Contacts of the strand formed by residues 25 - 30 (chain A) in PDB entry 5BZR
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 GLN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN* 1.3 79.3 + - - +
26A ILE* 1.3 72.0 + - - +
27A ASP* 2.9 23.1 + - - +
43A ASN* 4.3 9.3 + - - +
148A VAL* 4.1 0.2 - - - -
149A THR* 2.8 43.5 + - - +
151A THR* 2.8 26.5 + - - -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 5.7 0.7 - - - +
25A GLN* 1.3 80.8 + - - +
27A ASP* 1.3 68.2 + - - +
28A LEU* 3.7 29.4 - - + -
42A LYS* 3.9 24.5 - - + -
43A ASN* 3.7 5.4 - - - +
148A VAL* 3.8 21.5 - - + +
149A THR 2.9 7.0 + - - +
150A ILE* 3.4 7.5 - - + +
151A THR 2.8 26.0 + - - +
165A GLU* 5.2 0.7 - - - +
166A TYR* 3.8 29.2 - - + +
167A ARG* 4.0 25.6 - - - +
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 2.9 33.3 + - - +
26A ILE* 1.3 73.4 - - - +
28A LEU* 1.3 63.7 + - - +
29A ASN* 4.0 5.6 - - - +
41A GLU 3.7 0.2 - - - +
42A LYS* 3.4 4.9 - - - -
43A ASN* 2.8 46.5 + - - +
151A THR* 3.4 12.6 - - - +
153A VAL* 4.1 8.9 - - + +
159A ARG* 3.2 26.3 + - - -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.7 18.4 - - + -
27A ASP* 1.3 81.6 - - - +
29A ASN* 1.3 64.1 + - - +
30A VAL* 3.6 5.3 + - + +
40A VAL* 4.0 12.8 - - + -
41A GLU 3.6 2.2 - - - -
42A LYS* 4.2 11.2 - - + -
56A LEU* 3.6 43.7 - - + -
60A PHE* 4.2 7.4 - - + -
140A LEU* 4.8 3.4 - - + -
150A ILE* 3.7 25.6 - - + -
151A THR 2.8 10.8 + - - +
152A ILE* 3.5 19.5 - - + -
153A VAL 2.8 25.6 + - - +
166A TYR* 4.3 4.3 - - + +
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 4.8 5.1 - - - +
28A LEU* 1.3 73.4 + - - +
30A VAL* 1.3 58.7 + - - +
39A HIS* 3.6 2.4 + - - +
40A VAL* 3.3 5.7 - - - -
41A GLU* 2.9 63.9 + - + +
44A GLY* 4.2 13.9 - - - +
153A VAL* 3.3 27.0 - - - +
202A 4XM 3.5 42.0 + - + +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU 3.9 11.2 - - - +
29A ASN* 1.3 77.7 - - - +
31A THR* 1.3 63.1 + - - +
38A PHE* 4.5 7.6 - - + -
39A HIS 3.3 5.6 - - - +
40A VAL* 4.2 12.8 - - + -
60A PHE* 4.0 28.7 - - + -
137A VAL* 3.8 17.3 - - + -
152A ILE* 3.8 15.0 - - + -
153A VAL 3.0 9.9 + - - +
154A ASN* 3.5 23.5 - - - +
155A ARG* 3.9 8.8 + - - +
201A DMS 5.6 0.7 - - - -
202A 4XM 3.2 20.6 + - - -
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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