Contacts of the strand formed by residues 71 - 77 (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 VAL 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A HIS* 5.4 5.2 - - + +
62A HIS* 3.3 41.7 - - + +
63A GLY 3.8 4.5 - - - +
64A GLU* 4.3 4.9 - - + +
69A LYS* 5.7 1.8 - - + -
70A LEU* 1.3 76.5 - - - +
72A VAL* 1.3 60.7 + - - +
73A LEU 3.6 17.9 - - - +
74A GLU* 4.1 12.3 - - + -
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Residues in contact with VAL 72 (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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22A VAL* 3.7 25.8 - - + -
35A GLN* 3.8 22.5 + - - +
36A GLU* 3.7 39.6 - - + +
37A GLY 4.1 0.9 - - - +
41A SER* 4.4 0.9 - - - +
63A GLY 2.9 16.6 + - - +
64A GLU 3.7 4.0 - - - +
65A ARG* 3.6 34.5 - - + +
70A LEU* 3.0 16.9 + - + +
71A VAL* 1.3 75.6 - - - +
73A LEU* 1.3 58.8 + - - +
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Residues in contact with LEU 73 (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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22A VAL* 3.7 24.0 - - + -
23A MET 5.2 0.2 - - - +
35A GLN* 3.4 30.5 - - - +
43A VAL* 5.2 3.6 - - + -
61A ILE* 3.3 35.7 - - + +
62A HIS* 3.5 2.9 - - - +
63A GLY* 2.9 35.5 + - - +
71A VAL* 3.5 6.7 - - - +
72A VAL* 1.3 80.2 - - - +
74A GLU* 1.3 66.1 + - - +
75A CYS* 3.6 22.9 - - - -
93A TRP* 4.1 14.6 - - + -
100A PHE* 4.7 8.3 - - + -
101A GLY 5.5 1.6 - - - +
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Residues in contact with GLU 74 (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 7.2 - - + -
60A LEU* 4.2 5.6 - - + -
61A ILE 3.4 3.8 - - - -
62A HIS* 4.0 15.7 - - + +
71A VAL* 4.1 13.7 - - + -
73A LEU* 1.3 79.4 - - - +
75A CYS* 1.3 68.4 + - - +
76A TYR* 2.9 38.8 + - - +
100A PHE* 4.8 2.9 - - - -
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Residues in contact with CYS 75 (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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60A LEU* 3.8 0.6 - - - -
61A ILE* 2.8 48.3 + - + +
73A LEU* 3.6 17.7 - - - -
74A GLU* 1.3 79.4 + - - +
76A TYR* 1.3 64.3 + - - +
77A VAL* 3.7 5.7 + - + +
93A TRP* 3.5 14.8 - - - +
95A VAL* 4.8 9.9 - - + -
100A PHE* 3.0 43.7 - - + -
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Residues in contact with TYR 76 (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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48A VAL* 3.5 28.9 - - + +
49A MET 4.9 9.6 + - - -
50A HIS* 5.5 2.3 + - - +
58A GLY* 5.8 1.1 - - - -
59A PHE 4.0 0.4 - - - -
60A LEU* 3.8 30.3 - - + +
74A GLU* 2.9 19.4 + - - +
75A CYS* 1.3 72.2 - - - +
77A VAL* 1.3 82.2 + - - +
78A ARG* 4.5 31.3 + - + +
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Residues in contact with VAL 77 (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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58A GLY* 4.1 0.9 - - - -
59A PHE* 2.9 50.1 + - + +
61A ILE* 5.5 0.7 - - + -
75A CYS* 4.0 9.9 - - + +
76A TYR* 1.3 92.2 - - - +
78A ARG* 1.3 63.0 + - - +
80A ASP* 3.1 32.8 - - - +
81A LEU* 3.6 38.1 - - + -
95A VAL* 5.0 11.7 - - + -
124A LEU* 4.4 7.6 - - + -
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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