Contacts of the helix formed by residues 81 - 87 (chain E) 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 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59E PHE* 3.5 24.5 - - + -
63E SER* 4.0 15.5 - - - +
76E ASP 5.3 0.2 - - - -
77E VAL* 3.2 26.0 + - + +
80E LYS* 1.3 85.6 - - + +
82E ALA* 1.3 68.3 + - - +
83E PHE 3.6 0.7 - - - -
84E LYS* 3.5 6.2 + - - +
85E MET* 3.1 29.0 + - + +
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Residues in contact with ALA 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PHE* 3.8 15.9 - - + -
77E VAL 2.7 16.1 + - - +
78E ILE* 3.3 17.0 - - - +
81E VAL* 1.3 73.4 - - - +
83E PHE* 1.3 64.7 + - - +
85E MET 3.2 1.7 + - - -
86E TYR* 3.0 32.4 + - + -
1068E PLM 3.7 36.8 - - + -
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Residues in contact with PHE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 2.8 53.9 + - + +
79E ALA* 3.7 4.7 + - - +
81E VAL 3.6 0.2 - - - -
82E ALA* 1.3 72.6 - - - +
84E LYS* 1.3 57.0 + - - +
87E LEU* 2.9 54.3 + - + +
88E GLY 3.1 4.9 + - - -
89E ILE* 3.1 16.8 - - + +
91E PRO* 3.4 24.2 - - + -
105E LEU* 3.7 20.0 - - + -
107E LEU* 4.0 19.7 - - + -
131E LEU* 4.6 10.3 - - + -
135E LEU* 4.4 13.0 - - + -
163E ILE* 4.8 7.2 - - + -
1068E PLM 4.1 26.2 - - + -
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 4.5 0.2 - - - +
13E LYS* 4.1 8.1 + - - +
79E ALA 4.2 1.4 + - - -
80E LYS 3.8 24.7 + - - +
81E VAL* 3.5 5.9 + - - +
82E ALA 3.2 1.2 - - - -
83E PHE* 1.3 78.6 - - - +
85E MET* 1.3 60.3 + - - +
88E GLY* 3.0 31.9 + - - +
89E ILE 3.0 15.1 + - - +
90E THR* 3.8 16.4 - - - +
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Residues in contact with MET 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 4.0 1.4 - - - -
25B SER* 3.1 36.6 + - - +
13E LYS* 3.7 14.6 + - - +
59E PHE* 3.9 21.3 - - + -
62E ARG* 3.5 50.5 - - + +
81E VAL* 3.1 21.2 + - + +
82E ALA 3.6 4.3 - - - +
84E LYS* 1.3 81.5 - - - +
86E TYR* 1.3 90.3 + - + +
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Residues in contact with TYR 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 2.8 29.0 - - - +
25B SER* 4.2 7.9 - - - -
27B SER* 4.5 4.0 - - - -
28B ALA* 3.6 21.9 - - + +
31B LEU* 4.5 6.3 - - + -
55E LEU* 3.6 41.3 + - + -
58E ASP* 3.7 16.2 + - - -
59E PHE* 3.0 46.9 + + - +
82E ALA* 3.0 27.5 + - + +
85E MET* 1.3 101.9 - - + +
87E LEU* 1.3 62.0 + - - +
88E GLY 3.6 0.2 - - - -
1068E PLM 3.6 27.4 - - + -
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Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 3.8 6.9 - - - +
24B VAL* 3.8 10.9 - - + +
16E SER* 4.4 0.2 + - - -
19E PHE* 4.1 25.8 - - + -
83E PHE* 2.9 40.6 + - + +
86E TYR* 1.3 80.1 - - - +
88E GLY* 1.3 56.8 + - - +
89E ILE* 3.1 23.9 + - + +
107E LEU* 5.7 0.2 - - + -
110E ASN* 4.0 18.6 - - - +
111E PRO* 3.6 30.9 - - + +
112E LEU* 4.5 7.4 - - + -
131E LEU* 4.2 17.0 - - + -
1068E PLM 4.1 18.2 - - + -
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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