Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 5Y39
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 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 3.2 26.5 - - - +
15B ASN* 3.6 32.3 - - - +
16B THR 3.1 11.2 + - - +
17B GLY 3.5 1.0 - - - -
18B GLY* 1.3 74.5 + - - +
20B GLN* 1.3 62.6 + - - +
21B SER 4.1 1.1 - - - +
22B THR* 4.1 1.1 - - - +
37B TYR* 3.8 6.9 - - - -
93B MET* 3.6 41.3 - - + -
94B TYR 3.9 4.7 - - - +
95B ALA* 3.7 7.9 - - + -
99B VAL* 3.9 8.3 - - + +
104B LEU* 4.3 10.5 - - + -
107B LYS* 3.6 12.1 - - + +
117G GLU* 4.8 1.6 - - - +
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Residues in contact with GLN 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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15B ASN* 4.5 1.1 - - - -
18B GLY 3.1 8.1 + - - +
19B VAL* 1.3 74.1 - - - +
21B SER* 1.3 57.6 + - - +
36B GLY* 3.2 1.3 - - - -
37B TYR* 2.9 63.7 + - + +
94B TYR* 2.7 34.1 + - + +
95B ALA* 4.3 2.7 - - - -
96B LYS* 3.5 20.4 - - - +
65C LEU* 6.3 0.2 - - + -
117G GLU* 2.8 41.4 + - - +
120G THR* 4.2 14.3 - - - +
121G GLN 4.9 1.0 + - - -
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Residues in contact with SER 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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15B ASN* 3.6 2.4 + - - -
19B VAL* 3.6 2.0 - - - +
20B GLN* 1.3 82.4 - - - +
22B THR* 1.3 66.3 + - - +
23B LEU* 3.3 5.8 - - - +
34B TYR* 2.9 36.5 - - - -
35B SER 3.5 6.5 - - - -
36B GLY* 4.0 0.7 - - - -
37B TYR 5.0 0.7 - - - -
93B MET* 3.4 4.9 - - - +
94B TYR* 3.0 60.8 + - - +
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Residues in contact with THR 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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11B LEU* 3.7 24.9 + - + +
14B ALA* 3.8 6.2 - - - +
15B ASN* 2.8 21.6 + - - -
19B VAL* 4.1 0.3 - - - +
21B SER* 1.3 75.0 + - - +
23B LEU* 1.3 64.3 + - - +
33B ALA 4.1 0.7 - - - +
34B TYR* 3.5 2.6 - - - -
35B SER 2.8 36.7 + - - -
91B LEU* 3.8 15.7 - - + -
92B CYS 3.5 4.5 - - - +
93B MET* 3.8 15.1 - - + +
111B LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 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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11B LEU* 4.7 1.8 - - - -
21B SER* 3.3 18.8 - - - +
22B THR* 1.3 77.3 - - - +
24B LEU* 1.3 58.9 + - - +
25B LEU* 4.2 12.1 - - + -
31B LEU* 4.3 8.1 - - + -
33B ALA 3.4 6.1 - - - +
34B TYR* 3.7 20.0 - - + -
42B ALA* 3.5 26.9 - - + +
45B THR* 3.7 24.0 - - + -
46B ALA* 4.0 7.4 - - - +
91B LEU* 3.4 11.1 - - - +
92B CYS* 2.7 59.9 + - + +
94B TYR* 4.1 5.6 - - + -
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Residues in contact with LEU 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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7B LEU* 3.9 35.9 - - + -
11B LEU* 4.3 10.1 - - + -
23B LEU* 1.3 74.5 - - - +
25B LEU* 1.3 55.2 + - - +
31B LEU* 3.4 5.4 - - - +
32B LEU* 2.7 43.5 + - + -
33B ALA 2.7 21.7 + - - +
86B VAL* 3.7 26.9 - - + -
89B LEU* 4.2 21.8 - - + -
90B LEU 3.4 16.6 - - - +
91B LEU* 4.5 7.2 - - + -
115B LEU* 4.8 6.1 - - + -
119B LEU* 4.3 9.2 - - + -
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Residues in contact with LEU 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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23B LEU* 4.2 9.0 - - + +
24B LEU* 1.3 77.8 - - - +
26B ASN* 1.3 73.0 + - - +
29B GLY* 4.4 0.7 - - - -
30B SER 3.2 15.3 - - - +
32B LEU* 4.1 8.3 - - - -
46B ALA* 3.4 45.1 - - + +
49B ALA* 4.3 2.9 - - + -
50B SER* 3.8 17.0 - - - +
89B LEU* 3.5 4.0 - - - +
90B LEU* 2.7 61.9 + - + +
92B CYS* 3.9 27.4 - - + -
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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