Contacts of the strand formed by residues 147 - 151 (chain B) in PDB entry 1O2D
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 TYR 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ASP* 3.5 1.2 - - - +
103B LYS* 2.8 24.8 + - - +
145B THR* 3.2 18.9 + - + -
146B PRO* 1.3 94.7 - - + +
148B SER* 1.3 61.9 + - - +
149B ILE* 4.5 9.4 - - + -
160B CYS 3.3 6.1 - - - +
161B THR* 3.7 25.4 - - + -
247B ILE* 2.7 44.4 + - + -
248B ALA* 3.8 8.9 + - - -
249B GLN 5.1 0.7 - - - -
251B GLY* 3.8 15.5 + - - -
252B THR* 6.3 0.4 - - + -
1801B NAP 3.0 36.7 + + - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASP* 2.9 35.4 + - - +
103B LYS* 4.4 2.5 - - - -
104B ALA* 4.1 4.9 - - - +
147B TYR* 1.3 76.0 - - - +
149B ILE* 1.3 63.3 + - - +
150B LEU* 3.9 15.6 + - - +
158B ARG 3.8 0.9 - - - +
159B GLY* 3.4 0.7 - - - -
160B CYS* 2.9 39.2 + - - -
162B LEU* 3.9 23.6 - - - -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN 5.2 0.2 - - - -
70B PRO* 4.2 14.7 - - - +
100B ASP* 3.0 20.8 + - - +
147B TYR* 4.5 14.1 - - + -
148B SER* 1.3 75.8 + - - +
150B LEU* 1.3 68.0 + - - +
157B LYS* 3.9 28.8 + - + +
158B ARG 3.6 7.6 - - - +
159B GLY* 3.6 19.5 - - - -
260B TYR* 4.0 23.3 - - + +
1801B NAP 3.7 46.1 + - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN 5.6 0.4 - - - -
70B PRO* 3.3 21.8 - - + +
72B PHE* 3.8 11.2 - - + +
75B VAL* 3.9 27.4 - - + -
100B ASP 5.0 3.1 - - - +
101B PHE* 5.0 2.0 - - - -
104B ALA* 4.3 15.9 - - + -
116B VAL* 3.9 26.9 - - + -
119B LEU* 4.4 7.2 - - + -
120B TYR* 3.5 19.6 + - + +
148B SER* 3.9 18.4 - - - +
149B ILE* 1.3 81.6 - - - +
151B THR* 1.3 63.5 + - - +
152B ASP 3.7 0.7 + - - -
156B ASN 3.7 0.3 - - - +
157B LYS* 4.4 2.0 - - - -
158B ARG* 2.9 32.6 + - - +
160B CYS* 5.1 1.8 - - - -
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 3.2 28.5 + - - +
70B PRO 2.9 8.6 + - - -
71B SER* 3.2 10.7 - - - -
72B PHE* 3.0 24.6 + - - -
150B LEU* 1.3 71.1 - - - +
152B ASP* 1.3 69.9 + - - +
155B GLY* 3.7 29.8 - - - +
156B ASN 3.6 6.5 - - - +
157B LYS* 3.6 17.0 + - - +
264B THR* 4.6 7.1 - - + +
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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