Contacts of the strand formed by residues 240 - 244 (chain B) in PDB entry 1O01
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 LYS 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B VAL* 3.8 20.9 - - + -
161B VAL 3.2 2.0 + - - -
162B CYS* 3.3 9.1 - - + -
163B GLY 2.7 32.1 + - - +
238B VAL* 3.4 5.8 - - - +
239B ASP* 1.3 81.2 - - - +
241B VAL* 1.3 71.4 + - - +
242B ALA* 4.0 3.1 - - + +
263B LYS* 4.3 1.1 - - - -
264B ARG* 3.3 20.3 + - + +
265B VAL 4.1 0.6 - - - -
266B THR* 2.7 40.9 + - - +
484B ALA* 3.6 29.7 - - - +
485B TYR* 3.6 37.7 - - + -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY* 3.2 14.8 - - - +
165B ILE* 4.2 22.2 - - + -
232B ILE* 4.8 1.8 - - + -
233B ALA* 4.8 8.1 - - - -
238B VAL* 5.1 1.1 - - + -
240B LYS* 1.3 90.7 + - - +
242B ALA* 1.3 64.9 + - - +
243B PHE* 4.1 0.9 - - + +
253B ILE* 3.8 27.8 - - + -
257B ALA* 4.8 0.9 - - + -
263B LYS* 4.0 20.2 - - + -
264B ARG 2.8 8.3 + - - +
265B VAL* 3.7 26.7 - - + -
266B THR 3.3 12.1 + - - +
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Residues in contact with ALA 242 (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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163B GLY 2.9 9.5 + - - +
164B GLN* 3.5 4.1 - - + -
165B ILE* 3.0 25.1 + - - +
178B LYS* 3.5 21.9 - - + -
240B LYS* 4.0 4.7 - - + +
241B VAL* 1.3 73.1 - - - +
243B PHE* 1.3 60.9 + - - +
266B THR* 3.7 17.3 - - - +
476B GLU* 4.8 2.7 - - - +
485B TYR* 3.2 27.4 - - - +
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Residues in contact with PHE 243 (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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165B ILE* 3.5 23.3 - - + -
178B LYS* 4.6 0.6 + - - -
241B VAL* 4.1 1.1 - - + -
242B ALA* 1.3 74.5 - - - +
244B THR* 1.3 66.8 + - - +
245B GLY* 3.4 27.6 - - - -
246B SER 3.6 17.0 - - - -
249B ILE* 3.4 24.9 - - + -
250B GLY* 3.8 7.4 - - - -
253B ILE* 3.9 22.2 - - + -
266B THR 3.2 6.7 + - - +
267B LEU* 3.4 22.8 - - + -
268B GLU* 2.9 25.6 + - - +
269B LEU* 3.7 13.7 - - + -
5502B NAD 3.1 35.7 - - - -
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Residues in contact with THR 244 (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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165B ILE 3.1 10.3 + - - +
166B ILE* 4.8 0.4 - - - -
167B PRO* 3.2 44.7 - - + +
174B MET* 3.9 16.2 - - - -
178B LYS* 2.7 30.1 + - - -
243B PHE* 1.3 81.2 - - - +
245B GLY* 1.3 59.8 + - - +
268B GLU* 3.1 29.5 - - + +
302B CYS* 6.2 1.1 - - + -
476B GLU* 4.2 1.2 + - - -
5502B NAD 3.9 15.1 - - - +
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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