Contacts of the strand formed by residues 31 - 37 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E TYR* 3.8 3.4 - - - -
28E VAL* 2.9 36.7 + - - +
29E ASP 3.3 1.4 + - - -
30E ASP* 1.3 77.9 - - - +
32E GLN* 1.3 74.5 + - - +
33E PHE* 3.4 1.4 + - - +
49E ALA* 4.9 2.0 - - + -
51E TRP* 4.4 11.9 - - + +
179E LEU* 4.0 21.9 - - + +
209E TYR* 2.8 33.1 + - - -
239E GLY* 6.6 0.2 - - - -
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E VAL* 3.7 11.2 - - + +
26E GLY 3.3 17.9 - - - +
27E TYR* 3.7 33.3 + - + +
30E ASP 4.2 0.2 + - - -
31E THR* 1.3 83.0 - - - +
33E PHE* 1.3 58.1 + - - +
34E VAL 3.1 18.8 + - - +
35E ARG* 3.6 2.6 - - - +
48E ARG* 3.5 30.0 + - + +
49E ALA* 3.7 2.1 - - - +
52F SER* 5.3 4.0 - - - -
53F ASP* 2.7 42.9 + - - +
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Residues in contact with PHE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 3.5 23.3 - - + -
7E TYR* 3.3 24.5 - + - -
26E GLY* 3.0 17.9 + - - -
27E TYR 3.4 21.5 - - - -
28E VAL* 3.5 15.5 - - + -
31E THR 4.4 0.2 - - - +
32E GLN* 1.3 74.6 - - - +
34E VAL* 1.3 98.6 + - + +
47E PRO* 4.0 0.5 - - - +
48E ARG* 3.2 20.2 + - - -
49E ALA* 3.6 11.1 + - + -
51E TRP* 3.5 31.2 - + + -
52E MET* 4.0 19.7 - - + +
59E TYR* 4.1 1.3 - - - -
171E TYR* 3.6 27.8 - + - -
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 3.9 13.0 - - + +
26E GLY* 3.2 37.3 + - - +
32E GLN* 3.1 12.6 + - - +
33E PHE* 1.3 114.2 - - + +
35E ARG* 1.3 68.6 + - - +
45E MET* 4.1 15.0 - - + -
46E VAL 3.4 8.7 - - - +
48E ARG* 3.7 6.1 - - - +
52E MET* 4.4 2.5 - - + -
59E TYR* 4.5 2.7 - - - +
60E TRP* 4.0 29.6 - - + -
63E GLU* 6.1 0.2 - - - +
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 5.5 1.3 - - - -
24E SER 3.0 14.4 - - - +
25E VAL* 4.0 1.6 - - + -
32E GLN* 3.6 1.6 - - - +
34E VAL* 1.3 83.2 - - - +
36E PHE* 1.3 73.0 + - - +
37E ASP* 3.9 19.1 - - - +
40E ALA* 4.2 18.8 - - - +
42E SER 5.8 1.4 + - - -
44E ARG 5.5 0.8 + - - -
45E MET* 3.4 7.5 - - - +
46E VAL* 2.9 50.4 + - + +
48E ARG* 3.7 27.5 - - + +
53F ASP* 2.9 48.3 + - - +
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Residues in contact with PHE 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E PHE* 3.9 25.4 - + - -
23E ILE* 3.2 7.6 - - - +
24E SER* 2.8 35.4 + - - -
35E ARG* 1.3 78.2 - - - +
37E ASP* 1.3 63.4 + - - +
38E ASN* 3.7 29.8 - - + -
43E PRO* 4.0 9.0 - - + -
44E ARG* 3.4 43.1 - - - -
45E MET* 3.4 15.0 - - - -
64E THR* 4.4 2.9 - - - -
67E ALA* 3.4 32.5 - - + -
68E ARG* 4.1 25.6 - - + -
71E ALA* 5.1 1.8 - - + -
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Residues in contact with ASP 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ARG* 3.0 36.6 + - - -
22E PHE 3.6 4.5 - - - -
23E ILE* 3.9 12.4 - - + +
35E ARG* 3.9 21.7 - - - +
36E PHE* 1.3 81.6 - - - +
38E ASN* 1.3 57.7 + - - +
39E ASP* 2.7 35.6 + - - +
40E ALA* 3.0 27.7 + - + +
42E SER 4.7 0.7 + - - +
43E PRO* 4.1 10.5 - - - +
44E ARG 4.8 2.4 + - - -
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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