Contacts of the strand formed by residues 37 - 44 (chain C) in PDB entry 4YO0
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 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLY 3.6 25.4 - - - +
28C GLY* 4.1 11.7 - - - +
29C GLY 4.6 1.1 - - - +
30C LEU 5.1 4.9 - - - +
31C VAL* 4.2 17.9 - - + -
36C SER* 1.3 80.1 - - - +
38C LYS* 1.3 55.5 + - - +
39C LEU* 4.1 5.6 - - + -
101C GLN* 3.6 4.2 + - - -
102C MET* 2.6 47.4 + - + +
105C LEU* 3.8 11.0 - - + -
132C VAL* 3.6 43.5 - - + -
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Residues in contact with LYS 38 (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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27C GLY* 3.5 18.5 - - - +
37C LEU* 1.3 73.2 - - - +
39C LEU* 1.4 71.8 + - - +
40C SER* 4.9 3.7 + - - +
90C SER* 5.0 4.6 + - - -
99C TYR* 4.0 40.4 - - + +
100C LEU 3.4 7.4 - - - +
101C GLN* 3.5 30.3 - - - +
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Residues in contact with LEU 39 (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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26C SER 3.6 5.4 - - - +
27C GLY 3.5 26.9 - - - +
28C GLY* 3.8 11.7 - - - +
37C LEU* 4.1 7.2 - - + -
38C LYS* 1.4 74.6 - - - +
40C SER* 1.3 61.2 + - - +
55C TRP* 3.7 26.2 - - + -
99C TYR* 3.2 10.4 - - - +
100C LEU* 2.9 35.6 + - + +
102C MET* 3.6 24.5 - - - -
113C TYR* 3.4 36.1 - - + -
130C VAL* 4.3 7.9 - - + -
132C VAL* 4.0 10.8 - - + -
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Residues in contact with SER 40 (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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24C VAL 4.4 0.7 - - - -
25C GLU* 3.1 6.4 - - - +
26C SER* 2.9 47.9 + - - +
27C GLY* 5.9 0.7 - - - -
38C LYS* 4.9 4.2 + - - +
39C LEU* 1.3 72.7 - - - +
41C CYS* 1.3 60.8 + - - +
42C ALA* 4.2 0.9 - - - -
55C TRP* 3.8 3.9 - - - -
97C THR* 4.1 13.7 - - - -
98C HIS 3.5 5.2 - - - -
99C TYR* 3.5 19.3 - - - -
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Residues in contact with CYS 41 (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 LEU* 3.9 21.8 - - - -
24C VAL 3.5 5.4 - - - -
40C SER* 1.3 75.8 - - - +
42C ALA* 1.3 59.6 + - - +
43C ALA* 3.9 1.0 + - - +
55C TRP* 3.7 7.2 - - + -
97C THR* 3.2 5.9 - - - +
98C HIS* 2.8 55.5 + - + +
115C CYS* 2.2 49.4 - - + -
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Residues in contact with ALA 42 (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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22C GLN 3.7 0.9 - - - +
23C LEU* 3.6 2.2 - - - -
24C VAL* 2.9 46.3 + - + +
40C SER* 4.2 1.5 - - - -
41C CYS* 1.3 72.5 - - - +
43C ALA* 1.3 60.6 + - - +
96C THR 3.8 4.3 - - - +
97C THR* 3.9 14.1 - - + +
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Residues in contact with ALA 43 (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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22C GLN 3.4 4.7 - - - -
23C LEU* 3.7 21.1 - - + -
41C CYS* 3.9 1.3 + - - +
42C ALA* 1.3 73.6 - - - +
44C SER* 1.3 63.5 + - - +
46C PHE* 3.7 8.7 - - + -
48C PHE* 3.4 37.0 - - + +
96C THR* 3.0 27.0 + - - +
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Residues in contact with SER 44 (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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20C GLU 4.5 1.0 + - - -
22C GLN* 3.0 49.2 + - - +
42C ALA 5.6 0.2 - - - -
43C ALA* 1.3 76.8 - - - +
45C GLY* 1.3 60.0 + - - +
46C PHE* 3.3 17.8 - - - -
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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