Contacts of the strand formed by residues 18 - 25 (chain B) in PDB entry 5U17
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 VAL 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B MET* 3.7 31.6 - - + -
11B THR 5.5 0.9 - - - +
12B ALA* 4.0 16.8 - - + +
17B ILE* 1.3 77.9 - - - +
19B GLN* 1.3 64.8 + - - +
20B ILE* 4.8 3.8 - - + -
73B LEU 3.8 1.2 - - - +
74B LEU* 3.5 5.9 - - - +
75B LEU* 3.0 40.6 + - + +
78B LEU* 3.7 26.0 - - + +
105B LEU* 3.9 25.8 - - + -
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Residues in contact with GLN 19 (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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10B MET* 3.2 20.9 - - - +
17B ILE* 4.9 1.1 - - + +
18B VAL* 1.3 76.3 - - - +
20B ILE* 1.3 60.0 + - - +
21B ASN* 3.0 30.8 + - - +
70B TYR* 5.0 3.6 + - - -
72B TYR* 3.5 52.5 - - + -
73B LEU 3.5 2.7 - - - -
74B LEU* 4.1 11.6 - - + +
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Residues in contact with ILE 20 (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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7B PRO* 4.5 1.1 - - + -
10B MET* 3.9 13.5 - - - -
18B VAL* 4.8 6.7 - - + -
19B GLN* 1.3 74.8 - - - +
21B ASN* 1.3 65.5 + - - +
34B TRP* 3.6 21.5 - - + -
72B TYR* 3.1 4.4 - - - -
73B LEU* 2.8 44.6 + - + +
75B LEU* 4.3 15.9 - - + -
86B TYR* 3.7 39.5 - - + -
103B THR* 3.4 37.7 - - + +
105B LEU* 4.7 9.4 - - + -
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Residues in contact with ASN 21 (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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5B ASP 4.5 0.2 - - - -
6B GLN* 3.4 21.1 - - - +
7B PRO* 3.4 16.4 - - + +
10B MET* 5.0 0.8 - - - +
19B GLN* 3.0 36.1 + - - +
20B ILE* 1.3 75.9 - - - +
22B CYS* 1.3 61.1 + - - +
23B THR* 4.3 5.6 - - + +
34B TRP* 4.2 1.9 - - - -
70B TYR* 4.0 14.2 - - + -
71B SER 3.6 2.9 - - - +
72B TYR* 3.5 8.5 - - - +
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Residues in contact with CYS 22 (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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4B ILE* 3.4 22.4 - - - -
5B ASP 3.4 6.5 - - - -
6B GLN* 4.5 0.7 - - + -
21B ASN* 1.3 75.7 - - - +
23B THR* 1.3 65.0 + - - +
24B TYR* 4.4 1.9 - - - -
32B LEU* 4.5 3.8 - - - -
34B TRP* 3.5 15.7 - - + -
70B TYR* 3.3 2.0 - - - -
71B SER* 2.8 42.6 + - - +
88B CYS* 2.0 50.5 - - + -
90B VAL* 5.4 1.1 - - - -
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Residues in contact with THR 23 (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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4B ILE* 3.4 4.9 - - - +
5B ASP* 2.9 49.9 + - - +
21B ASN* 5.5 5.2 - - + -
22B CYS* 1.3 78.6 - - - +
24B TYR* 1.3 63.8 + - - +
68B LYS 5.6 1.3 - - - +
69B GLY 3.5 8.7 - - - +
70B TYR* 3.8 18.4 - - + -
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Residues in contact with TYR 24 (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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3B ASN* 3.5 8.3 - - - +
4B ILE* 4.1 6.1 - - + -
23B THR* 1.3 80.0 - - - +
25B GLN* 1.3 65.2 + - - +
26B THR* 3.7 21.8 - - + -
29B PHE* 3.5 37.5 - + + -
32B LEU* 3.7 30.5 - - + -
64B LEU* 3.7 15.6 - - + +
66B ARG* 3.9 14.6 + - - +
69B GLY* 3.2 44.3 + - - +
70B TYR* 3.7 4.7 - - - -
90B VAL* 3.7 19.7 - - + -
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Residues in contact with GLN 25 (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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2B GLN* 3.3 8.3 + - + +
3B ASN* 2.9 49.4 + - - +
24B TYR* 1.3 76.9 - - - +
26B THR* 1.3 66.0 + - - +
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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