Contacts of the strand formed by residues 103 - 107 (chain W) in PDB entry 1O19
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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8W LEU* 3.9 18.8 - - + +
10W CYS* 4.9 3.8 - - + -
90W PHE* 4.4 17.9 - - + -
101W HIS 3.4 9.0 + - - -
102W PRO* 1.3 74.3 + - - +
104W LEU* 1.4 61.1 + - - +
105W LEU* 3.7 28.7 + - + +
123W MET* 4.6 7.2 - - - -
129W VAL* 3.4 20.0 - - - +
131W ALA 2.9 11.8 + - - -
132W MET* 3.2 28.0 - - - +
133W TYR 3.3 1.7 + - - -
356W TRP* 3.8 3.1 - - - -
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Residues in contact with LEU 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W LEU 2.9 14.4 + - - +
9W VAL* 3.3 22.9 - - + -
10W CYS* 2.9 26.0 + - - +
103W THR* 1.4 68.9 - - - +
105W LEU* 1.3 78.1 + - - +
106W THR* 4.1 9.9 - - + -
133W TYR* 3.5 31.4 - - + +
135W ALA* 4.2 7.4 - - + -
343W GLY* 4.3 10.1 - - - +
346W LEU* 4.2 16.8 - - + -
347W ALA* 4.2 12.8 - - + -
352W PHE* 4.1 12.3 - - + -
356W TRP* 3.9 12.7 - - + -
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Residues in contact with LEU 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W CYS* 3.5 34.8 - - + +
12W ASN* 4.3 7.9 - - - +
86W TRP* 4.4 9.9 - - + +
90W PHE* 6.1 0.4 - - + -
103W THR* 3.9 19.1 - - + +
104W LEU* 1.3 80.4 - - - +
106W THR* 1.3 65.2 + - - +
119W MET* 3.7 28.7 - - + -
123W MET* 3.7 34.8 - - + -
132W MET* 3.7 14.1 - - + -
133W TYR 2.8 10.4 + - - +
134W VAL* 3.4 3.3 - - + -
135W ALA 2.9 23.6 + - - -
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Residues in contact with THR 106 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 5.4 2.5 - - + -
10W CYS 3.4 10.6 + - - +
11W ASP* 2.9 30.5 + - + +
12W ASN* 3.7 18.6 + - - +
104W LEU* 4.1 5.8 - - + -
105W LEU* 1.3 80.1 - - - +
107W GLU* 1.3 62.0 + - - +
119W MET* 4.1 8.0 - - - +
134W VAL* 4.4 2.9 - - - -
135W ALA 3.3 8.1 - - - +
137W GLN* 3.8 16.6 + - - +
140W LEU* 3.4 31.4 - - + -
339W VAL* 4.2 9.2 - - + -
340W TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74W GLY 5.8 0.2 - - - -
106W THR* 1.3 74.4 - - - +
108W ALA* 1.3 65.7 + - - +
109W PRO 5.3 1.0 - - - +
111W ASN* 2.9 42.9 + - - +
116W ARG* 3.1 50.7 + - - +
119W MET* 5.0 4.0 - - - -
134W VAL* 3.6 12.6 - - + +
135W ALA 3.0 12.3 + - - +
136W ILE* 3.7 14.5 - - + +
137W GLN* 3.0 37.2 + - - +
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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