Contacts of the strand formed by residues 31 - 37 (chain G) in PDB entry 3BZE
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 THR 31 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G TYR* 3.7 2.9 - - - -
28G VAL* 2.8 39.9 + - - +
29G ASP 3.4 1.2 + - - -
30G ASP* 1.3 75.7 - - - +
32G GLN* 1.3 74.4 + - - +
33G PHE* 3.5 1.2 + - - +
49G ALA* 4.9 2.2 - - + -
51G TRP* 4.5 11.7 - - + +
179G LEU* 4.0 25.4 - - + +
209G TYR* 2.8 31.5 + - - -
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Residues in contact with GLN 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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25G VAL* 3.5 14.0 - - + +
26G GLY 3.3 17.9 - - - +
27G TYR* 3.5 36.0 + - + +
31G THR* 1.3 81.5 - - - +
33G PHE* 1.3 60.0 + - - +
34G VAL 3.1 20.2 + - - +
35G ARG* 3.6 2.0 - - - +
48G ARG* 3.7 26.5 + - + +
49G ALA* 3.7 2.6 - - - +
52H SER* 5.4 2.8 - - - -
53H ASP* 3.2 42.6 + - - +
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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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5G LEU* 3.6 21.3 - - + -
7G TYR* 3.5 20.9 - + - -
26G GLY* 3.0 32.2 + - - -
27G TYR* 3.4 6.5 - - - -
28G VAL* 3.5 16.4 - - + -
32G GLN* 1.3 74.2 - - - +
34G VAL* 1.3 100.4 + - + +
47G PRO 3.8 0.2 - - - -
48G ARG* 3.1 20.7 + - - -
49G ALA* 3.7 10.2 + - + +
51G TRP* 3.3 30.7 - + + -
52G MET* 3.7 22.5 - - + +
59G TYR* 4.1 2.7 - - - -
171G TYR* 3.7 27.8 - + - -
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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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7G TYR* 4.1 13.0 - - + +
25G VAL* 3.5 0.4 - - - -
26G GLY* 3.1 36.6 + - - +
32G GLN* 3.1 15.2 + - - +
33G PHE* 1.3 116.0 - - + +
35G ARG* 1.3 61.7 + - - +
45G MET* 4.2 15.0 - - + -
46G VAL 3.4 15.3 - - - +
48G ARG* 3.6 7.0 - - - +
52G MET* 3.9 13.2 - - + -
59G TYR* 4.4 4.0 - - - +
60G TRP* 4.1 12.6 - - + -
63G GLU* 5.7 0.7 - - - +
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Residues in contact with ARG 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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23G ILE* 5.8 2.2 - - - -
24G SER 3.0 14.1 - - - +
25G VAL* 3.9 2.7 - - + -
32G GLN* 3.6 4.0 - - - +
34G VAL* 1.3 80.3 - - - +
36G PHE* 1.3 70.2 + - - +
37G ASP* 4.5 15.8 - - - +
40G ALA* 4.9 12.3 - - - +
44G ARG 4.0 1.0 + - - +
45G MET* 3.6 5.6 - - - -
46G VAL* 3.0 48.6 + - + +
48G ARG* 2.9 42.5 - - + +
53H ASP* 3.1 33.8 + - - +
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Residues in contact with PHE 36 (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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22G PHE* 3.9 26.9 - + - -
23G ILE* 3.3 9.5 - - - +
24G SER* 2.9 34.8 + - - -
35G ARG* 1.3 77.6 - - - +
37G ASP* 1.3 62.4 + - - +
38G ASN* 3.5 32.1 - - + -
43G PRO* 3.7 10.1 - - + -
44G ARG* 3.3 43.3 - - - -
45G MET* 3.4 17.9 - - - -
64G THR* 4.4 3.1 - - - -
67G ALA* 3.4 29.6 - - + -
68G ARG* 4.1 23.1 - - + -
71G ALA* 5.1 2.0 - - + -
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Residues in contact with ASP 37 (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 ARG* 3.1 27.2 + - - -
22G PHE 3.6 3.6 - - - -
23G ILE* 4.0 13.7 - - + +
35G ARG* 4.5 15.0 - - - +
36G PHE* 1.3 80.8 - - - +
38G ASN* 1.3 59.8 + - - +
39G ASP* 2.7 46.0 + - - +
40G ALA* 2.9 29.2 + - + +
42G SER 4.0 6.3 + - - +
43G PRO* 4.3 2.1 - - - +
44G ARG 4.7 3.0 + - - -
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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