Contacts of the helix formed by residues 81 - 88 (chain A) in PDB entry 2J3R
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.4 24.7 - - + -
63A SER* 4.7 13.9 - - - +
77A VAL* 3.2 24.3 + - + +
80A LYS* 1.3 83.7 - - + +
82A ALA* 1.3 58.6 + - - +
83A PHE 3.4 0.7 - - - -
84A LYS* 2.9 6.1 + - - +
85A MET* 2.7 42.2 + - + +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.7 25.8 - - + -
77A VAL 2.8 17.8 + - - +
78A ILE* 3.6 5.6 - - - +
81A VAL* 1.3 73.1 - - - +
83A PHE* 1.3 63.7 + - - +
84A LYS 3.1 0.2 + - - -
85A MET* 3.1 1.9 + - - -
86A TYR* 3.0 31.6 + - + +
1068A PLM 4.0 37.0 - - + -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 2.7 39.6 + - + +
79A ALA* 3.9 2.0 - - - +
82A ALA* 1.3 74.1 - - - +
84A LYS* 1.3 59.8 + - - +
87A LEU* 3.3 45.1 + - + +
88A GLY 3.3 4.7 + - - -
89A ILE* 3.1 19.1 + - + +
91A PRO* 3.6 39.7 - - + -
105A LEU* 4.0 22.2 - - + -
107A LEU* 4.4 15.3 - - + -
111A PRO* 4.7 2.2 - - + -
131A LEU* 4.5 15.0 - - + -
135A LEU* 4.8 8.7 - - + -
163A ILE* 4.7 8.5 - - + -
1068A PLM 4.2 23.8 - - + -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 5.0 2.3 + - - -
79A ALA 4.6 1.0 + - - -
80A LYS 3.4 19.7 - - - +
81A VAL 2.9 8.1 + - - +
83A PHE* 1.3 79.0 - - - +
85A MET* 1.3 61.4 + - - +
88A GLY* 3.1 25.9 + - - -
89A ILE 2.9 20.5 + - - +
90A THR* 4.0 12.1 - - - +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU 4.7 1.3 - - - +
11A SER* 4.2 18.6 - - - +
13A LYS* 3.1 23.4 + - - +
58A ASP* 5.3 1.8 - - - +
59A PHE* 4.0 15.9 - - + -
62A ARG* 3.6 37.2 - - + +
63A SER* 4.7 7.2 - - - -
81A VAL* 2.7 26.4 + - + +
82A ALA 3.8 3.6 - - - +
84A LYS* 1.3 74.7 - - - +
86A TYR* 1.3 88.3 + - + +
25B SER* 3.0 21.6 + - - +
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.6 42.1 + - + -
58A ASP* 2.9 28.0 + - - -
59A PHE* 3.0 44.2 + + - +
82A ALA* 3.0 28.5 + - + +
85A MET* 1.3 86.6 - - + +
87A LEU* 1.3 61.2 + - - +
88A GLY 3.3 1.3 - - - -
1068A PLM 3.9 22.7 - - + -
24B VAL* 3.0 11.6 - - - +
25B SER* 2.9 31.5 + - - -
27B SER* 3.9 23.8 - - - -
28B ALA* 3.9 8.5 - - + +
31B LEU* 4.8 3.6 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.5 9.6 - - + -
83A PHE* 3.3 32.7 + - + +
86A TYR* 1.3 77.9 - - - +
88A GLY* 1.3 62.2 + - - +
89A ILE* 3.3 8.7 + - + +
111A PRO* 3.2 54.3 - - + +
112A LEU* 3.9 20.4 - - + -
131A LEU* 4.2 11.0 - - + -
1068A PLM 4.3 12.6 - - + -
22B THR* 3.8 7.8 - - + +
24B VAL* 3.7 19.9 - - + +
28B ALA* 5.6 0.2 - - - -
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE 3.3 0.2 + - - -
84A LYS* 3.1 26.4 + - - +
86A TYR 3.3 2.8 + - - -
87A LEU* 1.3 78.4 - - - +
89A ILE* 1.3 64.9 + - - +
22B THR* 3.8 9.2 - - - +
23B GLU 3.4 21.0 + - - -
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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