Contacts of the strand formed by residues 29 - 35 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E MET* 3.7 44.2 - - + +
53E ARG* 4.8 4.5 - - + +
56E GLY* 4.3 18.8 - - - -
23G TYR* 3.6 9.0 - - - -
24G ASN* 2.7 36.6 + - - +
27G ALA* 3.2 17.7 - - + +
28G GLY* 1.3 84.0 - - - +
30G CYS* 1.3 72.5 + - - +
31G GLN* 4.6 10.8 - - + +
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Residues in contact with CYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E MET* 3.1 33.3 - - + +
21G TYR* 4.6 9.0 - - + -
22G PHE 3.1 4.5 - - - -
23G TYR* 3.9 15.9 - - - -
29G LEU* 1.3 79.8 - - - +
31G GLN* 1.3 67.1 + - - +
48G ALA 5.0 0.2 - - - +
51G CYS* 2.0 63.9 - - + -
52G MET* 3.5 8.1 - - - -
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Residues in contact with GLN 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G TYR* 3.1 9.1 - - - -
22G PHE* 2.8 48.5 + - + -
24G ASN* 2.7 34.1 + - + +
27G ALA* 4.1 15.3 - - - +
29G LEU* 4.2 15.8 - - + +
30G CYS* 1.3 80.9 - - - +
32G THR* 1.3 66.2 + - - +
39H ARG* 5.4 4.0 + - - -
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Residues in contact with THR 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU* 3.2 27.1 - - - +
53E ARG* 4.6 4.5 + - - +
19G ILE* 3.9 17.5 - - + -
20G ARG 3.1 7.2 - - - -
21G TYR* 3.5 19.5 - - + -
22G PHE* 3.4 10.2 - - - -
31G GLN* 1.3 77.8 - - - +
33G PHE* 1.3 65.5 + - - +
20H ARG* 4.5 3.1 - - - +
35H TYR* 3.0 19.3 + - + +
37H GLY 2.9 17.7 + - - +
38H CYS* 3.9 9.7 - - - +
39H ARG* 4.9 2.8 + - - -
40H ALA* 5.2 0.2 - - - +
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Residues in contact with PHE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G PRO* 3.7 21.3 - - + -
10G TYR 3.5 28.5 - - - -
11G THR* 4.3 5.2 - - - -
19G ILE* 3.4 3.5 - - - -
20G ARG* 2.9 55.6 + - + -
21G TYR 3.6 14.4 - - - -
22G PHE* 3.6 28.5 - + + -
32G THR* 1.3 77.2 - - - +
34G VAL* 1.3 76.7 + - - +
35G TYR* 4.2 3.4 - - + -
43G ASN 4.3 5.8 - - - -
44G ASN* 3.9 23.8 - - + -
37H GLY 3.6 10.3 - - - -
38H CYS* 4.6 5.2 - - + -
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G THR* 2.7 33.7 + - + +
16G ALA 4.5 1.1 - - - +
17G ARG* 3.6 35.0 - - + +
18G ILE 3.3 4.5 - - - +
19G ILE* 5.1 1.3 - - + -
33G PHE* 1.3 77.2 - - - +
35G TYR* 1.3 62.8 + - - +
14H CYS* 4.2 13.1 - - + -
15H LYS* 4.0 25.6 - - + +
16H ALA* 3.9 12.6 - - + +
36H GLY 3.7 22.9 - - - +
37H GLY* 4.0 9.6 - - - -
38H CYS* 5.3 1.2 - - - +
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Residues in contact with TYR 35 (chain G).
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* 5.1 0.2 - - - -
19F ILE* 4.0 17.9 - - + -
32F THR* 2.7 25.8 + - + -
10G TYR 3.9 8.3 - - - -
11G THR* 3.6 8.7 - - - -
16G ALA 3.3 3.0 - - - +
18G ILE* 2.6 34.8 + - + +
20G ARG* 3.4 39.0 - - + -
33G PHE* 3.7 6.0 + + + -
34G VAL* 1.3 73.2 - - - +
36G GLY* 1.3 66.5 + - - +
37G GLY* 3.4 20.7 + - - -
38G CYS* 3.1 33.6 + - - -
40G ALA* 3.1 36.0 + - + +
44G ASN* 3.4 17.3 - - - -
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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