Contacts of the strand formed by residues 33 - 42 (chain C) in PDB entry 3BX7
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 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C ALA 3.4 3.4 + - - +
32C THR* 1.3 74.0 - - - +
34C VAL* 1.3 59.7 + - - +
53C THR* 3.4 31.1 - - + +
54C TYR 3.8 6.1 - - - +
55C MET* 4.2 15.0 - - - +
99C MET* 2.9 33.6 + - + +
100C TYR* 2.7 40.5 + - + +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 4.1 4.0 - - + +
28C PRO* 3.7 30.1 - - + -
32C THR* 3.9 15.0 - - + +
33C GLU* 1.3 78.2 - - - +
35C ARG* 1.3 63.5 + - - +
53C THR* 3.1 3.3 - - - +
54C TYR* 2.7 76.6 + - + +
56C MET 5.8 1.8 - - - +
96C VAL* 3.6 25.4 - - + -
97C GLU 3.3 6.7 - - - +
98C LEU* 4.3 7.6 - - + -
99C MET* 4.8 0.2 - - - -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 6.1 0.4 - - - +
72A SER* 4.2 0.8 + - - -
75A LYS* 5.8 0.4 - - - +
77A GLU* 2.7 44.6 + - - -
34C VAL* 1.3 77.8 - - - +
36C VAL* 1.3 64.3 + - - +
37C THR* 4.1 15.6 + - - +
51C ALA* 4.8 8.1 - - + -
52C ALA 3.2 13.5 - - - +
53C THR* 3.6 18.2 - - - +
95C LYS* 3.5 2.6 - - - +
96C VAL* 3.5 2.3 - - - -
97C GLU* 2.9 65.2 + - - +
99C MET* 3.5 40.3 - - + +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 1.3 75.0 - - - +
37C THR* 1.3 67.5 + - - +
38C VAL* 4.3 2.7 - - + -
50C CYS 4.1 0.2 - - - +
51C ALA* 3.2 4.3 - - - +
52C ALA* 2.8 43.7 + - + +
54C TYR* 3.7 24.1 - - + +
60C LEU* 4.4 12.6 - - + -
62C PHE* 4.5 8.6 - - + -
77C VAL* 4.3 20.9 - - + -
79C LEU* 4.7 6.5 - - + -
94C CYS* 4.4 14.8 - - - -
95C LYS 3.3 8.5 - - - +
96C VAL* 4.4 10.8 - - + +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 4.1 13.7 + - - +
36C VAL* 1.3 79.2 + - - +
38C VAL* 1.3 63.2 + - - +
39C LEU* 3.8 13.9 + - + +
48C GLU* 3.5 40.6 - - + +
50C CYS 3.4 5.6 - - - +
51C ALA* 4.0 7.3 - - + +
93C ILE 3.3 2.8 - - - +
94C CYS* 3.8 1.0 - - - -
95C LYS* 2.8 59.9 + - - +
97C GLU* 4.1 4.7 + - - -
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 5.4 1.3 - - + -
36C VAL* 4.9 4.5 - - + -
37C THR* 1.3 76.3 - - - +
39C LEU* 1.3 55.3 + - - +
48C GLU* 3.6 2.8 - - - +
49C VAL* 2.7 39.5 + - + +
50C CYS* 2.8 36.1 + - - +
62C PHE* 5.5 1.3 - - + -
68C CYS* 4.7 1.3 - - - -
79C LEU* 4.0 28.0 - - + -
81C ILE* 4.1 11.7 - - + -
92C TYR* 3.9 34.8 - - + -
93C ILE 3.4 7.2 - - - +
94C CYS* 4.7 7.6 - - - -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A HIS* 4.3 21.1 - - + +
37C THR* 4.0 20.0 - - + +
38C VAL* 1.3 74.1 - - - +
40C ARG* 1.3 60.5 + - - +
41C GLN 3.9 0.4 + - - -
46C VAL* 4.2 18.6 - - + -
47C THR 3.3 5.4 - - - +
48C GLU* 3.8 24.0 - - + -
49C VAL* 4.2 2.2 - - - -
91C LEU 3.3 2.6 - - - +
92C TYR* 3.4 2.7 - - - -
93C ILE* 2.8 58.1 + - + +
95C LYS* 4.6 27.4 - - + +
108C ILE* 5.8 3.6 - - + -
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 1.3 72.1 - - - +
41C GLN* 1.3 64.2 + - - +
42C ALA* 3.3 27.4 + - - +
45C GLN* 3.4 2.9 + - - +
46C VAL* 3.4 4.0 - - - -
47C THR* 2.7 49.9 + - - +
49C VAL* 3.5 20.7 - - + +
87C MET 3.0 23.3 + - - -
88C ASP* 3.0 21.8 + - - +
89C THR 2.8 21.6 + - - -
90C GLY* 4.9 0.9 - - - -
91C LEU 3.5 4.3 - - - +
92C TYR* 3.5 26.2 - - + +
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Residues in contact with GLN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 3.9 0.4 + - - -
40C ARG* 1.3 73.0 - - - +
42C ALA* 1.3 64.8 + - - +
44C SER* 4.9 9.6 - - - +
45C GLN 3.2 13.2 - - - +
46C VAL* 4.2 18.0 - - + +
90C GLY* 3.8 0.9 - - - -
91C LEU* 2.8 63.1 + - + +
93C ILE* 4.0 21.1 - - + +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ARG* 3.3 41.5 + - - +
41C GLN* 1.3 77.2 - - - +
43C ASP* 1.3 74.5 + - + +
44C SER 3.1 1.3 - - - -
45C GLN* 2.8 24.9 + - - +
89C THR 4.1 7.6 - - - +
90C GLY* 4.6 1.6 - - - -
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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