Contacts of the helix formed by residues 72 - 79 (chain B) in PDB entry 2J3T
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.2 8.7 - - + +
53B PRO* 3.2 29.9 - - + +
68B PHE* 2.7 47.2 + - + +
71B LYS* 1.3 83.4 - - - +
73B LEU* 1.3 59.7 + - - +
75B VAL* 3.3 2.8 + - - +
76B ALA* 2.8 31.9 + - - +
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Residues in contact with LEU 73 (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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48B LEU* 3.8 33.0 - - + -
52B LEU* 3.7 22.3 - - + +
68B PHE* 3.2 8.5 + - + -
69B LEU* 3.3 38.8 - - + +
72B ASP* 1.3 77.8 - - - +
74B TRP* 1.3 62.4 + - + +
76B ALA* 3.1 2.3 + - - +
77B VAL* 2.8 38.0 + - + +
126B LEU* 4.2 13.0 - - + +
127B LEU* 3.8 21.8 - - + -
130B ALA* 3.9 16.6 - - + -
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Residues in contact with TRP 74 (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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69B LEU 3.0 20.4 + - - +
70B CYS 3.7 12.8 - - - +
72B ASP 3.4 0.6 - - - -
73B LEU* 1.3 80.2 - - + +
75B VAL* 1.3 56.0 + - - +
77B VAL* 4.5 1.6 - - + +
78B PHE* 2.7 60.2 + + - +
79B GLN 3.3 1.7 + - - -
80B LYS* 2.9 34.0 - - + +
81B GLN 3.9 2.7 - - - -
82B MET* 3.3 40.5 - - + +
97B ASP* 2.9 25.9 + - + -
100B PHE* 3.9 7.0 - + - -
123B THR* 3.5 25.8 - - + -
126B LEU* 6.1 2.0 - - + -
127B LEU* 3.6 27.8 - - + -
152B PHE* 3.8 24.2 - + - -
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Residues in contact with VAL 75 (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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71B LYS 2.9 26.2 + - - +
72B ASP* 3.3 3.1 + - - +
73B LEU 3.3 0.4 - - - -
74B TRP* 1.3 78.0 - - - +
76B ALA* 1.3 60.4 + - - +
79B GLN* 3.0 25.0 + - - +
80B LYS* 3.5 9.9 - - - +
81B GLN* 3.3 39.3 - - + +
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Residues in contact with ALA 76 (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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18A LEU* 4.7 6.8 - - - +
48B LEU* 5.8 2.9 - - + -
52B LEU* 4.1 26.7 - - + -
72B ASP 2.8 18.9 + - - +
73B LEU* 3.6 3.4 - - + +
75B VAL* 1.3 80.6 - - - +
77B VAL* 1.3 64.8 + - + +
79B GLN* 4.4 3.8 - - - +
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Residues in contact with VAL 77 (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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18A LEU* 3.8 32.5 - - + +
4B THR* 5.6 1.2 - - - +
7B PHE* 4.7 5.4 - - + -
48B LEU* 3.7 30.3 - - + -
73B LEU* 2.8 23.7 + - + +
74B TRP* 4.9 0.9 - - + -
76B ALA* 1.3 79.4 - - + +
78B PHE* 1.3 91.4 + - + +
79B GLN* 2.7 18.8 - - - +
126B LEU* 4.0 19.5 - - + -
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Residues in contact with PHE 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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7B PHE* 4.5 10.8 - + - -
74B TRP* 2.7 58.6 + + + +
77B VAL* 1.3 97.7 - - + +
79B GLN* 1.3 78.6 + - - +
80B LYS* 2.9 20.1 + - + +
100B PHE* 3.4 28.7 - + - -
101B PRO* 3.8 34.0 - - + +
102B LEU* 4.2 17.7 - - + -
123B THR* 3.7 19.3 - - + -
126B LEU* 4.9 2.0 - - + -
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Residues in contact with GLN 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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4B THR* 3.4 39.0 + - - +
75B VAL* 3.0 27.4 + - - +
76B ALA 4.4 3.9 - - - +
77B VAL 2.7 28.9 - - - +
78B PHE* 1.3 81.9 + - - +
80B LYS* 1.3 59.7 + - - +
101B PRO* 6.0 3.0 - - - +
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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