Contacts of the strand formed by residues 29 - 35 (chain F) in PDB entry 1BHC
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 LEU 29 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A MET* 3.7 32.8 - - + +
53A ARG* 4.8 4.3 - - - +
56A GLY* 4.3 26.5 - - - -
23F TYR* 3.8 8.3 - - - -
24F ASN* 2.7 36.8 + - - +
27F ALA* 3.2 18.8 - - + +
28F GLY* 1.3 84.8 - - - +
30F CYS* 1.3 73.0 + - - +
31F GLN* 4.5 10.8 - - + +
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Residues in contact with CYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A MET* 2.9 35.3 - - + +
21F TYR* 4.6 8.1 - - + -
22F PHE 3.0 4.9 - - - +
23F TYR* 3.9 13.9 - - - -
29F LEU* 1.3 79.9 - - - +
31F GLN* 1.3 62.6 + - - +
48F ALA 5.1 0.2 - - - +
51F CYS* 2.0 65.3 - - + -
52F MET* 3.5 8.7 - - - -
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Residues in contact with GLN 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TYR* 3.1 8.0 - - - +
22F PHE* 2.8 44.1 + - + -
24F ASN* 2.6 35.3 + - + +
27F ALA* 4.2 14.5 - - - +
29F LEU* 4.0 17.5 - - + +
30F CYS* 1.3 80.7 - - - +
32F THR* 1.3 65.3 + - - +
59F SCN 3.4 29.5 + - - -
39G ARG* 5.9 0.2 + - - -
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Residues in contact with THR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.1 27.6 - - + +
53A ARG* 4.5 4.7 - - - +
19F ILE* 4.0 15.9 - - + -
20F ARG 3.1 7.6 - - - -
21F TYR* 3.6 19.3 - - + -
22F PHE* 3.3 4.6 - - - -
31F GLN* 1.3 76.8 - - - +
33F PHE* 1.3 64.6 + - - +
59F SCN 2.9 29.0 + - - -
20G ARG* 4.3 3.6 - - - +
35G TYR* 2.7 27.9 + - + -
37G GLY 3.1 8.2 + - - +
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Residues in contact with PHE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F PRO* 3.5 23.1 - - + -
10F TYR 3.5 27.6 - - - -
11F THR* 4.4 5.2 - - - -
19F ILE* 3.4 4.7 - - - -
20F ARG* 2.9 56.1 + - + +
21F TYR 3.6 14.4 - - - -
22F PHE* 3.6 27.1 - + + -
32F THR* 1.3 76.8 - - - +
34F VAL* 1.3 73.1 + - - +
35F TYR* 3.6 6.7 + - + -
43F ASN 4.3 4.3 - - - -
44F ASN* 3.7 26.9 - - + -
59F SCN 5.4 0.2 - - - +
37G GLY 3.4 11.4 - - - +
38G CYS* 4.4 6.1 - - + -
39G ARG* 6.4 0.2 - - - +
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F THR* 2.7 36.3 + - + +
16F ALA 4.6 1.6 - - - +
17F ARG* 3.7 34.5 - - + +
18F ILE 3.4 4.0 - - - +
19F ILE* 5.0 0.9 - - + -
33F PHE* 1.3 76.6 - - - +
35F TYR* 1.3 61.8 + - - +
14G CYS* 4.1 10.9 - - + -
15G LYS* 4.0 24.2 - - + +
16G ALA* 3.7 14.4 - - + +
36G GLY 3.4 25.1 - - - +
37G GLY* 3.8 11.0 + - - +
38G CYS* 5.0 1.6 - - - +
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Residues in contact with TYR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 5.0 0.2 - - - -
10F TYR 3.9 7.9 - - - -
11F THR* 3.6 9.2 - - - -
16F ALA 3.5 2.6 - - - +
17F ARG* 3.9 0.3 - - - -
18F ILE* 2.7 34.0 + - + +
20F ARG* 3.4 49.1 - - + -
33F PHE* 3.6 5.7 + - + -
34F VAL* 1.3 73.5 - - - +
36F GLY* 1.3 67.5 + - - +
37F GLY* 3.5 18.2 + - - -
38F CYS* 3.1 35.1 + - - -
40F ALA* 3.1 34.9 + - + +
44F ASN* 3.4 17.0 - - - +
19J ILE* 4.3 9.6 - - + -
32J THR* 2.9 24.9 + - + +
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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