Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 4OD9
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY* 3.2 2.2 - - - -
21A ILE 2.9 34.4 + - - +
24A PRO* 4.3 5.6 - - + +
25A PRO* 1.3 73.4 - - - +
27A CYS* 1.3 60.6 + - - +
28A PHE* 3.1 18.6 - - + -
58A LYS 3.9 4.9 + - - -
59A TYR* 3.5 20.2 - - - +
60A ASN* 2.8 52.7 - - - +
63A LYS* 3.8 23.8 - - + +
64A SER* 4.4 4.2 + - - -
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Residues in contact with CYS 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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18A GLU* 3.7 24.0 - - - +
19A ILE 3.3 4.0 - - - +
25A PRO 4.0 0.2 + - - -
26A GLN* 1.3 73.3 - - - +
28A PHE* 1.3 69.6 + - - +
57A HIS* 3.8 19.1 - - + +
96A CYS* 2.0 44.0 - - - -
98A SER* 3.3 17.9 - - - -
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Residues in contact with PHE 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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18A GLU* 3.3 5.2 - - - -
19A ILE* 2.8 40.5 + - + +
21A ILE* 4.0 29.6 - - + -
26A GLN* 3.1 43.3 - - + -
27A CYS* 1.3 74.2 - - - +
29A THR* 1.3 64.5 + - - +
41A VAL* 3.7 32.5 - - + -
57A HIS* 3.6 29.2 - - + -
58A LYS 3.7 4.7 - - - -
59A TYR* 3.5 43.1 - - + -
132B ASP* 3.4 11.9 - - + +
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Residues in contact with THR 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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8A LYS* 6.4 1.3 - - + -
16A TYR* 3.8 30.3 - - + -
17A GLY 3.3 11.7 - - - +
18A GLU* 4.6 11.0 - - + +
28A PHE* 1.3 76.8 - - - +
30A VAL* 1.3 61.4 + - - +
57A HIS* 5.2 5.3 + - + +
130B LYS 3.9 4.0 + - - +
131B PHE* 3.3 7.3 - - - -
132B ASP* 2.9 50.3 + - - +
133B GLY 3.0 8.0 + - - -
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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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16A TYR* 3.2 6.9 - - - -
17A GLY 2.9 32.7 + - - +
19A ILE* 3.8 47.3 - - + -
28A PHE* 4.7 0.2 - - + -
29A THR* 1.3 80.9 - - - +
31A VAL* 1.3 61.0 + - - +
32A PHE* 3.6 10.3 + - + -
39A LEU* 4.4 2.5 - - + -
41A VAL* 4.3 11.0 - - + -
131B PHE* 4.4 0.7 - - - -
133B GLY* 3.2 25.1 - - - +
134B ILE 4.0 4.7 - - - +
135B LEU* 3.8 23.1 - - + +
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Residues in contact with VAL 31 (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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15A TYR 3.5 25.1 - - - +
16A TYR* 4.4 0.9 - - + -
30A VAL* 1.3 71.9 - - - +
32A PHE* 1.4 70.0 + - - +
33A ASP* 3.2 16.4 + - + +
103A 2RZ 4.5 12.8 - - - -
131B PHE* 3.4 39.5 - - + -
133B GLY 3.2 5.5 + - - -
134B ILE* 3.7 16.6 - - + -
135B LEU 2.9 23.5 + - - -
232B THR 4.5 4.7 - - - +
233B GLY* 4.2 15.9 - - - -
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Residues in contact with PHE 32 (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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5A GLU* 3.3 40.2 - - + -
7A LEU* 3.6 17.5 - - + -
15A TYR 4.3 2.3 + - - +
16A TYR* 5.2 0.2 - - - -
17A GLY* 3.8 15.3 - - - -
19A ILE* 3.6 18.2 - - + -
30A VAL* 3.8 10.3 - - + -
31A VAL* 1.4 72.6 - - - +
33A ASP* 1.3 52.1 + - - +
94A VAL* 4.3 8.7 - - + -
135B LEU* 3.5 34.1 - - + -
137B MET* 3.9 13.9 - - + -
167B PHE* 3.6 28.2 - - + -
181B LEU* 3.4 21.1 - - + -
183B LEU* 5.9 1.1 - - + -
232B THR* 2.7 26.4 + - - -
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Residues in contact with ASP 33 (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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31A VAL* 3.8 8.1 - - + +
32A PHE* 1.3 70.7 - - - +
34A THR* 1.3 55.2 + - - +
35A GLY 2.9 14.0 + - - -
36A SER* 2.9 28.5 + - - +
103A 2RZ 2.7 48.5 + - - +
134B ILE* 3.6 25.6 - - + +
135B LEU 3.0 8.8 + - - +
136B GLY* 3.4 0.2 - - - -
137B MET 2.7 27.6 + - - +
231B ASP* 2.9 5.0 - - - +
232B THR* 3.4 2.7 - - - -
233B GLY* 3.3 7.0 - - - +
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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