Contacts of the strand formed by residues 52 - 58 (chain C) in PDB entry 5EEY
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 THR 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B TRP* 2.8 34.1 + - + +
23C GLY* 4.0 6.5 - - - -
24C LEU 3.4 3.4 - - - +
26C ARG* 3.4 1.6 + - - -
33C HIS* 2.7 22.5 + - - -
47C GLN 4.6 1.3 - - - +
48C PHE* 3.6 5.4 - - + -
49C THR* 2.9 36.8 + - - +
51C HIS* 1.3 75.8 - - - +
53C SER* 1.3 58.3 + - - +
54C ALA 3.5 22.4 - - - +
55C ILE* 3.7 20.6 - - + -
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Residues in contact with SER 53 (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 LEU 3.2 3.6 + - - -
25C THR 3.7 1.0 + - - -
26C ARG* 3.2 39.3 - - - +
48C PHE* 3.8 5.6 - - - -
51C HIS 4.1 1.2 - - - -
52C THR* 1.3 73.0 - - - +
54C ALA* 1.3 61.1 + - - +
101C TRP* 3.0 32.9 + - - +
47D GLN* 3.0 35.8 + - - +
49D THR* 3.7 12.8 - - - -
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Residues in contact with ALA 54 (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 LEU* 2.8 53.0 + - + -
48C PHE* 3.9 1.5 - - - -
52C THR* 3.5 2.7 - - - +
53C SER* 1.3 82.3 + - - +
55C ILE* 1.3 67.9 + - - +
101C TRP* 4.0 15.0 - - + -
44D LEU* 4.4 5.4 - - + -
45D ILE 3.2 11.0 - - - +
46D ALA* 4.0 12.3 - - + -
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Residues in contact with ILE 55 (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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101B TRP* 3.9 18.6 - - + -
10C VAL* 3.9 21.1 - - + -
12C ILE* 4.7 3.6 - - + -
21C VAL* 3.9 27.6 - - + -
22C ILE 3.4 5.4 - - - +
46C ALA* 4.4 4.9 - - + +
47C GLN 4.3 9.9 - - - +
48C PHE* 3.9 23.8 - - + -
52C THR* 3.7 13.5 - - + -
54C ALA* 1.3 80.1 - - - +
56C LYS* 1.3 67.1 + - - +
57C VAL* 4.6 2.7 - - + -
44D LEU* 3.4 4.0 - - - -
45D ILE* 2.8 58.6 + - + +
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Residues in contact with LYS 56 (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 ASN 3.6 2.1 - - - +
21C VAL* 3.6 2.1 - - - -
22C ILE* 2.8 48.5 + - + +
24C LEU* 4.1 5.6 - - + +
32C PHE* 4.1 12.8 - - + -
55C ILE* 1.3 75.2 - - - +
57C VAL* 1.4 69.9 + - - +
58C ARG* 3.6 27.7 - - + +
36D GLU* 3.1 26.7 + - - +
37D LYS 2.7 29.3 + - - -
38D LEU* 3.7 16.9 - - + +
42D GLU* 3.6 21.4 + - + -
43D VAL 3.3 9.2 - - - +
44D LEU* 3.9 9.6 - - + -
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Residues in contact with VAL 57 (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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12C ILE* 4.1 27.8 - - + -
19C VAL* 4.0 19.7 - - + -
20C ASN 3.4 7.6 - - - +
21C VAL* 4.7 2.2 - - + -
55C ILE* 4.6 2.2 - - + -
56C LYS* 1.4 78.2 - - - +
58C ARG* 1.4 64.1 + - - +
61C ALA* 4.2 7.6 - - + -
63C ILE* 3.9 21.3 - - + -
72C SER* 3.5 23.5 - - - +
42D GLU* 3.7 8.7 - - - +
43D VAL* 2.7 33.8 + - + +
45D ILE* 4.4 14.6 - - + -
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Residues in contact with ARG 58 (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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18C GLY 4.5 1.0 - - - +
19C VAL* 3.4 5.0 - - - +
20C ASN* 2.9 50.2 + - + +
22C ILE* 3.7 25.6 - - + +
32C PHE* 4.1 20.0 - - - -
56C LYS* 3.6 29.7 - - - +
57C VAL* 1.4 74.2 - - - +
59C GLY* 1.3 62.9 + - - +
37D LYS 5.2 0.6 + - - -
42D GLU* 3.0 37.5 + - + +
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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