Contacts of the strand formed by residues 22 - 33 (chain A) in PDB entry 3BX9
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A THR* 3.2 4.8 - - - +
19A VAL 2.9 34.4 + - - +
20A ASN 3.2 1.9 + - - +
21A ASN* 1.3 75.5 - - - +
23A HIS* 1.3 83.0 + - - +
24A PHE* 3.7 5.6 - - - +
48A GLY* 2.4 36.4 + - - -
50A PRO 4.5 2.4 + - - -
51A LEU* 4.6 2.0 - - + -
52A PRO* 3.4 41.6 - - + +
53A PHE* 4.4 8.8 - - + -
133A MET* 6.2 0.9 - - + -
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Residues in contact with HIS 23 (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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16A GLU* 2.7 36.1 + - + +
17A GLY* 3.4 20.6 - - - -
18A THR* 3.6 16.3 - - + +
21A ASN 3.8 3.2 + - - -
22A HIS* 1.3 94.1 + - - +
24A PHE* 1.3 66.7 + - - +
25A LYS* 4.5 2.9 - - + -
47A GLU* 2.8 38.6 + - - +
48A GLY* 3.4 8.7 - - - -
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Residues in contact with PHE 24 (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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15A MET* 3.8 21.5 - - + -
16A GLU* 3.7 2.6 - - - +
17A GLY 3.0 56.4 + - - +
18A THR 3.7 3.8 - - - -
19A VAL* 3.8 10.1 - - + -
22A HIS* 3.7 11.0 - - - +
23A HIS* 1.3 77.2 - - - +
25A LYS* 1.3 69.6 + - - +
26A CYS* 4.0 14.6 - - - -
47A GLU* 3.2 18.8 - - - +
48A GLY* 4.6 0.2 - - - -
51A LEU* 3.6 24.2 - - + -
53A PHE* 3.8 19.1 - + - -
58A LEU* 3.8 36.3 - - + -
121A ILE* 4.1 11.2 - - + -
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Residues in contact with LYS 25 (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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15A MET 3.2 11.4 - - - +
16A GLU* 3.6 39.0 - - + +
23A HIS* 4.5 2.9 - - + -
24A PHE* 1.3 79.9 - - - +
26A CYS* 1.3 64.9 + - - +
45A VAL* 3.6 4.7 - - - +
46A VAL* 2.8 40.6 + - + -
47A GLU* 3.1 33.1 + - + +
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Residues in contact with CYS 26 (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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13A LEU* 4.8 0.2 - - - -
15A MET* 2.9 40.2 + - + +
24A PHE* 4.0 18.4 - - - -
25A LYS* 1.3 79.1 - - - +
27A THR* 1.3 68.4 + - - +
43A ILE* 4.1 13.0 - - + -
44A LYS 3.1 11.4 - - - +
45A VAL* 4.0 23.3 - - - -
46A VAL* 4.2 2.2 - - - +
51A LEU* 5.2 0.2 - - - -
55A PHE* 4.8 0.9 - - - -
58A LEU* 4.6 5.8 - - - -
62A PHE* 4.1 24.7 - - + -
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Residues in contact with THR 27 (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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13A LEU* 3.3 10.5 - - - -
14A TYR* 4.0 25.8 - - + -
26A CYS* 1.3 80.6 - - - +
28A SER* 1.3 63.6 + - - +
43A ILE* 3.5 2.5 - - - +
44A LYS* 2.9 37.0 + - - +
46A VAL* 3.5 27.9 - - + +
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Residues in contact with SER 28 (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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12A LYS* 3.4 5.1 - - - +
13A LEU* 2.9 53.4 + - - +
27A THR* 1.3 78.0 - - - +
29A GLU* 1.3 67.4 - - - +
41A MET* 3.4 20.0 - - - +
42A ARG 3.2 15.0 - - - -
43A ILE* 3.6 20.9 - - - -
62A PHE* 4.7 0.2 - - - -
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Residues in contact with GLU 29 (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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10A HIS* 2.8 34.6 + - + +
11A MET 3.4 5.6 - - - -
12A LYS* 2.5 43.6 + - - +
28A SER* 1.3 76.4 - - - +
30A GLY* 1.3 57.9 + - - +
41A MET* 4.4 4.0 - - - -
42A ARG* 2.8 46.0 + - + +
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Residues in contact with GLY 30 (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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10A HIS* 3.1 15.4 + - - -
11A MET* 2.9 38.5 + - - -
29A GLU* 1.3 74.7 - - - +
31A GLU* 1.3 61.8 + - - -
40A THR 3.1 16.6 - - - -
41A MET* 4.1 4.9 - - - +
42A ARG* 5.6 6.1 - - - -
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Residues in contact with GLU 31 (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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8A ASN* 3.4 27.0 - - - +
9A MET 3.0 27.0 + - - +
10A HIS* 3.2 27.5 + - + +
11A MET* 3.5 6.3 - - - +
30A GLY* 1.3 73.7 - - - +
32A GLY* 1.3 61.7 + - - +
39A GLN* 3.5 1.4 - - - -
40A THR* 2.9 29.3 + - - +
236A CIT 3.3 36.5 - - + +
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Residues in contact with GLY 32 (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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8A ASN* 3.5 5.4 - - - +
9A MET 2.9 32.3 + - - -
31A GLU* 1.3 79.0 - - - +
33A LYS* 1.3 66.4 + - - +
34A PRO* 3.4 1.0 - - - +
38A THR 3.2 13.5 - - - -
39A GLN* 3.9 0.9 - - - -
69A PHE* 3.4 14.0 - - - -
236A CIT 3.7 8.8 - - - +
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Residues in contact with LYS 33 (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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7A GLU* 3.4 29.0 + - + +
8A ASN* 2.5 33.4 + - - +
32A GLY* 1.3 76.2 - - - -
34A PRO* 1.3 68.7 - - - +
35A TYR 3.1 3.2 + - - -
36A GLU* 3.2 40.0 + - + +
37A GLY 3.0 18.2 + - - -
38A THR* 2.8 17.2 + - - +
236A CIT 3.6 32.5 + - - +
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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
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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