Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 1JNK
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 GLY 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A SER* 3.8 0.9 - - - -
73A GLY* 3.0 26.5 + - - -
74A ALA 3.5 2.8 - - - +
75A GLN* 1.3 81.4 - - - +
77A ILE* 1.3 65.2 + - - -
78A VAL* 4.0 1.7 + - - +
93A LYS* 4.6 9.4 - - - -
94A LYS 3.1 14.6 - - - -
96A SER* 5.1 1.6 - - - -
1001A ANP 3.6 8.5 + - - +
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Residues in contact with ILE 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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53A VAL* 5.3 6.3 - - + +
55A ASP* 6.1 0.7 - - + +
56A SER* 3.3 31.6 - - - +
58A PHE* 3.4 24.5 - - + -
69A PRO* 5.4 4.9 - - + -
71A GLY 3.6 12.6 - - - +
72A SER* 4.3 13.9 - - - +
76A GLY* 1.3 75.6 - - - -
78A VAL* 1.3 69.2 + - - +
79A CYS* 5.2 4.3 - - - -
94A LYS* 2.9 33.3 + - + +
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Residues in contact with VAL 78 (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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69A PRO* 3.9 3.1 - - - +
70A ILE* 3.0 34.0 + - + -
71A GLY 2.9 23.8 + - - +
76A GLY 4.4 3.8 - - - +
77A ILE* 1.3 76.6 - - - +
79A CYS* 1.3 66.3 + - - +
91A ALA* 4.4 4.9 - - + -
92A ILE 3.5 13.5 - - - +
93A LYS* 3.7 22.2 - - + -
146A MET* 4.5 0.7 - - + -
1001A ANP 3.4 63.3 - - + +
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Residues in contact with CYS 79 (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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53A VAL* 3.2 44.4 - - - -
58A PHE* 4.2 19.1 - - + -
67A LEU* 4.0 14.4 - - + -
68A LYS 3.3 4.7 - - - +
69A PRO* 3.8 15.3 - - - -
70A ILE* 4.0 4.0 - - - -
77A ILE* 4.1 2.0 + - - -
78A VAL* 1.3 74.3 - - - +
80A ALA* 1.3 64.1 + - - +
91A ALA* 3.4 4.0 - - - +
92A ILE* 2.7 41.0 + - + +
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Residues in contact with ALA 80 (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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66A ASN 3.4 1.6 - - - +
67A LEU* 3.3 3.5 - - - -
68A LYS* 2.7 38.0 + - + +
70A ILE* 3.5 28.4 - - + +
79A CYS* 1.3 73.3 - - - +
81A ALA* 1.3 65.2 + - - +
89A ASN* 5.4 1.1 - - - +
90A VAL 3.5 5.4 - - - -
148A LEU* 3.9 24.7 - - + -
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Residues in contact with ALA 81 (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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64A TYR* 4.5 2.0 - - + -
65A GLN 3.6 3.6 - - - +
66A ASN 3.5 6.1 - - - -
67A LEU* 3.2 30.5 - - + -
80A ALA* 1.3 75.8 - - - +
82A TYR* 1.3 62.8 + - - +
89A ASN* 3.0 13.0 + - - +
90A VAL* 2.7 46.1 + - + +
92A ILE* 3.8 17.7 - - + -
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Residues in contact with TYR 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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63A ARG 3.1 2.6 - - - +
64A TYR* 3.3 4.7 - - - -
65A GLN* 2.7 75.3 + - + +
66A ASN* 4.2 3.8 + - + -
81A ALA* 1.3 74.0 - - - +
83A ASP* 1.3 64.0 + - - +
84A ALA* 3.8 21.7 + - + -
87A ASP* 2.8 27.6 + - - +
88A ARG* 3.6 30.1 - - - -
89A ASN* 3.7 17.0 + - - +
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Residues in contact with ASP 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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63A ARG* 2.7 50.3 + - - +
64A TYR* 3.6 18.8 + - + -
81A ALA 4.1 0.4 + - - -
82A TYR* 1.3 74.8 - - - +
84A ALA* 1.3 51.6 + - - +
85A VAL 3.2 8.8 + - - -
86A LEU* 3.2 21.7 - - + +
87A ASP* 2.7 36.2 + - - -
88A ARG 2.8 19.8 + - - +
90A VAL* 4.2 13.4 - - + +
127A LEU* 5.6 0.3 - - - +
145A VAL* 5.8 0.2 - - - +
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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