Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 1O5L
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 SER 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.3 5.2 - - - +
15A PHE* 2.9 38.8 + - - +
34A LEU* 4.3 3.1 - - - -
36A GLU 3.3 11.7 - - - -
37A GLY* 4.2 0.2 - - - -
38A THR 3.2 26.9 + - - -
39A LEU* 4.0 17.4 - - - +
80A ALA* 4.7 4.3 - - - -
82A GLU 2.6 19.4 + - - -
83A ASN* 1.3 72.3 - - - +
85A LYS* 1.3 67.6 + - - +
86A ILE* 5.5 0.4 - - - -
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Residues in contact with LYS 85 (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 VAL* 4.6 9.4 - - + -
13A ILE 3.4 7.2 - - - +
14A VAL* 3.8 21.3 - - + -
34A LEU* 3.6 1.0 - - - +
35A LEU* 2.9 34.7 + - + +
36A GLU* 3.0 51.0 + - + +
84A SER* 1.3 80.3 - - - +
86A ILE* 1.3 66.2 + - - +
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Residues in contact with ILE 86 (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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11A LYS 3.8 0.2 - - - +
12A VAL* 3.4 7.3 - - - +
13A ILE* 2.8 40.7 + - + +
15A PHE* 3.8 25.8 - - + -
21A VAL* 3.8 21.3 - - + -
32A LEU* 4.1 25.1 - - + -
33A ILE 3.3 11.2 - - - +
34A LEU* 4.1 12.6 - - + +
35A LEU* 3.9 4.7 - - - -
39A LEU* 4.1 22.9 - - + -
62A ILE* 4.2 4.5 - - + -
84A SER* 5.6 0.7 - - - -
85A LYS* 1.3 80.5 - - - +
87A LEU* 1.3 74.3 + - - +
88A SER* 4.6 2.5 - - - +
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Residues in contact with LEU 87 (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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3A LEU 4.6 4.9 - - - +
6A LEU* 3.6 30.5 - - + +
7A LEU* 3.8 27.4 - - + +
10A GLY* 3.6 38.4 - - - +
11A LYS 3.5 5.4 - - - +
12A VAL* 4.8 2.0 - - + -
31A VAL 3.4 1.6 - - - +
32A LEU* 3.3 5.4 - - - -
33A ILE* 2.8 54.9 + - + +
35A LEU* 3.9 19.2 - - + +
86A ILE* 1.3 75.2 - - - +
88A SER* 1.3 58.7 + - - +
89A ILE* 4.0 18.2 - - + -
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Residues in contact with SER 88 (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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10A GLY* 3.2 2.6 - - - -
11A LYS* 2.9 44.8 + - - +
13A ILE* 3.9 25.3 - - - +
30A ASP* 2.7 35.1 + - - +
31A VAL 3.4 4.3 - - - -
32A LEU* 3.6 10.3 - - - +
86A ILE* 5.1 0.2 - - - -
87A LEU* 1.3 73.9 - - - +
89A ILE* 1.3 60.7 + - - +
90A PRO* 4.0 3.6 - - - +
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Residues in contact with ILE 89 (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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6A LEU* 4.0 37.5 - - + -
9A CYS* 3.8 23.8 - - + +
10A GLY* 4.3 1.1 - - - -
30A ASP* 3.4 3.5 - - - -
31A VAL* 2.9 45.0 + - + +
33A ILE* 4.2 9.4 - - + -
87A LEU* 4.0 20.6 - - + -
88A SER* 1.3 75.7 + - - +
90A PRO* 1.3 82.5 - - + +
93A VAL* 4.1 7.9 - - + -
94A PHE* 3.9 25.4 - - + +
97A LEU* 4.7 1.8 - - + -
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Residues in contact with PRO 90 (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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9A CYS 3.9 11.2 - - - +
10A GLY* 4.8 1.3 - - - -
30A ASP* 3.4 18.5 - - - +
88A SER 4.0 4.9 - - - +
89A ILE* 1.3 90.6 - - + +
91A LYS* 1.3 60.9 + - - +
92A GLU* 4.6 3.1 - - + +
93A VAL* 3.1 25.0 + - + +
94A PHE* 2.8 25.6 + - - +
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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