Contacts of the strand formed by residues 44 - 48 (chain S) in PDB entry 2JA7
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 TYR 44 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P ASP* 3.8 25.1 - - + -
37S SER 4.0 5.4 - - - -
38S CYS* 3.3 23.1 - - + -
43S GLY* 1.3 71.2 - - - -
45S ILE* 1.3 57.0 + - - +
46S LEU* 3.6 9.0 + - + +
78S VAL* 2.8 25.8 - - - +
79S PHE* 2.9 45.1 + + + +
81S PRO* 5.4 0.4 - - + -
105S PRO* 3.1 50.8 + - + -
106S MET* 4.2 7.1 - - + -
155S SER 5.2 1.8 - - - -
156S SER* 3.1 16.1 - - - -
157S ILE* 3.0 47.6 + - + -
158S HIS* 5.9 0.2 - - - -
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Residues in contact with ILE 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR* 5.5 6.3 - - + -
140P ASP* 5.5 0.2 - - - +
7S LEU* 3.2 35.4 - - + -
34S VAL* 3.1 40.8 - - + +
35S GLU* 3.8 4.5 - - + +
36S GLY* 3.0 21.5 + - - -
37S SER* 3.2 25.1 + - - +
39S THR* 5.9 1.1 - - - +
42S PHE* 5.0 7.4 - - + -
43S GLY 3.4 5.5 + - - +
44S TYR* 1.3 70.6 - - - +
46S LEU* 1.3 63.0 + - - +
47S CYS* 4.8 2.2 - - - +
74S TYR* 4.2 3.1 - - - +
76S ALA* 4.5 12.8 - - + -
77S VAL 4.8 0.2 - - - +
78S VAL* 3.8 17.9 - - + -
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Residues in contact with LEU 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P ILE* 5.3 1.6 - - + -
138P ASN* 3.9 11.8 + - - +
140P ASP* 4.1 15.9 - - + -
141P LEU* 3.3 31.0 - - + +
144P THR* 3.4 40.8 - - + +
2S PHE* 4.0 16.4 - - + -
35S GLU* 4.0 6.0 - - - +
36S GLY 4.8 0.9 - - - +
44S TYR* 4.0 10.3 - - + +
45S ILE* 1.3 79.9 - - - +
47S CYS* 1.3 66.5 + - + +
77S VAL* 3.0 22.5 + - + +
79S PHE* 4.2 17.5 - - + -
105S PRO* 4.0 17.9 - - + -
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Residues in contact with CYS 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P ILE* 4.6 19.1 - - + -
62P ALA* 4.9 5.6 - - - -
63P LEU* 3.3 34.8 - - - -
66P ARG* 4.0 0.4 - - - -
141P LEU* 4.3 11.2 - - + -
35S GLU* 3.4 9.8 - - - +
45S ILE* 4.8 1.0 - - - +
46S LEU* 1.3 85.4 - - + +
48S VAL* 1.3 71.9 + - - +
49S LEU* 3.2 13.9 - - + +
76S ALA* 2.8 23.0 - - - +
77S VAL* 3.0 14.7 + - + -
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Residues in contact with VAL 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P ALA* 4.4 4.0 - - - +
66P ARG* 3.0 19.6 + - - +
30S LEU* 4.5 4.7 - - + -
31S LEU* 3.3 24.0 - - + -
34S VAL* 4.7 5.4 - - + -
35S GLU* 2.6 38.5 + - + +
45S ILE* 5.9 0.2 - - + -
47S CYS* 1.3 73.7 - - - +
49S LEU* 1.3 70.1 + - - +
51S TYR* 4.4 5.3 + - - +
54S ILE* 4.6 7.6 - - + -
74S TYR* 3.4 43.1 - - + -
75S ARG 3.8 3.6 - - - +
76S ALA* 3.7 4.5 - - + -
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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
------------------------------------------------------------
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