Contacts of the strand formed by residues 33 - 40 (chain Q) in PDB entry 3J0S
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 33 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q VAL* 3.7 32.5 - - + -
17Q ASP* 3.2 36.5 + - - +
18Q MET* 4.0 24.2 - - + +
31Q LYS 4.3 3.8 + - - +
32Q ARG* 1.3 83.7 - - - +
34Q LYS* 1.3 64.0 + - - +
35Q ALA* 3.2 1.1 - - - -
36Q VAL* 3.4 29.1 - - + +
54Q GLU* 3.7 14.4 - - - +
55Q ILE 3.5 8.1 - - - +
56Q LEU* 3.8 13.7 - - + -
57Q VAL* 4.5 1.1 - - - -
86Q ASP* 3.4 13.0 - - - +
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Residues in contact with LYS 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q MET* 5.5 0.9 - - - +
32Q ARG 3.3 6.3 + - - -
33Q LYS* 1.3 74.6 - - - +
35Q ALA* 1.3 56.4 + - - +
55Q ILE* 2.8 9.7 + - + +
56Q LEU 4.0 1.3 - - - -
57Q VAL* 3.3 41.0 - - + +
60Q VAL* 3.7 10.8 - - - +
67Q PRO* 3.3 42.1 - - + +
84Q LEU 4.0 0.2 - - - +
85Q TYR* 3.4 22.9 - - + +
86Q ASP* 2.7 48.9 + - + +
88Q THR* 4.2 17.9 - - - +
162Q GLU* 3.4 24.0 + - - -
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Residues in contact with ALA 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q LYS* 4.4 0.4 - - - +
34Q LYS* 1.3 80.1 - - - +
36Q VAL* 1.3 68.4 + - - +
37Q LEU* 6.0 0.7 - - + -
54Q GLU* 3.7 0.7 - - - +
55Q ILE* 2.7 58.5 + - + +
71Q PHE* 4.4 7.6 - - + -
84Q LEU 3.0 8.5 - - - +
85Q TYR* 3.3 27.8 - - + -
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Residues in contact with VAL 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q VAL* 4.3 10.1 - - + -
18Q MET* 5.4 6.5 - - + -
33Q LYS* 3.4 43.3 - - + +
35Q ALA* 1.3 80.8 - - - +
37Q LEU* 1.3 64.8 + - - +
38Q PHE* 3.2 30.6 - - + -
49Q LEU* 6.2 1.6 - - + -
54Q GLU* 4.3 10.3 - - + +
83Q ALA* 3.3 6.1 - - - +
84Q LEU* 2.8 51.3 + - + +
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Residues in contact with LEU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q ALA* 6.0 0.7 - - + -
36Q VAL* 1.3 75.1 - - - +
38Q PHE* 1.3 61.7 + - - +
49Q LEU* 3.8 5.0 - - - +
50Q GLU* 2.9 31.8 + - + +
53Q LYS* 3.3 53.1 + - + +
54Q GLU* 5.2 1.3 - - - -
55Q ILE* 6.4 1.3 - - + -
71Q PHE* 4.1 7.6 - - + -
74Q MET* 3.9 18.2 - - + +
75Q LEU* 3.4 35.0 - - + -
81Q ARG* 4.4 15.9 - - + -
82Q TYR 3.6 4.0 - - - +
83Q ALA* 3.4 24.0 - - + -
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Residues in contact with PHE 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q VAL* 3.5 39.7 - - + -
14Q VAL* 3.2 36.1 - - + -
15Q PHE 5.0 0.7 - - - -
36Q VAL* 3.2 36.8 - - + -
37Q LEU* 1.3 75.3 - - - +
39Q CYS* 1.3 62.0 + - - +
47Q ILE* 5.2 3.1 - - + -
48Q ILE 3.5 9.2 - - - +
49Q LEU* 4.2 6.3 - - + -
81Q ARG* 3.7 3.0 - - - +
82Q TYR* 2.5 57.2 + - + +
83Q ALA* 4.1 2.0 - - - -
84Q LEU* 3.3 36.6 - - + -
101Q PHE* 4.7 6.3 - + + -
124Q ILE* 6.0 1.1 - - + -
127Q LYS* 6.0 0.7 - - - -
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Residues in contact with CYS 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q PHE* 1.3 77.6 - - - +
40Q LEU* 1.3 75.0 + - + +
41Q SER* 5.6 0.7 - - - -
47Q ILE* 4.0 4.3 - - - +
48Q ILE* 3.0 44.7 + - - +
50Q GLU* 3.4 36.1 - - - -
80Q CYS 5.2 2.2 - - - +
81Q ARG* 4.6 18.6 - - + +
82Q TYR* 4.3 3.6 - - - -
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Residues in contact with LEU 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q VAL* 4.1 16.6 - - + -
39Q CYS* 1.3 83.4 - - + +
41Q SER* 1.3 64.8 + - - +
42Q GLU* 5.1 0.7 - - - +
44Q LYS* 3.5 45.8 + - + +
46Q ASN 3.5 15.7 - - - +
47Q ILE* 4.3 10.3 - - + +
80Q CYS 5.6 3.1 - - - +
82Q TYR* 3.4 33.7 - - + +
113Q SER* 5.7 1.8 - - - +
116Q ILE* 3.6 24.2 - - + -
117Q TYR* 4.6 10.1 - - + -
120Q SER* 5.0 1.3 - - - +
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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