Contacts of the strand formed by residues 26 - 33 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASP* 6.1 1.3 - - - +
19B GLN* 6.0 1.8 - - - +
20B GLY* 3.9 14.4 - - - -
21B GLY* 2.9 23.2 + - - +
22B LYS* 4.8 0.7 - - - +
24B PHE* 3.2 16.5 - - + +
25B ASN* 1.3 86.5 - - - +
27B PRO* 1.3 84.4 - - + +
28B LEU 3.6 0.2 + - - -
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Residues in contact with PRO 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN 3.6 0.3 - - - +
20B GLY* 3.5 10.7 - - - -
25B ASN 4.8 0.9 - - - +
26B MET* 1.3 98.8 - - + +
28B LEU* 1.3 62.7 + - - +
29B THR* 3.4 18.5 + - + +
49B VAL* 3.8 31.0 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.5 14.6 - - + -
19B GLN 3.4 5.2 - - - +
20B GLY 3.6 22.7 - - - +
21B GLY* 3.6 13.7 - - - -
26B MET 3.6 0.8 + - - -
27B PRO* 1.3 70.0 - - - +
29B THR* 1.3 57.9 + - - +
49B VAL* 3.3 8.0 - - - +
50B VAL* 2.9 46.1 + - + +
53B ILE* 4.8 1.6 - - + -
58B ALA* 3.9 35.4 - - + +
61B MET* 4.7 3.1 - - + -
62B THR 4.8 0.4 - - - +
63B HIS* 4.3 9.9 - - - +
66B ALA* 3.4 34.3 - - + -
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.2 10.6 - - - +
19B GLN* 2.8 70.4 + - - +
27B PRO* 3.8 15.9 + - + +
28B LEU* 1.3 80.1 - - - +
30B ILE* 1.3 63.9 + - - +
47B GLY* 3.8 15.7 - - - +
48B ASP 3.2 5.4 - - - -
49B VAL* 3.7 24.5 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.6 29.8 - - + -
17B ARG 3.5 3.8 - - - +
18B LEU* 3.9 9.6 - - + -
19B GLN* 5.8 0.2 - - - -
29B THR* 1.3 70.5 + - - +
31B SER* 1.3 61.6 - - - +
32B SER 3.6 18.8 - - - +
33B LEU* 4.1 17.5 - - + -
44B VAL* 3.5 25.6 - - + -
45B ARG 3.6 18.8 - - - +
46B ILE* 3.5 10.7 - - - +
47B GLY* 2.8 27.9 + - - -
48B ASP 2.9 19.0 + - - +
50B VAL* 4.2 9.4 - - + -
79B MET* 5.1 2.5 - - + -
81B LEU* 4.1 8.5 - - + -
64D LEU* 5.0 1.9 - - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG 2.9 10.4 + - - -
18B LEU 3.2 17.0 - - - -
19B GLN* 3.9 34.1 - - - -
29B THR 3.2 0.4 + - - -
30B ILE* 1.3 74.4 - - - +
32B SER* 1.3 61.2 + - - +
46B ILE* 4.3 7.9 - - - +
1088B CL 2.9 29.0 - - - +
23D ASP* 5.1 2.1 - - - +
64D LEU* 3.7 27.0 - - - +
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.3 8.3 - - - +
17B ARG* 3.0 56.1 + - - -
30B ILE* 3.6 6.2 - - - +
31B SER* 1.3 80.3 + - - +
33B LEU* 1.3 63.2 + - - +
46B ILE* 4.1 8.2 - - - +
1089B EDO 2.7 29.9 + - - -
23D ASP* 4.9 9.6 + - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.5 13.7 - - - +
16B PHE* 3.9 9.6 - - + -
30B ILE* 4.1 9.2 - - + -
32B SER* 1.3 76.5 + - - +
34B LYS* 1.3 66.3 + - - +
35B ASP 3.5 0.3 + - - -
39B ALA* 3.8 21.8 - - + -
40B ALA* 4.0 17.3 - - + +
44B VAL* 3.3 25.8 - - + +
45B ARG* 4.1 1.3 - - - -
46B ILE* 4.0 31.6 - - + +
1089B EDO 3.5 8.6 + - - -
23D ASP* 5.4 1.9 + - - +
24D PHE* 3.5 29.1 - - + -
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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