Contacts of the strand formed by residues 227 - 232 (chain B) in PDB entry 1X7O
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 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 2.9 18.2 + - - -
127B LEU* 3.4 15.6 - - + -
128B GLY 2.9 25.3 + - - +
205B ILE* 4.6 0.2 - - - -
206B VAL* 3.6 4.1 - - - +
208B VAL* 4.0 18.6 - - + -
221B PHE* 4.4 1.9 - - - -
222B ASP 4.4 0.3 + - - -
223B PHE* 4.0 32.9 - - + -
225B GLN* 2.6 29.4 + - - +
226B PRO* 1.3 73.7 + - - +
228B LEU* 1.3 70.7 + - - +
229B LEU* 4.3 3.8 - - + +
278B ARG* 4.8 1.8 - - - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 4.3 9.9 - - + -
128B GLY* 3.7 26.0 - - - -
129B VAL 3.8 15.9 - - - +
130B LEU* 4.2 14.4 - - + +
156B ILE* 4.3 14.4 - - + -
191B VAL* 4.5 5.2 - - + -
194B TRP* 4.9 2.0 - - + -
195B VAL* 4.2 17.0 - - + -
205B ILE* 4.0 10.0 - - + +
206B VAL 3.1 8.1 + - - +
207B LEU* 3.5 31.0 - - + -
208B VAL* 2.9 27.7 + - - +
227B THR* 1.3 74.2 - - - +
229B LEU* 1.3 58.9 + - - +
230B LEU* 3.8 17.0 + - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 5.4 1.3 - - + -
128B GLY 2.9 18.9 + - - +
129B VAL* 3.4 7.2 - - + +
130B LEU 2.9 25.8 + - - +
208B VAL* 3.5 28.3 - - + +
210B THR* 4.1 14.4 - - + -
223B PHE* 4.6 5.6 - - + -
227B THR* 4.0 6.2 - - + -
228B LEU* 1.3 70.9 - - - +
230B LEU* 1.3 61.5 + - - +
231B ILE* 3.5 28.0 - - + -
250B VAL* 4.8 1.3 - - + -
267B ALA 4.5 3.4 - - - +
270B ILE* 3.6 38.8 - - + -
271B LEU* 4.3 19.7 - - + -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.6 22.7 - - + +
207B LEU* 4.3 9.4 - - + -
208B VAL 2.7 15.8 + - - +
209B GLY* 4.1 0.2 - - - -
210B THR* 3.2 31.4 + - - +
228B LEU* 3.8 27.1 - - + +
229B LEU* 1.3 77.2 - - - +
231B ILE* 1.3 60.4 + - - +
238B LEU* 3.9 17.1 - - + +
242B TRP* 2.9 54.5 - - + +
246B CYS* 3.9 20.2 - - - -
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Residues in contact with ILE 231 (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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129B VAL* 3.7 20.9 - - + -
130B LEU 2.9 9.7 + - - +
131B PHE* 3.6 18.1 - - + -
132B ASP* 3.0 27.5 + - - +
143B ILE* 4.3 7.6 - - + -
210B THR* 3.8 18.4 - - + +
229B LEU* 3.5 25.4 - - + -
230B LEU* 1.3 76.7 - - - +
232B GLY* 1.3 70.8 + - - +
238B LEU* 4.5 3.1 - - - -
263B ALA* 4.1 15.7 - - + +
266B ALA* 6.3 1.1 - - + -
267B ALA* 3.3 33.4 - - + +
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Residues in contact with GLY 232 (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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131B PHE* 3.5 16.8 - - - -
132B ASP 4.1 3.4 - - - -
210B THR* 4.2 6.9 + - - -
231B ILE* 1.3 80.7 - - - +
233B ASN* 1.3 70.0 + - - +
237B GLY* 3.7 13.0 - - - -
238B LEU* 3.8 18.7 - - - +
263B ALA* 3.9 6.6 - - - +
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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