Contacts of the strand formed by residues 28 - 33 (chain C) in PDB entry 5YXK
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 LEU 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PHE* 4.5 6.5 - - + -
23C GLN* 3.8 26.9 - - + +
24C SER 3.5 19.3 - - - +
25C LEU* 2.9 12.5 + - - +
26C SER 3.5 0.2 - - - -
27C GLU* 1.3 81.7 - - - +
29C VAL* 1.3 58.4 + - - +
30C VAL* 4.1 11.1 - - + +
43C VAL 3.7 1.9 - - - +
45C LEU* 2.8 32.1 + - - +
68C TRP* 3.8 33.4 - - + -
87C ILE* 4.1 10.5 - - + -
88C HIS 3.1 16.4 - - - +
89C HIS* 4.1 2.7 - - - -
90C LYS 4.5 0.2 - - - +
98C ILE* 3.8 24.2 - - + -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 1.3 76.8 - - - +
30C VAL* 1.3 62.6 + - - +
31C PHE* 4.3 10.5 - - + -
42C GLU* 3.3 31.6 - - + +
43C VAL 3.5 3.4 - - - +
44C TYR* 3.8 26.7 - - + -
45C LEU* 4.4 9.9 - - + -
88C HIS* 2.8 44.4 + - + +
90C LYS* 4.6 13.9 - - + -
95C MET* 4.2 29.2 - - + -
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C CYS* 4.5 2.2 - - - -
25C LEU* 4.4 11.0 - - + +
28C LEU* 4.2 17.7 - - + -
29C VAL* 1.3 77.5 - - - +
31C PHE* 1.3 67.2 + - - +
32C TRP* 3.7 30.6 - - + -
42C GLU* 3.3 2.4 - - - +
43C VAL* 2.8 44.7 + - + +
63C PHE* 5.2 1.1 - - + -
68C TRP* 4.3 22.7 - - + -
85C CYS* 4.3 5.6 - - - -
86C ILE 3.4 8.3 - - - +
87C ILE* 4.2 17.3 - - + -
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.3 8.3 - - + -
30C VAL* 1.3 76.5 - - - +
32C TRP* 1.3 66.7 + - - +
33C GLN* 4.0 27.4 - - + -
39C VAL* 4.2 15.3 - - + -
41C ASN 3.1 16.4 - - - +
42C GLU* 4.0 21.5 - - + -
52C SER* 6.0 2.2 - - - -
84C GLN 3.7 0.5 - - - +
85C CYS* 3.5 1.9 - - - -
86C ILE* 2.8 65.2 + - + +
88C HIS* 3.5 29.8 - + - -
95C MET* 4.2 14.4 - - + -
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Residues in contact with TRP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.1 37.0 + - + -
15C CYS* 3.5 23.0 - - - -
30C VAL* 3.7 19.1 - - + -
31C PHE* 1.3 81.3 - - - +
33C GLN* 1.3 62.7 + - - +
39C VAL* 3.3 7.8 - - - +
40C LEU* 2.9 35.7 + - + -
41C ASN* 3.3 25.1 + - - -
43C VAL* 4.3 5.2 - - + -
63C PHE* 3.4 33.0 - + - -
68C TRP 4.4 0.2 - - - -
69C THR 4.0 3.1 - - - -
70C LEU* 3.3 52.7 - - + -
83C TYR* 6.0 0.9 - - + -
84C GLN 3.2 6.1 - - - +
85C CYS* 3.6 24.3 - - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE* 4.0 15.8 - - + -
32C TRP* 1.3 73.1 - - - +
34C ASP* 1.3 64.7 + - - +
37C ASN* 2.7 43.6 + - - +
38C LEU 3.1 7.0 - - - +
39C VAL* 3.4 26.5 - - + +
40C LEU* 3.8 4.3 - - - -
83C TYR* 3.3 6.2 - - - +
84C GLN* 2.8 39.3 + - + +
86C ILE* 3.6 21.5 - - + +
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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