Contacts of the strand formed by residues 18 - 24 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35K ARG* 5.8 0.9 - - - +
39K GLU* 3.2 47.3 - - + +
40K LEU* 3.7 15.0 - - + -
57K HIS 4.2 9.9 - - - +
58K CYS 5.0 0.4 - - - +
60K PRO* 4.4 12.6 - - - +
16Q ALA* 3.9 12.6 - - + -
17Q ARG* 1.3 75.6 - - - +
19Q ILE* 1.3 61.7 + - - +
20Q ARG* 3.3 14.5 + - + +
33Q PHE 3.5 0.2 - - - +
35Q TYR* 2.7 54.2 + - + +
37Q GLY* 3.8 28.9 - - - +
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Residues in contact with ILE 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K PRO* 5.2 2.1 - - - -
38K GLN* 4.0 30.3 - - + +
39K GLU* 3.0 37.8 + - - +
17Q ARG* 3.8 36.3 - - + +
18Q ILE* 1.3 69.2 - - - +
20Q ARG* 1.3 61.1 + - - +
21Q TYR* 5.4 3.8 - - + -
32Q THR* 3.9 30.5 - - + -
33Q PHE 3.4 10.8 - - - +
34Q VAL* 4.0 14.8 - - + -
46Q LYS 5.2 2.4 - - - +
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Residues in contact with ARG 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K GLU* 3.0 35.5 + - - -
60K PRO* 2.7 74.7 + - - +
18Q ILE* 3.9 8.3 - - + +
19Q ILE* 1.3 76.3 - - - +
21Q TYR* 1.3 64.9 + - - +
32Q THR* 3.0 10.4 - - - -
33Q PHE* 2.8 52.1 + - + +
35Q TYR* 3.8 16.2 - - + -
44Q ASN* 2.9 23.6 + - - +
45Q PHE 3.2 24.7 + - - -
46Q LYS* 3.9 8.8 - - - +
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Residues in contact with TYR 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q ILE* 5.4 3.8 - - + -
20Q ARG* 1.3 78.1 - - - +
22Q PHE* 1.3 60.8 + - - +
30Q CYS 4.5 4.5 - - - -
31Q GLN* 3.1 23.1 - - - -
32Q THR* 3.4 25.7 - - + +
33Q PHE* 4.0 0.9 - - - -
44Q ASN* 3.5 4.3 - - - -
45Q PHE* 2.7 45.2 + - + +
46Q LYS 4.0 6.7 - - - -
47Q SER* 3.4 36.8 - - - +
48Q ALA* 3.6 27.5 - - + +
51Q CYS* 4.4 5.4 - - + -
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Residues in contact with PHE 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K THR* 4.9 4.9 - - + -
7Q GLU 5.1 0.2 - - - -
8Q PRO* 5.4 0.7 - - + -
9Q PRO* 3.6 35.0 - - + -
21Q TYR* 1.3 74.3 - - - +
23Q TYR* 1.3 69.4 + - - +
24Q ASN* 3.4 20.8 + - + -
30Q CYS* 3.1 1.6 - - - -
31Q GLN* 2.8 73.5 + - + -
32Q THR 3.8 11.4 - - - -
33Q PHE* 3.8 26.7 - + + -
43Q ASN* 3.6 28.7 - - - +
45Q PHE* 4.3 0.9 - - - -
51Q CYS* 3.7 4.5 - - - -
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Residues in contact with TYR 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q CYS* 3.4 32.3 - - + +
7Q GLU 4.7 0.9 - - - +
22Q PHE* 1.3 75.1 - - - +
24Q ASN* 1.3 58.9 + - - +
25Q ALA* 3.3 29.7 + - + -
28Q GLY* 3.3 39.8 + - - -
29Q LEU* 3.6 4.0 - - - -
30Q CYS* 3.8 17.3 - - - -
43Q ASN* 2.7 31.9 + - - +
51Q CYS* 3.6 7.2 - - - -
52Q MET* 4.2 7.9 - - + -
55Q CYS* 3.5 35.2 - - + -
57Q GLY* 4.2 6.3 + - - -
58Q ALA* 3.5 33.4 + - + -
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Residues in contact with ASN 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q PHE* 3.4 14.9 + - + -
23Q TYR* 1.3 70.3 - - - +
25Q ALA* 1.3 54.5 + - - +
26Q LYS* 3.2 19.4 + - - +
27Q ALA* 3.3 19.7 + - + +
28Q GLY* 2.7 30.8 + - - -
29Q LEU 2.8 23.4 + - - +
31Q GLN* 2.8 38.8 + - + +
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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