Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 1H8O
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLN* 3.2 22.9 + - - +
10A SER* 4.3 2.3 + - - -
11A HIS 2.7 22.7 + - - +
12A LYS 3.6 0.7 - - - -
14A MET* 3.4 37.2 - - + +
24A ILE* 3.7 18.9 - - + +
87A ALA 3.6 0.5 - - - +
88A ASP* 4.4 3.2 + - - -
89A TYR* 3.1 31.1 + - - +
104A GLY* 1.3 72.2 + - - -
106A LYS* 1.3 70.5 + - - +
107A LEU* 3.5 3.7 + - + +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS 2.8 12.4 + - - +
13A PHE* 3.3 30.0 - - + +
14A MET 3.0 24.6 + - - -
43A PRO* 5.6 11.3 - - - +
87A ALA* 3.7 9.0 - - - +
88A ASP* 3.4 25.6 + - - +
105A THR* 1.3 72.1 - - - +
107A LEU* 1.3 63.8 + - - +
108A GLU* 3.6 24.4 + - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.3 28.7 - - + +
16A THR* 3.8 28.3 - - + -
22A VAL* 4.1 17.0 - - + -
24A ILE* 5.1 5.6 - - + -
78A ILE* 3.7 29.4 - - + -
81A VAL* 4.7 7.0 - - + -
85A ASP 3.8 17.7 - - - +
86A LEU* 3.4 24.5 - - + +
87A ALA 2.9 20.2 + - - +
89A TYR* 4.0 9.6 - - + -
105A THR* 3.5 1.5 + - + +
106A LYS* 1.3 74.6 - - - +
108A GLU* 1.3 58.2 + - - +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.6 32.2 - - + +
14A MET 3.1 9.3 + - - +
15A SER* 3.2 13.3 + - - +
16A THR* 2.9 27.0 + - - +
86A LEU* 3.9 9.0 - - - -
106A LYS* 3.9 26.2 + - + +
107A LEU* 1.3 75.5 - - - +
109A LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 4.7 3.7 + - - -
16A THR* 3.1 19.5 - - + +
17A SER* 3.6 16.2 - - - -
18A VAL* 4.2 17.5 - - + +
81A VAL* 6.0 0.4 - - + -
83A SER* 6.0 1.3 - - - +
86A LEU* 3.7 37.1 - - + +
108A GLU* 1.3 82.5 - - - +
110A LYS* 1.3 63.1 + - - +
111A ARG 4.4 1.6 - - - +
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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