Contacts of the strand formed by residues 60 - 67 (chain P) 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 THR 60 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10180 A 2.9 29.5 + - - -
10190 C 3.5 43.9 - - - +
38P LYS* 4.4 3.9 + - + -
39P VAL 3.2 18.6 - - - +
40P HIS* 2.9 30.8 - - + -
58P GLY 4.2 0.9 + - - -
59P GLN* 1.3 74.8 - - - +
61P GLY* 1.3 63.8 + - - +
75P ILE* 4.6 4.7 - - - +
94P GLN* 4.0 14.1 - - + +
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Residues in contact with GLY 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LYS* 3.3 9.8 - - - +
39P VAL 2.9 31.7 + - - -
41P LEU* 3.9 6.1 - - - +
60P THR* 1.3 75.1 - - - +
62P THR* 1.3 64.6 + - - -
73P VAL* 3.6 14.1 - - - -
74P ASP 3.2 15.0 - - - -
75P ILE* 3.8 5.6 - - - +
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Residues in contact with THR 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P GLY* 3.7 25.6 - - - +
37P GLU 3.5 2.9 - - - -
38P LYS* 3.3 28.7 + - - -
61P GLY* 1.3 71.3 - - - -
63P VAL* 1.3 75.3 + - - +
64P GLU* 3.3 22.6 + - - +
73P VAL* 3.6 1.7 - - - +
74P ASP* 2.9 35.3 + - - -
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Residues in contact with VAL 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PHE* 3.9 14.8 - - + -
34P ASP 3.6 27.1 - - - +
35P ASP* 4.0 9.0 - - - +
36P GLY 2.7 28.6 + - - -
37P GLU 3.0 10.9 + - - +
39P VAL* 3.7 34.1 - - + -
61P GLY 4.1 0.6 - - - -
62P THR* 1.3 70.7 - - - +
64P GLU* 1.3 67.2 + - - +
65P GLY 4.1 4.9 - - - +
71P TYR* 3.9 27.8 - - + -
72P LYS 3.8 5.6 - - - +
73P VAL* 4.3 9.0 - - + +
91P LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P ASP* 3.9 8.6 - - - +
36P GLY* 3.7 9.7 + - - -
62P THR* 3.4 23.5 - - + +
63P VAL* 1.3 86.4 - - - +
65P GLY* 1.3 63.2 + - - +
72P LYS* 2.8 25.6 + - - +
74P ASP* 2.9 32.7 - - + +
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Residues in contact with GLY 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P ASP* 2.9 30.8 + - - -
63P VAL* 4.1 6.5 - - - +
64P GLU* 1.3 77.9 + - - +
66P LYS* 1.3 63.6 + - - +
71P TYR* 4.0 2.2 - - - -
72P LYS* 3.0 25.1 + - - +
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Residues in contact with LYS 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P GLU* 4.2 16.8 + - - -
65P GLY* 1.3 75.8 - - - +
67P GLN* 1.3 57.9 + - - +
68P GLY 3.7 14.3 + - - +
69P ASP* 3.7 20.2 + - - +
70P ALA 3.0 16.2 - - - +
71P TYR* 3.4 40.2 + - + -
72P LYS* 3.8 18.1 + - - +
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Residues in contact with GLN 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23850 G 3.2 8.6 - - - +
23860 U 3.0 41.8 + - - -
24030 C 2.6 60.7 + - - +
24040 G 3.7 18.2 - - - +
66P LYS* 1.3 73.9 - - - +
68P GLY* 1.3 63.7 + - - +
69P ASP 3.4 0.2 + - - -
70P ALA* 2.9 19.4 + - - +
72P LYS* 3.9 22.3 + - + +
85P ILE* 4.1 11.0 - - + +
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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