Contacts of the strand formed by residues 22 - 33 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H THR* 3.4 4.2 - - - +
19H VAL 3.3 29.8 + - - +
20H ASN 3.3 4.1 - - - +
21H ASN* 1.3 78.5 - - - +
23H HIS* 1.3 78.9 + - - +
24H PHE* 3.8 3.3 + - - +
48H GLY* 3.0 30.3 + - - -
50H PRO 4.4 2.0 + - - -
51H LEU* 4.3 7.6 - - + -
52H PRO* 3.4 43.3 - - + +
53H PHE* 4.5 6.3 - - + -
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Residues in contact with HIS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H GLU* 3.7 20.0 + - - -
17H GLY* 3.4 15.5 - - - -
18H THR* 4.3 10.5 - - + +
21H ASN 3.6 4.8 + - - +
22H HIS* 1.3 97.8 + - - +
24H PHE* 1.3 83.7 + - - +
25H LYS* 3.8 21.9 - - + +
47H GLU* 4.0 24.9 + - - +
48H GLY* 3.4 8.1 + - - -
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Residues in contact with PHE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H MET* 4.0 18.6 - - + -
16H GLU 4.9 0.4 - - - -
17H GLY* 2.9 59.4 + - - +
18H THR 4.0 3.1 - - - -
19H VAL* 4.3 8.5 - - + -
22H HIS* 4.3 4.9 - - + -
23H HIS* 1.3 87.5 - - - +
25H LYS* 1.3 71.4 + - - +
26H CYS* 3.6 25.4 - - + -
47H GLU 3.5 14.8 - - - +
48H GLY* 4.4 0.2 - - - -
51H LEU* 3.6 24.5 - - + -
53H PHE* 4.1 18.4 - + - -
58H LEU* 3.6 36.6 - - + -
121H ILE* 4.5 9.6 - - + -
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Residues in contact with LYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H MET 3.4 9.2 - - - +
16H GLU* 3.7 31.2 + - + +
23H HIS* 3.8 16.6 - - + -
24H PHE* 1.3 80.2 - - - +
26H CYS* 1.3 68.3 + - - +
45H VAL* 3.8 1.0 - - - +
46H VAL* 3.1 36.4 + - + -
47H GLU* 3.2 37.6 + - + +
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Residues in contact with CYS 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 4.9 0.2 - - - -
14H TYR* 3.8 0.3 - - - +
15H MET* 2.8 46.5 + - + +
24H PHE* 3.6 23.1 - - - -
25H LYS* 1.3 82.0 - - - +
27H THR* 1.3 69.1 + - - +
43H ILE* 4.5 1.6 - - + -
44H LYS 3.3 8.7 - - - +
45H VAL* 3.8 25.8 - - - -
46H VAL* 3.8 1.7 - - - +
55H PHE* 4.7 7.4 - - - -
58H LEU* 4.8 1.1 - - - -
62H PHE* 4.3 22.9 - - + -
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Residues in contact with THR 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.2 12.3 - - - +
14H TYR* 4.4 19.1 - - + -
26H CYS* 1.3 80.0 - - - +
28H SER* 1.3 62.4 + - - +
43H ILE* 3.5 2.6 - - - +
44H LYS* 2.7 43.0 + - - +
46H VAL* 3.7 29.9 - - + +
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Residues in contact with SER 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H MET 4.0 0.2 - - - +
12H LYS* 3.5 5.5 - - - +
13H LEU* 2.8 55.5 + - - +
27H THR* 1.3 79.6 - - - +
29H GLU* 1.3 61.2 + - - +
41H MET* 3.4 19.2 - - - +
42H ARG 3.2 15.0 - - - -
43H ILE* 3.8 19.1 - - - -
44H LYS* 6.1 0.2 - - - -
62H PHE* 4.0 5.6 - - - -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H MET 3.3 10.5 - - - +
12H LYS* 4.7 8.1 - - + +
28H SER* 1.3 73.7 - - - +
30H GLY* 1.3 66.4 + - - +
41H MET* 3.6 5.9 - - - +
42H ARG* 2.4 80.2 + - + +
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Residues in contact with GLY 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H HIS* 3.2 8.0 - - - +
11H MET* 2.8 34.1 + - - -
29H GLU* 1.3 80.9 + - - +
31H GLU* 1.3 64.0 + - - +
40H THR 3.4 14.1 - - - -
41H MET* 3.6 5.1 - - - +
42H ARG* 3.7 13.0 - - - -
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H MET 3.1 18.6 - - - +
10H HIS* 4.0 7.4 - - + +
11H MET* 3.7 8.0 - - - -
29H GLU* 4.6 0.2 - - - +
30H GLY* 1.3 74.1 - - - +
32H GLY* 1.3 57.7 + - - +
39H GLN* 3.7 0.3 - - - -
40H THR* 3.2 36.0 + - - -
42H ARG* 2.4 41.7 + - - -
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Residues in contact with GLY 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ASN* 3.5 4.6 - - - +
9H MET 2.9 32.9 + - - +
31H GLU* 1.3 78.4 - - - +
33H LYS* 1.3 69.1 + - - -
34H PRO* 3.2 2.9 - - - +
38H THR 3.1 13.5 - - - -
39H GLN* 4.0 1.3 - - - -
69H PHE* 3.6 12.9 - - - -
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU* 3.3 18.4 - - + +
8H ASN* 3.6 22.9 - - - +
32H GLY* 1.3 75.1 - - - -
34H PRO* 1.3 58.9 - - - +
35H TYR 3.3 0.7 - - - -
36H GLU* 3.7 32.8 - - + +
37H GLY* 2.7 33.1 + - - -
38H THR* 2.8 31.7 + - - +
69H PHE* 3.8 3.0 - - - -
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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