Contacts of the strand formed by residues 103 - 107 (chain Z) in PDB entry 1O18
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 103 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8Z LEU* 3.9 19.4 - - + +
10Z CYS* 4.9 4.0 - - + -
90Z PHE* 4.4 17.5 - - + -
101Z HIS 3.4 9.9 + - - -
102Z PRO* 1.3 73.4 + - - +
104Z LEU* 1.4 61.0 + - - +
105Z LEU* 3.7 28.4 + - + +
123Z MET* 4.6 7.2 - - - -
129Z VAL* 3.4 19.1 - - - +
131Z ALA 2.9 12.0 + - - -
132Z MET* 3.2 28.3 - - - +
133Z TYR 3.3 2.1 + - - -
356Z TRP* 3.8 3.5 - - - -
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Residues in contact with LEU 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z LEU 2.9 15.2 + - - +
9Z VAL* 3.3 22.0 - - + -
10Z CYS* 2.9 25.5 + - - +
103Z THR* 1.4 69.9 - - - +
105Z LEU* 1.3 79.2 + - - +
106Z THR* 4.1 9.2 - - + -
133Z TYR* 3.5 30.3 - - + +
135Z ALA* 4.2 7.4 - - + -
343Z GLY* 4.3 11.2 - - - +
346Z LEU* 4.2 16.8 - - + -
347Z ALA* 4.2 14.1 - - + -
352Z PHE* 4.1 12.3 - - + -
356Z TRP* 3.9 12.3 - - + -
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Residues in contact with LEU 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z CYS* 3.5 34.3 - - + +
12Z ASN* 4.3 7.6 - - - +
86Z TRP* 4.4 9.0 - - + +
90Z PHE* 6.1 0.4 - - + -
103Z THR* 3.9 19.3 - - + +
104Z LEU* 1.3 81.8 - - - +
106Z THR* 1.3 64.6 + - - +
119Z MET* 3.7 28.7 - - + -
123Z MET* 3.7 35.4 - - + -
132Z MET* 3.7 14.6 - - + -
133Z TYR 2.8 10.6 + - - +
134Z VAL* 3.4 4.2 - - + -
135Z ALA 2.9 23.3 + - - -
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Residues in contact with THR 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z VAL* 5.4 2.5 - - + -
10Z CYS 3.4 10.8 + - - +
11Z ASP* 2.9 31.3 + - + +
12Z ASN* 3.7 18.8 + - - +
104Z LEU* 4.1 5.6 - - + -
105Z LEU* 1.3 80.8 - - - +
107Z GLU* 1.3 61.3 + - - +
119Z MET* 4.1 8.0 - - - +
134Z VAL* 4.4 2.9 - - - -
135Z ALA 3.3 7.0 - - - -
137Z GLN* 3.8 16.5 + - - +
140Z LEU* 3.4 32.3 - - + -
339Z VAL* 4.2 9.0 - - + -
340Z TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Z GLY 5.8 0.2 - - - -
106Z THR* 1.3 74.8 - - - +
108Z ALA* 1.3 66.3 + - - +
109Z PRO 5.3 0.9 - - - +
111Z ASN* 2.9 43.1 + - - +
116Z ARG* 3.1 51.1 + - - +
119Z MET* 5.0 3.6 - - - -
134Z VAL* 3.6 12.2 - - + +
135Z ALA 3.0 12.7 + - - +
136Z ILE* 3.7 14.1 - - + +
137Z GLN* 3.0 36.9 + - - +
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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