Contacts of the strand formed by residues 53 - 60 (chain L) in PDB entry 1O5F
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 ALA 53 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41L ALA* 3.8 30.1 - - + +
42L GLY* 4.0 8.0 - - - +
45L CYS* 3.7 19.8 - - - +
52L ARG* 1.3 82.2 - - - +
54L LEU* 1.3 64.3 + - - +
55L THR 4.2 8.3 - - - +
56L HIS* 6.2 0.4 - - + -
103L ALA* 4.9 0.7 - - + -
104L ILE 3.4 8.7 - - - +
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Residues in contact with LEU 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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52L ARG* 4.5 17.7 - - + +
53L ALA* 1.3 75.6 - - - +
55L THR* 1.3 64.7 + - + +
104L ILE* 2.6 28.0 + - + +
105L CYS 4.4 4.0 - - - +
106L GLN* 4.1 38.8 - - + +
107L ASP 5.3 0.9 - - - +
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Residues in contact with THR 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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53L ALA* 3.4 7.2 - - - +
54L LEU* 1.3 82.6 - - + +
56L HIS* 1.3 79.1 + - - +
103L ALA* 3.7 0.7 - - - -
104L ILE* 2.8 52.3 + - + +
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Residues in contact with HIS 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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37L ASN* 3.8 22.4 + - + +
38L ALA* 3.8 28.9 - - + +
41L ALA* 3.5 23.8 - - + -
53L ALA* 6.2 0.4 - - + -
55L THR* 1.3 89.2 + - - +
57L SER* 1.3 66.7 + - - +
101L LEU* 3.6 14.2 - - + +
102L ALA 3.1 18.4 - - - +
103L ALA* 4.1 0.9 - - - +
104L ILE* 4.6 2.0 - - - +
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Residues in contact with SER 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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37L ASN* 5.8 0.4 - - - -
56L HIS* 1.3 80.7 - - - +
58L GLU* 1.3 65.6 + - - +
59L LEU* 4.8 7.3 - - - +
101L LEU* 3.5 10.4 - - - +
102L ALA* 2.9 42.2 + - - +
104L ILE* 6.0 1.7 - - - +
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Residues in contact with GLU 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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33L SER* 2.7 31.7 + - - +
37L ASN* 4.6 5.6 + - - +
57L SER* 1.3 77.6 - - - +
59L LEU* 1.3 67.9 + - - +
97L ARG* 3.6 14.9 + - - -
99L ARG* 2.7 51.6 + - + +
100L PHE 3.1 6.7 - - - +
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Residues in contact with LEU 59 (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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15L ASP* 4.0 28.3 - - + +
17L ARG* 4.0 9.4 - - + +
57L SER* 4.8 7.6 - - - +
58L GLU* 1.3 80.4 - - - +
60L ASP* 1.3 61.6 + - - +
64L ALA* 4.2 10.5 - - + -
99L ARG* 3.1 10.3 - - - +
100L PHE* 2.8 64.1 + - + +
102L ALA* 3.9 24.9 - - + -
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Residues in contact with ASP 60 (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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59L LEU* 1.3 76.5 - - - +
61L VAL* 1.3 61.3 + - - +
62L ARG* 2.9 39.1 + - - +
63L THR* 2.9 22.2 + - + +
64L ALA* 2.8 32.3 + - - +
97L ARG 4.2 5.7 - - - +
98L GLY 3.6 7.5 - - - +
99L ARG* 3.1 36.9 + - - +
100L PHE* 3.9 2.0 - - - -
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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