Contacts of the strand formed by residues 22 - 33 (chain C) in PDB entry 3BXB
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 HIS 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C THR* 3.3 3.6 - - - +
19C VAL* 2.9 36.8 + - - +
20C ASN 3.2 2.9 + - - +
21C ASN* 1.3 78.3 - - - +
23C HIS* 1.3 74.6 + - - +
24C PHE* 4.0 3.3 - - + -
48C GLY* 2.7 34.0 + - - -
50C PRO 4.0 3.4 - - - -
51C LEU* 3.9 11.5 - - + +
52C PRO* 3.4 41.0 - - + +
53C PHE* 4.2 4.3 - + + -
133C MET* 6.4 0.2 - - + -
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Residues in contact with HIS 23 (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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16C GLU* 3.0 34.3 + - + +
17C GLY* 3.1 24.0 - - - -
18C THR* 3.8 13.2 - - - +
21C ASN 3.7 5.1 + - - +
22C HIS* 1.3 89.7 + - - +
24C PHE* 1.3 78.9 + - - +
25C LYS* 4.4 5.4 - - + -
47C GLU* 3.4 25.6 + - - -
48C GLY* 3.5 8.7 + - - -
122C ARG* 6.3 0.4 - - - -
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Residues in contact with PHE 24 (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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15C MET* 4.0 14.1 - - + -
17C GLY 3.3 42.6 + - - +
18C THR 3.9 3.8 - - - -
19C VAL* 4.1 8.3 - - + -
22C HIS* 4.0 7.2 - - + -
23C HIS* 1.3 85.9 - - - +
25C LYS* 1.3 70.3 + - - +
26C CYS* 3.7 23.6 - - - -
47C GLU* 3.6 14.1 - - - +
51C LEU* 3.2 30.7 - - + -
53C PHE* 4.0 16.4 - + - -
58C LEU* 3.6 36.3 - - + -
121C ILE* 4.4 14.1 - - + -
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Residues in contact with LYS 25 (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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15C MET 3.4 7.9 - - - +
16C GLU* 3.5 34.8 - - + -
23C HIS* 4.4 2.9 - - + -
24C PHE* 1.3 78.4 - - - +
26C CYS* 1.3 66.9 + - - +
45C VAL* 3.6 2.8 - - - +
46C VAL* 2.8 43.7 + - + -
47C GLU* 3.4 35.9 + - + +
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Residues in contact with CYS 26 (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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13C LEU* 4.6 0.4 - - - -
14C TYR* 3.6 0.3 - - - +
15C MET* 2.8 52.6 + - + +
24C PHE* 3.7 24.7 - - - -
25C LYS* 1.3 81.5 - - - +
27C THR* 1.3 69.2 + - - +
43C ILE* 4.5 2.5 - - + -
44C LYS 3.4 13.0 - - - +
45C VAL* 4.0 16.8 - - - -
46C VAL* 4.3 1.8 - - - -
51C LEU* 5.3 0.2 - - - -
55C PHE* 4.8 4.0 - - - -
58C LEU* 5.1 0.4 - - - -
62C PHE* 4.1 24.5 - - + -
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Residues in contact with THR 27 (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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13C LEU* 3.1 10.1 - - - -
14C TYR* 4.0 24.2 - - + -
26C CYS* 1.3 81.2 - - - +
28C SER* 1.3 62.6 + - - +
29C GLU* 6.5 0.2 - - - -
43C ILE* 3.8 2.3 - - - +
44C LYS* 3.0 37.4 + - - +
46C VAL* 4.0 26.6 - - + +
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Residues in contact with SER 28 (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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11C MET 4.0 0.3 - - - +
12C LYS* 3.4 1.4 - - - -
13C LEU* 2.8 54.0 + - - +
27C THR* 1.3 75.3 - - - +
29C GLU* 1.3 66.9 + - - +
41C MET* 3.4 23.7 - - - +
42C ARG 3.1 20.2 - - - -
43C ILE* 3.5 20.8 - - - +
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Residues in contact with GLU 29 (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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11C MET 3.5 5.6 - - - +
12C LYS* 3.0 35.1 - - - +
27C THR* 6.5 0.4 - - - -
28C SER* 1.3 79.4 - - - +
30C GLY* 1.3 59.9 + - - +
41C MET* 3.4 6.5 - - - +
42C ARG* 2.7 45.1 + - + +
44C LYS* 6.1 3.4 - - - +
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Residues in contact with GLY 30 (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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10C HIS* 3.4 9.4 + - - +
11C MET* 3.1 35.4 + - - +
29C GLU* 1.3 78.9 - - - +
31C GLU* 1.3 68.3 + - - +
40C THR 3.2 13.9 - - - -
41C MET* 4.1 0.4 - - - +
42C ARG* 3.8 12.1 - - - +
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Residues in contact with GLU 31 (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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9C MET 3.3 13.2 - - - +
10C HIS* 3.8 26.6 + - + +
11C MET* 3.7 6.9 - - - +
30C GLY* 1.3 77.2 - - - +
32C GLY* 1.3 60.1 + - - +
39C GLN* 3.6 0.3 - - - -
40C THR* 2.9 37.9 + - - +
42C ARG* 2.6 41.0 + - - -
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Residues in contact with GLY 32 (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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8C ASN* 3.7 4.7 - - - +
9C MET 2.9 32.8 + - - +
31C GLU* 1.3 78.4 - - - +
33C LYS* 1.3 66.7 + - - -
34C PRO* 3.2 1.7 - - - +
38C THR* 3.3 12.8 - - - -
39C GLN* 3.9 2.2 - - - -
69C PHE* 3.6 12.3 - - - -
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Residues in contact with LYS 33 (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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7C GLU* 3.3 17.6 + - + +
8C ASN* 2.9 41.2 + - - +
32C GLY* 1.3 74.6 - - - -
34C PRO* 1.4 66.8 - - - +
35C TYR 3.0 3.2 + - - +
36C GLU* 3.0 41.4 + - + +
37C GLY 2.9 19.2 + - - -
38C THR* 2.8 25.0 + - - +
69C PHE* 3.9 0.4 - - - -
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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