Contacts of the strand formed by residues 52 - 58 (chain L) in PDB entry 5EF3
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23L GLY* 3.8 17.9 - - - -
24L LEU 3.3 4.0 - - - +
26L ARG* 3.6 1.8 + - - -
33L HIS* 2.4 26.0 + - - -
47L GLN 4.5 1.6 - - - +
48L PHE* 3.6 5.6 - - + -
49L THR* 2.9 36.7 + - - +
51L HIS* 1.4 76.1 - - - +
53L SER* 1.3 58.3 + - - +
54L ALA 3.5 20.4 - - - +
55L ILE* 3.9 16.6 - - + -
101M TRP* 2.7 30.6 + - + +
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Residues in contact with SER 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU 3.2 5.3 + - - -
25L THR 3.8 0.5 + - - -
26L ARG* 3.3 38.4 - - - +
48L PHE* 3.8 7.1 - - - -
52L THR* 1.3 73.1 - - - +
54L ALA* 1.3 58.9 + - - +
101L TRP* 2.8 38.3 + - - +
47V GLN* 3.1 38.6 + - - +
49V THR* 3.8 6.3 - - - -
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Residues in contact with ALA 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU* 2.8 52.9 + - + -
48L PHE* 3.9 1.1 - - - -
52L THR* 3.5 7.7 - - - +
53L SER* 1.3 79.2 + - - +
55L ILE* 1.3 63.6 + - - +
101L TRP* 4.1 16.8 - - + -
44V LEU* 4.4 5.4 - - + -
45V ILE 3.1 12.6 - - - +
46V ALA* 4.1 11.2 - - + -
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Residues in contact with ILE 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L VAL* 3.9 23.8 - - + -
12L ILE* 4.6 3.4 - - + -
21L VAL* 3.7 29.4 - - + -
22L ILE 3.2 6.5 - - - +
24L LEU* 4.7 0.2 - - - -
46L ALA* 4.4 10.3 - - + +
47L GLN 4.4 4.9 - - - +
48L PHE* 3.8 25.4 - - + -
52L THR* 3.9 11.7 - - + -
54L ALA* 1.3 80.8 - - - +
56L LYS* 1.3 65.5 + - - +
57L VAL* 4.4 7.6 - - + -
101M TRP* 4.1 15.9 - - + -
43V VAL 3.8 0.7 - - - +
44V LEU* 3.5 5.4 - - - +
45V ILE* 2.9 44.5 + - + +
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Residues in contact with LYS 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L ASN 3.5 2.6 - - - +
21L VAL* 3.7 1.9 - - - -
22L ILE* 2.8 44.9 + - + +
24L LEU* 4.1 17.4 - - + +
32L PHE* 5.1 1.8 - - + -
55L ILE* 1.3 74.6 - - - +
57L VAL* 1.4 70.4 + - - +
58L ARG* 3.3 27.6 - - + +
36V GLU* 2.7 33.4 + - + +
37V LYS 3.8 4.8 + - - -
38V LEU* 4.3 11.4 - - + -
42V GLU* 3.8 19.5 + - + +
43V VAL 3.3 9.2 - - - +
44V LEU* 4.1 8.1 - - + -
101W G 6.0 0.2 - - - +
102W A 3.6 8.7 - - - +
103W G 2.8 21.8 + - - -
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Residues in contact with VAL 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 4.2 26.2 - - + -
19L VAL* 4.0 14.6 - - + -
20L ASN 3.5 2.9 - - - +
21L VAL* 4.7 3.4 - - + -
55L ILE* 4.4 8.5 - - + -
56L LYS* 1.4 77.9 - - - +
58L ARG* 1.4 64.1 - - - +
59L GLY 4.9 0.4 - - - -
61L ALA* 3.9 17.0 - - + -
63L ILE* 4.0 22.0 - - + -
72L SER* 3.6 24.7 - - - +
42V GLU* 3.7 11.4 - - - +
43V VAL* 2.7 33.3 + - + +
45V ILE* 4.9 6.3 - - + -
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Residues in contact with ARG 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L GLY 5.5 0.4 - - - -
19L VAL* 3.2 9.4 - - - +
20L ASN* 3.0 46.3 + - + +
22L ILE* 3.8 24.7 - - + +
32L PHE* 4.4 2.2 - - - -
56L LYS* 3.3 32.7 - - + +
57L VAL* 1.4 74.4 - - - +
59L GLY* 1.3 62.4 + - - +
42V GLU* 3.2 30.4 + - - +
101W G 5.6 4.9 - - - +
102W A 5.0 1.8 + - - +
103W G 3.4 13.9 + - - -
104W U 3.3 35.3 + - - +
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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