Contacts of the strand formed by residues 62 - 68 (chain R) in PDB entry 1JJ2
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 LYS 62 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16740 C 4.2 8.3 + - - -
16750 C 3.0 35.0 + - - -
27R ALA* 3.4 6.6 - - - +
28R VAL* 2.9 58.6 + - + +
29R ASP 4.2 0.2 - - - +
30R ASP* 3.5 31.3 + - + +
31R ARG 4.9 0.4 - - - -
32R ALA 2.9 26.4 + - - +
54R THR* 4.1 16.6 - - + -
55R GLN 3.3 13.7 - - - +
56R ASN* 3.5 13.0 - - - +
61R GLU* 1.3 76.2 - - - +
63R LYS* 1.3 68.0 + - - +
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Residues in contact with LYS 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14450 G 4.0 21.2 + - - -
14460 U 2.8 27.8 + - - -
9R HIS* 3.8 33.8 + - + +
13R LYS* 5.7 2.0 - - - +
25R GLN* 3.9 16.5 + - - +
26R PHE 3.4 9.6 - - - +
27R ALA* 4.8 0.7 - - - +
53R ASN 3.8 0.3 - - - +
54R THR* 3.2 5.2 - - - -
55R GLN* 2.8 59.3 + - + +
57R THR* 4.1 12.5 + - - +
61R GLU 4.1 0.4 + - - -
62R LYS* 1.3 76.1 - - - +
64R ALA* 1.3 69.6 + - - +
65R VAL* 4.3 10.0 + - + +
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Residues in contact with ALA 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R LEU 3.6 1.7 - - - +
25R GLN* 3.4 6.1 - - - +
26R PHE* 3.0 32.6 + - + +
28R VAL* 4.2 17.5 - - + -
37R VAL* 3.9 28.5 - - + -
52R VAL* 4.1 7.2 - - + -
53R ASN 3.2 7.0 - - - +
54R THR* 4.3 7.0 - - + -
62R LYS 4.2 0.2 + - - -
63R LYS* 1.3 75.0 - - - +
65R VAL* 1.3 61.6 + - - +
66R VAL* 3.6 4.5 + - + +
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Residues in contact with VAL 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14470 U 3.6 32.8 - - + +
17R ASP* 3.8 12.6 - - - +
23R LYS* 3.6 34.8 - - + +
24R LEU 3.7 2.2 - - - -
25R GLN* 4.2 23.1 - - + +
51R GLN 3.6 2.1 - - - +
52R VAL* 3.5 3.1 - - - -
53R ASN* 2.7 39.0 + - + +
54R THR 6.4 0.2 - - - -
63R LYS* 5.1 12.3 - - + +
64R ALA* 1.3 73.2 - - - +
66R VAL* 1.3 60.5 + - - +
67R ARG 3.8 0.5 + - - -
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Residues in contact with VAL 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R LYS* 3.2 2.8 - - - -
24R LEU* 2.6 46.9 + - + +
26R PHE* 4.0 21.8 - - + -
37R VAL* 3.9 27.4 - - + -
38R ALA* 5.4 0.2 - - - -
41R VAL* 4.3 11.0 - - + -
49R VAL* 3.5 43.5 - - + -
51R GLN 3.4 3.6 - - - +
52R VAL* 4.1 5.6 - - + -
64R ALA* 4.2 6.1 - - + +
65R VAL* 1.3 73.2 - - - +
67R ARG* 1.3 61.3 + - - +
68R LEU* 3.8 5.8 + - + +
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Residues in contact with ARG 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15080 C 3.0 30.2 + - - -
21R GLN 3.8 14.6 - - - +
22R ASN* 3.8 0.4 - - + -
23R LYS* 3.6 28.0 - - + +
49R VAL* 3.7 3.8 - - - +
50R GLU* 2.8 51.2 + - - +
51R GLN* 2.8 59.6 + - + +
65R VAL 3.8 2.2 + - - +
66R VAL* 1.3 73.1 - - - +
68R LEU* 1.3 71.6 + - - +
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Residues in contact with LEU 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R ASN* 3.0 32.4 + - - +
24R LEU* 3.7 29.2 - - + -
41R VAL* 4.9 1.1 - - + -
47R VAL* 3.7 25.8 - - + -
48R THR 3.5 8.3 - - - +
49R VAL* 4.2 11.4 - - + -
50R GLU* 3.9 4.8 - - - +
66R VAL* 4.3 12.8 - - + +
67R ARG* 1.3 91.2 + - - +
69R SER* 1.3 61.5 + - - +
70R GLU 3.9 0.5 + - - -
72R ASP* 4.0 14.4 - - + -
74R ALA* 4.0 24.0 - - - +
77R VAL* 4.1 12.8 - - + -
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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