Contacts of the strand formed by residues 19 - 26 (chain C) in PDB entry 5Y3A
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 19 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS 4.7 0.4 - - - +
13C LEU* 3.9 40.7 - - + +
16C VAL* 3.3 33.1 + - + +
17C GLU 3.4 1.6 + - - -
18C GLY* 1.3 75.0 - - - +
20C HIS* 1.3 61.7 + - - +
21C ALA 3.6 15.9 - - - +
22C ILE* 4.2 4.5 - - + -
37C ASN* 3.9 12.6 + - - -
39C ASN* 4.8 0.5 + - - -
92C PHE* 3.9 21.8 - - + -
93C ILE 3.5 17.9 - - - +
94C ALA* 3.8 10.9 - - + +
98C ALA* 4.6 0.6 - - - +
103C ILE* 4.5 5.4 - - + -
106C LEU* 3.8 28.7 - - + -
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Residues in contact with HIS 20 (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* 3.7 6.4 - - - +
18C GLY* 3.1 17.0 + - - -
19C LEU* 1.3 74.2 - - - +
21C ALA* 1.3 58.1 + - - +
36C ALA* 3.3 4.3 - - - +
37C ASN* 3.0 34.5 + - - +
39C ASN* 2.9 40.4 + - + -
40C ALA* 3.8 20.2 - - + -
78C TYR* 3.2 35.8 - + - -
93C ILE* 2.8 15.7 + - + +
94C ALA* 3.5 20.6 - - - -
95C SER* 3.3 17.3 + - - -
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.1 2.8 - - - +
19C LEU* 3.6 6.9 - - - +
20C HIS* 1.3 80.7 - - - +
22C ILE* 1.3 63.3 + - - +
23C VAL* 4.1 2.9 - - + -
35C VAL 3.3 11.9 - - - +
36C ALA* 3.9 3.6 - - + -
40C ALA* 4.2 2.9 - - + -
45C LEU* 3.6 29.6 - - + -
91C SER 4.4 0.2 - - - -
92C PHE* 3.3 5.0 - - - -
93C ILE* 2.9 42.7 + - + -
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Residues in contact with ILE 22 (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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9C LEU* 4.1 36.9 - - + +
12C LYS* 4.7 5.6 - - + -
13C LEU* 3.8 20.6 - - + +
19C LEU* 4.2 9.6 - - + -
21C ALA* 1.3 76.8 - - - +
23C VAL* 1.3 62.8 + - - +
24C VAL* 4.6 12.1 - - + -
33C ILE 3.7 3.6 - - - +
35C VAL* 3.0 38.5 + - + +
90C VAL* 4.9 1.6 - - + -
91C SER 3.3 8.3 - - - +
92C PHE* 3.7 36.6 - - + -
106C LEU* 4.3 9.2 - - + -
110C LEU* 4.7 2.5 - - + -
114C PHE* 4.6 7.2 - - + -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 4.5 5.2 - - + -
22C ILE* 1.3 75.9 - - - +
24C VAL* 1.3 69.1 + - - +
25C SER* 3.9 2.1 + - - -
31C PRO* 4.6 9.0 - - + -
33C ILE 3.4 9.2 - - - +
34C LYS* 3.8 28.0 - - + -
45C LEU* 3.9 24.2 - - + +
50C LEU* 3.8 39.0 - - + -
89C VAL 3.5 1.9 - - - +
91C SER* 2.8 45.1 + - - +
93C ILE* 5.1 3.8 - - + -
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Residues in contact with VAL 24 (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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9C LEU* 4.7 7.2 - - + -
22C ILE* 4.1 7.6 - - + -
23C VAL* 1.3 74.8 - - - +
25C SER* 1.3 55.7 + - - +
31C PRO* 3.7 1.2 - - - +
32C VAL* 2.7 33.6 + - + +
33C ILE 2.9 17.7 + - - +
88C LEU* 3.8 31.9 - - + -
89C VAL 3.6 6.3 - - - +
90C VAL* 4.3 12.8 - - + -
114C PHE* 3.6 31.6 - - + -
117C LEU* 3.8 24.0 - - + -
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Residues in contact with SER 25 (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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23C VAL* 4.6 1.7 + - - -
24C VAL* 1.3 74.5 - - - +
26C ASP* 1.3 66.2 + - - +
29C GLY* 3.8 18.8 - - - -
30C VAL 3.4 17.0 - - - -
31C PRO* 4.4 2.0 - - - -
32C VAL* 4.2 2.9 - - - +
50C LEU* 4.3 16.0 - - - +
88C LEU* 3.3 15.5 - - - +
89C VAL* 2.7 46.8 + - - +
91C SER* 4.4 2.4 + - - -
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Residues in contact with ASP 26 (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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84A ARG* 3.4 25.1 + - - -
88A TYR* 3.2 26.8 + - + +
25C SER* 1.3 83.3 + - - +
27C ARG* 1.3 63.3 + - + +
28C ASP* 3.7 6.8 - - - +
29C GLY* 2.9 16.6 + - - -
30C VAL* 2.7 40.3 + - - +
32C VAL* 4.6 2.0 - - - +
50C LEU 5.5 1.0 - - - +
87C PRO 3.8 13.7 - - - +
88C LEU* 4.7 0.4 - - - +
89C VAL* 4.0 7.9 - - - +
121C VAL* 4.4 13.5 - - + -
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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