Contacts of the strand formed by residues 29 - 35 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B MET* 3.6 41.5 - - + +
53B ARG* 4.8 4.5 - - + +
56B GLY* 4.3 19.1 - - - -
23J TYR* 3.8 9.9 - - - -
24J ASN* 2.7 29.4 + - - +
27J ALA* 3.9 17.9 - - + +
28J GLY* 1.3 85.0 - - - +
30J CYS* 1.3 79.5 + - - +
31J GLN* 4.5 10.5 - - + +
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Residues in contact with CYS 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 3.0 36.3 - - + +
21J TYR* 4.6 9.2 - - + -
22J PHE 3.2 4.5 - - - -
23J TYR* 3.9 14.1 - - - -
29J LEU* 1.3 79.1 - - - +
31J GLN* 1.3 65.3 + - - +
51J CYS* 2.0 54.5 - - + -
52J MET* 3.4 19.7 - - - -
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Residues in contact with GLN 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ARG* 5.4 4.2 + - - -
21J TYR* 3.0 9.5 - - - +
22J PHE* 2.9 48.7 + - + -
24J ASN* 2.9 30.7 + - + +
27J ALA* 4.1 18.1 - - - +
29J LEU* 4.3 13.9 - - + +
30J CYS* 1.3 79.8 - - - +
32J THR* 1.3 66.5 + - - +
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Residues in contact with THR 32 (chain J).
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* 3.2 27.1 - - - +
53B ARG* 4.7 3.3 + - - +
20F ARG* 4.5 3.6 - - - +
35F TYR* 2.9 25.3 + - + -
37F GLY 3.0 12.2 + - - +
38F CYS* 3.9 9.2 - - - +
39F ARG* 4.9 2.8 + - - -
40F ALA* 5.3 0.3 - - - +
19J ILE* 3.9 17.5 - - + -
20J ARG 3.2 7.2 - - - -
21J TYR* 3.5 20.9 - - + -
22J PHE* 3.5 8.8 - - - -
31J GLN* 1.3 79.6 - - - +
33J PHE* 1.3 65.9 + - - +
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Residues in contact with PHE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLY 3.5 10.1 - - - -
38F CYS* 4.7 5.6 - - + -
9J PRO* 3.6 21.8 - - + -
10J TYR 3.6 25.8 - - - -
11J THR* 4.3 5.6 - - - -
19J ILE* 3.5 3.6 - - - -
20J ARG* 2.9 61.2 + - + +
21J TYR 3.7 12.8 - - - -
22J PHE* 3.6 30.5 - + + -
32J THR* 1.3 77.0 - - - +
34J VAL* 1.3 85.8 + - - +
35J TYR* 4.2 4.0 - - + -
43J ASN 4.3 3.4 - - - -
44J ASN* 3.7 27.8 - - + -
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Residues in contact with VAL 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F CYS* 4.1 6.8 - - + -
15F LYS* 3.7 34.1 - - + +
16F ALA* 3.9 11.2 - - + -
36F GLY 3.7 23.3 - - - +
37F GLY* 4.0 8.7 - - - +
38F CYS* 5.3 0.6 - - - +
11J THR* 2.9 30.9 + - + +
16J ALA 4.7 1.1 - - - +
17J ARG* 3.7 35.7 - - + +
18J ILE 3.4 3.4 - - - +
19J ILE* 5.2 1.6 - - + -
33J PHE* 1.3 81.7 - - - +
35J TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ILE* 4.1 8.5 - - + -
32I THR* 2.8 26.8 + - + -
10J TYR 4.0 7.4 - - - -
11J THR* 3.6 8.5 - - - -
16J ALA 3.4 3.7 - - - +
18J ILE* 2.7 32.9 + - - +
20J ARG* 3.3 52.9 - - + -
33J PHE* 3.7 6.4 + - + -
34J VAL* 1.3 73.0 - - - +
36J GLY* 1.3 68.5 + - - +
37J GLY* 3.4 17.7 + - - -
38J CYS* 3.0 40.0 + - - -
40J ALA* 3.3 29.8 + - + +
44J ASN* 3.4 13.2 - - - -
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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