Contacts of the strand formed by residues 18 - 24 (chain P) in PDB entry 1BTH
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 ILE 18 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35H ARG* 5.1 1.6 - - - +
39H GLU* 2.8 43.3 - - + +
40H LEU* 3.8 17.7 - - + -
57H HIS 4.3 10.1 - - - +
58H CYS 5.0 1.3 - - - +
60H TYR* 4.4 14.1 - - + +
16P ALA* 4.2 11.4 - - + -
17P ARG* 1.3 72.3 - - - +
19P ILE* 1.3 61.5 + - - +
20P ARG* 3.2 14.0 + - + +
34P VAL* 4.4 0.4 - - - +
35P TYR* 2.9 53.0 + - + +
37P GLY* 3.9 26.9 - - - -
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Residues in contact with ILE 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PRO* 5.4 1.2 - - - -
38H GLN* 3.9 34.5 - - + +
39H GLU* 3.0 40.8 - - - +
17P ARG* 3.6 33.0 - - + +
18P ILE* 1.3 68.7 - - - +
20P ARG* 1.3 64.7 + - - +
21P TYR* 5.7 2.8 - - + -
32P THR* 4.0 28.9 - - + -
33P PHE 3.6 4.7 - - - +
34P VAL* 3.9 19.3 - - + -
46P LYS 5.3 1.7 - - - +
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Residues in contact with ARG 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLU* 3.5 13.5 + - - -
60H PRO* 2.7 83.9 + - - +
18P ILE* 3.2 19.2 + - + +
19P ILE* 1.3 79.2 - - - +
21P TYR* 1.3 65.2 + - - +
32P THR* 2.8 7.9 - - - -
33P PHE* 2.7 57.8 + - + -
35P TYR* 4.2 9.6 - - + -
44P ASN* 2.7 36.5 + - - +
45P PHE 3.7 8.2 + - - -
46P LYS* 3.6 19.8 - - - +
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Residues in contact with TYR 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P ILE* 5.8 2.7 - - + -
20P ARG* 1.3 75.8 - - - +
22P PHE* 1.3 60.0 + - - +
30P CYS 4.5 3.6 - - - -
31P GLN* 3.0 24.5 - - - -
32P THR* 3.2 28.2 - - + +
33P PHE* 4.0 1.6 - - - -
44P ASN* 3.6 3.8 - - - -
45P PHE* 2.7 45.2 + - - +
46P LYS 3.8 7.6 - - - -
47P SER* 3.4 23.6 - - - +
48P ALA* 3.4 40.1 - - + +
51P CYS* 4.2 9.6 - - + -
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Residues in contact with PHE 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H THR* 5.2 3.1 - - + -
7P GLU 5.1 0.4 - - - -
9P PRO* 3.5 38.6 - - + -
21P TYR* 1.3 74.8 - - - +
23P TYR* 1.3 69.8 + - - +
24P ASN* 3.9 22.4 - - + -
30P CYS* 3.2 2.8 - - - -
31P GLN* 2.7 91.5 + - + -
32P THR 3.8 9.9 - - - -
33P PHE* 4.0 24.2 - + + -
43P ASN* 3.4 27.1 - - - +
51P CYS* 3.6 5.4 - - - -
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Residues in contact with TYR 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P CYS* 3.2 37.2 - - + +
7P GLU 4.6 1.0 - - - +
22P PHE* 1.3 76.1 - - - +
24P ASN* 1.3 58.3 + - - +
25P ALA* 3.3 24.6 + - + +
28P GLY* 3.4 39.5 + - - -
29P LEU* 4.0 2.2 - - - -
30P CYS* 4.0 14.6 - - - -
43P ASN* 2.7 31.0 + - - +
51P CYS* 3.6 8.1 - - - -
52P MET* 4.4 4.5 - - - -
55P CYS* 3.4 40.8 - - + -
57P GLY* 3.7 9.0 - - - -
58P ALA* 3.3 33.9 + - + -
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Residues in contact with ASN 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P PHE* 3.4 19.4 + - + -
23P TYR* 1.3 71.4 - - - +
25P ALA* 1.3 54.0 + - - +
26P LYS* 3.5 19.2 + - - +
27P ALA* 3.8 14.9 - - + +
28P GLY* 2.6 31.4 + - - -
29P LEU 2.8 23.0 + - - +
31P GLN* 2.6 38.1 + - + +
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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