Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 2UZC
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 MET 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLN* 3.8 34.5 - - + +
20A GLY* 3.6 15.3 - - - +
21A GLY 2.8 29.4 + - - +
24A PHE* 3.0 12.0 + - - +
25A ASN* 1.3 80.4 - - - +
27A PRO* 1.3 78.1 - - + +
29A THR* 3.7 23.1 - - + +
64B LEU* 5.3 3.8 - - + -
68B ASN* 5.9 4.0 - - - +
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Residues in contact with PRO 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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20A GLY* 3.5 3.5 - - - -
21A GLY 3.9 0.7 - - - -
26A MET* 1.3 102.1 - - + +
28A LEU* 1.3 59.9 + - - +
29A THR* 2.9 19.5 + - - +
49A VAL* 3.8 36.3 - - + -
59A GLN* 5.9 4.3 - - + +
84A GLU* 5.4 3.1 - - - +
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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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18A LEU* 4.5 13.9 - - + -
19A GLN 3.5 4.7 - - - +
20A GLY 3.5 22.7 - - - +
21A GLY* 3.7 12.9 - - - +
26A MET 3.7 0.8 + - - -
27A PRO* 1.3 70.8 - - - +
29A THR* 1.3 56.2 - - - +
49A VAL* 3.3 7.5 - - - +
50A VAL* 2.8 51.3 + - + +
53A ILE* 4.7 0.4 - - + -
58A ALA* 3.4 40.6 - - + +
59A GLN* 6.0 3.5 - - - +
61A MET* 4.6 2.0 - - + -
62A THR 4.7 0.7 - - - +
63A HIS* 4.3 9.0 - - - +
66A ALA* 3.4 34.3 - - + -
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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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18A LEU* 3.3 9.4 - - - +
19A GLN* 2.9 35.8 + - - -
26A MET* 3.7 15.4 - - + +
27A PRO* 2.9 20.3 + - - +
28A LEU* 1.3 74.4 - - - +
30A ILE* 1.3 69.7 + - - +
47A GLY* 3.5 35.2 - - - +
48A ASP 3.4 4.0 - - - +
49A VAL* 4.1 8.9 - - + +
64B LEU* 4.3 12.3 - - + -
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Residues in contact with ILE 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 PHE* 3.9 25.8 - - + -
17A ARG 3.6 4.3 - - - +
18A LEU* 4.0 1.8 - - + -
29A THR* 1.3 73.0 - - - +
31A SER* 1.3 58.6 + - - +
32A SER 3.7 18.8 - - - +
33A LEU* 3.9 18.4 - - + -
44A VAL* 3.6 20.0 - - + -
45A ARG 3.7 18.2 - - - +
46A ILE* 3.5 8.6 - - - +
47A GLY 2.9 26.5 + - - -
48A ASP 2.9 19.7 + - - +
50A VAL* 3.9 13.9 - - + +
79A MET* 5.0 3.6 - - + -
81A LEU* 3.8 21.3 - - + -
64B LEU* 4.3 0.5 - - - +
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Residues in contact with SER 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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17A ARG* 2.9 17.4 + - - +
18A LEU 3.2 20.4 + - - -
19A GLN* 3.4 33.9 + - - +
29A THR 3.2 1.0 + - - -
30A ILE* 1.3 73.3 - - - +
32A SER* 1.3 61.5 + - - +
46A ILE* 4.0 16.3 - - - +
23B ASP* 4.3 6.2 - - - +
62B THR* 6.0 0.9 - - - -
64B LEU* 3.7 25.0 + - - +
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Residues in contact with SER 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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16A PHE* 3.3 8.4 - - - +
17A ARG* 3.1 55.6 + - - +
30A ILE* 3.7 4.3 - - - +
31A SER* 1.3 80.7 + - - +
33A LEU* 1.3 71.6 + - - +
46A ILE* 4.0 8.0 - - - +
23B ASP* 4.4 12.4 + - - +
24B PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 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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15A GLY 3.6 6.3 - - - +
16A PHE* 3.9 5.6 - - + +
30A ILE* 3.9 9.4 - - + -
32A SER* 1.3 86.0 + - - +
34A LYS* 1.3 65.5 + - - +
35A ASP 3.5 0.5 + - - -
39A ALA* 3.7 29.6 - - + -
40A ALA* 3.9 17.0 - - + +
44A VAL* 3.2 27.4 - - + +
45A ARG* 3.9 1.1 - - - -
46A ILE* 3.7 36.9 - - + +
24B PHE* 3.5 24.1 - - + -
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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