Contacts of the helix formed by residues 38 - 45 (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 VAL 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B TYR* 2.9 50.2 + - + +
37B LYS* 1.3 87.5 - - + +
39B VAL* 1.3 60.5 + - - +
41B LYS* 4.1 2.2 - - - -
42B ASP* 3.0 37.9 + - - +
129B LYS* 3.9 25.9 - - + +
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Residues in contact with VAL 39 (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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34B TYR* 3.1 37.9 + - + +
35B LEU* 3.5 21.1 - - + +
38B VAL* 1.3 76.5 - - - +
40B LEU* 1.3 67.8 + - - +
42B ASP* 3.3 1.9 + - - +
43B LEU* 3.1 33.8 + - + +
98B PHE* 4.3 10.5 - - + -
126B PHE* 3.6 36.8 - - + -
129B LYS* 4.0 19.7 - - + -
130B LEU* 4.4 6.5 - - + -
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Residues in contact with LEU 40 (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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35B LEU 2.6 21.2 + - - +
36B GLN* 3.6 13.5 - - + +
39B VAL* 1.3 75.6 - - - +
41B LYS* 1.3 58.1 + - - +
43B LEU* 3.5 2.0 + - - -
44B TRP* 2.9 44.7 + - + +
76B LEU* 4.1 37.2 - - + +
79B ILE* 4.3 9.4 - - + -
80B LYS* 3.5 42.0 - - + +
83B LEU* 4.2 15.9 - - + -
98B PHE* 4.5 8.7 - - + -
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Residues in contact with LYS 41 (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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36B GLN 3.4 7.9 + - - +
37B LYS* 3.4 28.0 - - - +
38B VAL 4.2 0.2 - - - +
39B VAL 3.2 0.2 - - - -
40B LEU* 1.3 79.7 - - - +
42B ASP* 1.3 69.7 + - - +
44B TRP* 3.4 6.2 + - - +
45B LYS* 3.2 49.4 + - + +
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Residues in contact with ASP 42 (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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37B LYS 5.1 0.2 - - - +
38B VAL* 3.0 24.6 + - - +
39B VAL 3.3 3.2 + - - +
40B LEU 3.3 0.4 - - - -
41B LYS* 1.3 87.9 - - - +
43B LEU* 1.3 63.7 + - - +
45B LYS* 4.1 7.1 - - - +
46B HIS* 3.3 14.6 + - - +
125B LEU* 3.5 26.7 - - + +
129B LYS* 3.5 32.8 + - + +
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Residues in contact with LEU 43 (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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39B VAL* 3.1 30.5 + - + +
40B LEU* 3.9 4.0 - - - +
42B ASP* 1.3 76.5 - - + +
44B TRP* 1.3 65.2 + - - +
45B LYS 3.2 0.2 - - - -
46B HIS* 3.1 13.7 + - - +
49B SER* 3.0 21.7 - - - -
76B LEU* 4.3 12.3 - - + -
98B PHE* 3.7 27.8 - - + -
101B MET* 5.2 0.2 - - + -
102B PHE* 4.2 11.9 - - + -
122B LEU* 4.0 47.6 - - + +
125B LEU* 4.1 13.7 - - + -
126B PHE* 4.1 19.5 - - + -
129B LYS* 5.5 1.3 - - + -
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Residues in contact with TRP 44 (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* 2.9 33.0 + - + +
41B LYS* 3.6 8.3 - - - +
42B ASP 3.3 0.2 - - - -
43B LEU* 1.3 77.4 - - - +
45B LYS* 1.3 65.1 + - + +
46B HIS 4.0 0.2 - - - +
49B SER* 2.9 17.5 + - - -
53B GLN* 3.2 29.9 + - + +
76B LEU* 3.7 40.2 - - + -
77B ASN* 3.5 29.4 - - - -
80B LYS* 3.7 33.1 - - + +
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Residues in contact with LYS 45 (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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41B LYS* 3.2 34.1 + - + +
42B ASP* 4.1 6.5 - - - +
44B TRP* 1.3 84.7 - - + +
46B HIS* 1.3 65.0 + - - +
47B SER* 3.4 2.1 + - - -
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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