Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 3JT0
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 GLU 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY 3.4 2.9 + - - +
55A TRP* 1.3 75.3 - - - +
57A MSE 1.3 59.9 - - - +
58A ILE* 3.2 28.5 + - + +
67A SER* 3.2 23.3 + - - -
68A TYR 3.4 2.9 - - - -
69A LYS* 3.0 38.1 + - + -
116A ILE 3.6 1.9 - - - +
117A LEU* 3.6 5.8 - - - +
118A LYS* 2.9 56.7 + - + +
119A ASN 4.8 0.9 + - - +
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Residues in contact with MSE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.8 39.3 - - + -
42A LEU* 4.0 13.7 - - + -
55A TRP 4.3 0.2 - - - -
56A GLU* 1.3 70.6 - - - +
58A ILE* 1.3 62.4 + - - +
59A ARG 3.9 0.5 + - - -
66A VAL 3.6 2.1 - - - +
67A SER* 3.6 0.9 - - - -
68A TYR* 2.8 48.1 + - + +
70A TYR* 3.5 30.5 - - + +
84A ILE* 3.4 34.5 - - + -
101A TRP* 3.9 18.0 - - + -
115A VAL* 4.0 17.9 - - + -
116A ILE 3.5 3.4 - - - +
117A LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 6.1 0.2 - - - -
56A GLU* 3.2 28.3 - - + +
57A MSE 1.3 74.3 - - - +
59A ARG* 1.3 62.9 + - - +
60A LYS 4.7 0.2 - - - +
65A SER* 3.9 28.9 - - - +
66A VAL 3.5 4.5 - - - +
67A SER* 3.6 17.5 - - - +
114A LYS 3.5 2.1 - - - +
115A VAL* 3.3 8.9 - - - +
116A ILE* 2.9 57.8 + - + +
118A LYS* 3.8 30.5 - - + +
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Residues in contact with ARG 59 (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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40A ILE* 4.4 9.0 - - + -
57A MSE 3.9 1.0 + - - -
58A ILE* 1.3 70.6 - - - +
60A LYS* 1.3 61.1 + - - +
61A ILE* 4.1 17.8 - - + +
64A THR* 3.5 8.1 + - - +
65A SER* 3.3 2.9 - - - -
66A VAL* 2.8 66.2 + - - +
101A TRP* 3.6 28.1 - - + -
104A GLN* 3.3 20.2 + - - +
105A ASN 3.6 21.8 + - - -
107A TRP* 3.6 37.3 - - + +
113A VAL* 3.9 18.4 - - + -
114A LYS 3.7 2.5 - - - +
115A VAL* 4.8 2.0 - - - -
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.8 0.6 + - + -
59A ARG* 1.3 72.9 - - - +
61A ILE* 1.3 67.9 + - - +
62A GLY 2.7 31.8 + - - +
63A ASP* 4.4 6.9 - - - +
64A THR 3.5 4.7 - - - +
65A SER* 3.5 21.5 + - - +
112A ASP 4.1 0.5 - - - +
113A VAL* 3.6 1.4 - - - -
114A LYS* 2.8 69.8 + - + +
116A ILE* 4.5 11.7 - - + -
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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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59A ARG* 4.1 21.1 - - - +
60A LYS* 1.3 79.6 - - - +
62A GLY* 1.3 64.0 + - - +
63A ASP* 3.3 4.5 + - - +
64A THR* 3.1 20.5 + - - +
107A TRP* 3.5 31.6 - - + -
111A GLU* 4.1 27.4 - - + +
112A ASP 3.8 13.5 - - - +
113A VAL* 3.4 31.6 - - + -
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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