5.3 0.9 - - + -
151F LEU* 3.7 26.7 - - + -
154F SER* 3.5 25.6 - - - +
156F PHE* 3.8 32.1 - - + -
174F PHE* 4.7 3.6 - - + -
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Residues in contact with LEU 86 (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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82F VAL* 3.0 34.6 + - + +
83F LEU* 3.4 8.5 - - + +
85F ILE* 1.3 77.7 - - - +
87F LEU* 1.3 58.3 + - - +
89F ILE* 3.3 8.6 + - + +
90F LYS* 3.0 25.3 + - - +
105F LEU* 4.2 20.3 - - + +
115F TYR* 3.2 45.5 - - + -
117F ILE* 4.5 4.5 - - + +
151F LEU* 5.0 4.9 - - + -
172F ILE* 3.9 26.7 - - + -
174F PHE* 3.6 24.0 - - + -
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Residues in contact with LEU 87 (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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83F LEU* 2.9 39.9 + - + +
84F ASN* 3.5 13.9 - - - +
86F LEU* 1.3 74.1 - - - +
88F PHE* 1.3 60.3 + - - +
89F ILE 3.1 1.8 - - - -
90F LYS* 4.1 17.0 - - + -
91F VAL* 2.9 41.6 + - + +
92F ASN* 4.6 0.2 - - - -
105F LEU* 3.4 23.3 - - + -
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Residues in contact with PHE 88 (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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66F LEU* 4.7 5.4 - - + -
69F LEU* 4.2 17.7 - - + -
70F VAL* 3.6 35.2 - - + -
73F GLU* 6.2 0.4 - - + -
74F LYS* 3.8 22.9 - - + +
79F GLU* 4.9 5.8 - - + +
84F ASN 2.8 16.9 + - - +
85F ILE* 3.4 29.2 - - + +
86F LEU 3.3 0.2 - - - -
87F LEU* 1.3 72.5 - - - +
89F ILE* 1.3 60.3 + - + +
92F ASN* 3.2 47.1 + - + +
93F VAL* 3.0 44.7 + - + +
150F ILE* 3.7 20.9 - - + -
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Residues in contact with ILE 89 (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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85F ILE 3.3 15.2 + - - +
86F LEU* 3.4 11.0 - - + +
87F LEU 3.1 0.2 - - - -
88F PHE* 1.3 78.9 - - + +
90F LYS* 1.3 64.0 + - - +
93F VAL* 3.6 23.8 - - + -
94F TRP* 3.1 38.2 + - + +
117F ILE* 4.7 12.1 - - + -
147F VAL* 3.8 35.2 - - + -
150F ILE* 3.8 27.1 - - + -
151F LEU* 3.8 20.9 - - + -
172F ILE* 5.5 1.1 - - + -
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Residues in contact with LYS 90 (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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86F LEU 3.0 16.3 + - - +
87F LEU* 3.1 16.4 + - + +
89F ILE* 1.3 77.0 - - - +
91F VAL* 1.3 60.9 + - + +
94F TRP* 3.6 2.8 - - - +
101F GLU* 3.1 22.3 + - + +
102F ALA* 2.8 72.7 + - + -
103F ASP 3.5 14.6 + - - -
104F LYS* 4.5 0.4 - - - +
105F LEU* 3.5 35.7 - - + +
117F ILE* 4.0 11.4 - - + +
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Residues in contact with VAL 91 (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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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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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