Contacts of the helix formed by residues 75 - 85 (chain B) in PDB entry 2RFJ
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 ASP 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PHE 3.3 14.4 - - - +
54B ARG* 3.1 44.5 + - + +
73B PRO 4.9 4.2 - - - +
74B MET* 1.3 84.6 - - - +
76B LEU* 1.3 62.0 + - - +
77B ASN* 3.2 9.9 + - - +
78B THR* 2.8 45.0 + - - -
79B ILE* 3.4 16.2 + - - +
101B MET* 3.9 9.6 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.1 13.4 - - + +
43B LEU* 4.3 17.9 - - + +
44B TRP* 3.7 18.7 - - + -
49B SER* 3.8 28.7 - - - -
52B PHE* 2.8 33.4 + - + +
53B GLN* 4.2 9.9 - - + +
75B ASP* 1.3 68.8 - - - +
77B ASN* 1.3 58.4 + - - +
79B ILE* 3.4 7.1 + - + +
80B LYS* 2.9 29.1 + - - +
98B PHE* 3.8 28.5 - - + -
101B MET* 3.9 15.8 - - + -
122B LEU* 4.3 7.2 - - + -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.5 25.1 - - - -
53B GLN* 3.1 14.7 - - - +
54B ARG* 2.8 47.6 + - + +
75B ASP* 3.2 9.0 + - - +
76B LEU* 1.3 72.1 - - - +
78B THR* 1.3 66.1 + - - +
80B LYS* 3.3 4.8 + - - +
81B LYS* 2.9 31.4 + - + +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PRO 5.1 3.3 + - - -
74B MET* 4.0 15.5 - - + -
75B ASP* 2.8 32.6 + - - -
77B ASN* 1.3 74.1 - - - +
79B ILE* 1.3 57.1 + - - +
81B LYS* 3.3 4.9 + - - +
82B ARG* 2.9 62.3 + - + +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.3 6.3 - - + -
74B MET* 4.3 5.6 - - + -
75B ASP 3.4 13.8 + - - +
76B LEU* 3.4 14.1 + - + +
77B ASN 3.3 0.6 - - - -
78B THR* 1.3 77.4 - - - +
80B LYS* 1.3 64.4 + - - +
82B ARG* 3.2 2.9 + - - +
83B LEU* 2.9 32.8 + - + +
88B TYR* 3.9 8.0 + - - +
94B CYS* 4.1 13.7 - - - -
97B ASP* 3.8 21.8 - - + +
98B PHE* 3.7 72.0 - - + +
101B MET* 5.1 2.2 - - - -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 4.7 1.8 + - + +
40B LEU* 3.5 24.2 - - + +
44B TRP* 3.7 37.7 - - + +
76B LEU 2.9 18.1 + - - +
77B ASN* 3.4 6.3 - - - +
79B ILE* 1.3 77.1 - - - +
81B LYS* 1.3 59.6 + - + +
83B LEU* 3.6 2.6 + - - +
84B GLU* 2.9 59.1 + - - +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASN* 2.9 25.7 + - + +
78B THR* 3.9 4.9 - - - +
80B LYS* 1.3 76.4 - - + +
82B ARG* 1.3 57.9 + - + +
84B GLU* 3.1 13.9 + - - +
85B ASN* 2.8 47.8 + - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 4.0 8.3 - - - +
78B THR* 2.9 38.8 + - + +
79B ILE 3.6 0.9 - - - +
81B LYS* 1.3 76.7 - - + +
83B LEU* 1.3 60.0 + - - +
85B ASN* 3.5 1.3 + - - -
86B LYS 3.4 2.8 + - - -
87B TYR* 2.8 86.6 + - + +
88B TYR* 3.4 32.1 - - + +
97B ASP* 2.9 28.0 + - - -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.6 48.7 - - + +
35B LEU* 4.2 4.9 - - + +
36B GLN* 3.8 48.0 + - + +
40B LEU* 4.2 9.9 - - + -
79B ILE* 2.9 33.5 + - + +
80B LYS 3.9 4.0 - - - +
82B ARG* 1.3 73.3 - - - +
84B GLU* 1.3 63.6 + - - +
85B ASN 3.4 0.3 + - - -
86B LYS* 3.5 9.1 + - - +
88B TYR* 3.7 14.6 - - + -
94B CYS* 4.3 9.0 - - - -
98B PHE* 5.8 0.2 - - + -
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 3.6 18.7 + - - +
80B LYS* 2.9 56.7 + - + +
81B LYS* 3.1 17.0 + - - +
83B LEU* 1.3 76.1 - - - +
85B ASN* 1.3 68.0 + - - +
86B LYS* 3.3 1.7 + - - +
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 2.8 31.2 + - - +
82B ARG* 4.4 3.4 - - - +
84B GLU* 1.3 85.5 - - - +
86B LYS* 1.3 72.8 + - - +
87B TYR* 3.2 5.8 + - + +
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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