Contacts of the strand formed by residues 59 - 65 (chain A) in PDB entry 2JP2
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 PHE 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.8 7.9 - - + -
45A VAL* 4.3 19.1 - - + -
46A CYS 3.8 3.1 - - - -
47A LYS* 3.6 37.2 - - + -
48A VAL* 3.7 2.7 - - - +
57A SER* 4.8 5.6 - - - -
58A GLY* 1.3 82.4 - - - -
60A LEU* 1.3 61.6 + - - +
61A ILE* 5.7 1.3 - - + -
76A TYR* 4.0 1.4 - - - -
77A VAL* 2.9 48.8 + - + +
81A LEU* 4.5 7.6 - - + -
120A ALA* 3.6 42.8 - - + -
123A ASP* 4.7 12.1 - - + -
124A LEU* 3.8 32.1 - - + -
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Residues in contact with LEU 60 (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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7A THR* 5.3 1.1 - - + +
8A HIS* 3.5 30.5 - - + +
45A VAL* 3.8 3.9 - - - -
46A CYS* 3.1 46.0 + - - +
48A VAL* 4.0 16.4 - - + -
59A PHE* 1.3 75.6 - - - +
61A ILE* 1.3 77.6 + - - +
62A HIS* 3.2 27.2 + - + -
74A GLU* 4.2 5.4 - - + +
75A CYS 3.8 5.4 - - - +
76A TYR* 3.8 37.5 - - + +
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Residues in contact with ILE 61 (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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43A VAL* 4.8 8.3 - - + -
44A GLY 4.1 8.7 - - - +
45A VAL* 5.1 11.9 - - + +
59A PHE* 5.7 1.1 - - + -
60A LEU* 1.3 69.8 - - - +
62A HIS* 1.3 58.7 + - - +
73A LEU* 3.3 24.2 - - + +
74A GLU* 3.4 0.5 - - - -
75A CYS* 2.8 47.8 + - + +
81A LEU* 3.8 25.4 - - + -
83A TYR* 3.2 32.8 - - + +
93A TRP* 3.8 37.2 - - + +
113A PHE* 5.4 4.7 - - + -
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Residues in contact with HIS 62 (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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7A THR 5.0 1.3 - - - -
8A HIS* 3.0 54.8 + + - -
14A TYR* 2.7 34.6 + + + +
43A VAL* 3.7 3.3 - - - +
44A GLY 2.8 30.3 + - - +
46A CYS* 4.6 6.1 - - - -
60A LEU* 3.2 16.5 + - + +
61A ILE* 1.3 73.2 - - - +
63A GLY* 1.3 59.4 + - - +
64A GLU* 3.8 7.3 + - + -
71A VAL* 3.3 40.4 - - + +
73A LEU* 3.5 11.0 - - - -
74A GLU* 4.0 12.3 - - + +
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Residues in contact with GLY 63 (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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42A ARG 3.5 9.6 - - - -
43A VAL* 3.7 15.9 - - - -
62A HIS* 1.3 79.5 - - - +
64A GLU* 1.3 65.8 + - - -
71A VAL* 3.8 2.2 - - - -
72A VAL* 2.9 26.3 + - - +
73A LEU* 2.9 25.0 + - - +
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Residues in contact with GLU 64 (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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8A HIS 4.9 2.0 - - - +
11A ASP* 4.1 1.1 - - - -
14A TYR* 2.8 26.1 + - - -
17A ARG* 2.9 25.2 + - - -
41A SER* 3.4 5.0 - - - -
42A ARG* 2.6 43.5 + - + +
62A HIS* 3.8 8.8 + - + -
63A GLY* 1.3 76.6 - - - -
65A ARG* 1.3 61.9 + - - +
68A ASP 3.9 3.6 - - - +
69A LYS* 2.7 45.4 + - + +
70A LEU 3.2 24.0 - - - +
71A VAL* 4.7 4.7 - - + +
72A VAL* 3.7 2.2 - - - -
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Residues in contact with ARG 65 (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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36A GLU* 2.7 38.6 + - - -
37A GLY* 3.1 38.7 + - - -
39A GLY* 5.9 0.4 + - - -
41A SER* 4.0 5.8 - - - +
42A ARG* 3.9 5.9 - - - +
64A GLU* 1.3 81.3 - - - +
66A GLN* 1.3 53.7 + - - +
67A LYS* 2.7 42.8 + - + +
68A ASP 3.3 12.7 + - - +
70A LEU* 3.1 40.8 + - + +
72A VAL* 3.6 15.1 - - + +
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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