Contacts of the strand formed by residues 235 - 241 (chain B) in PDB entry 1OLY
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 LEU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 3.6 3.8 - - - +
165B LEU* 2.6 46.3 + - + +
185B LEU* 3.4 23.6 - - + -
186B ILE 3.4 32.8 - - - +
187B PRO* 3.5 4.0 - - + -
192B CYS* 3.9 3.1 - - - -
229B VAL* 4.2 2.5 - - + -
231B THR* 3.4 25.1 - - + +
233B HIS 3.2 0.2 + - - -
234B PRO* 1.3 74.2 - - - +
236B LEU* 1.3 57.6 + - - +
487B VIB 2.4 72.0 - - - +
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Residues in contact with LEU 236 (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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132A PHE* 3.5 38.4 - - + -
139B VAL* 4.5 18.6 - - + -
142B LEU* 3.9 17.9 - - + -
162B ILE* 3.9 7.4 - - + -
163B TYR 3.3 33.4 - - - +
164B LEU* 3.8 14.7 - - + +
184B GLY 3.8 0.5 - - - +
185B LEU* 3.4 4.2 - - - -
186B ILE* 2.8 49.7 + - + +
188B VAL* 4.6 12.5 - - + +
235B LEU* 1.3 74.5 - - - +
237B TRP* 1.3 64.2 + - - +
238B THR 3.9 0.3 + - - -
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Residues in contact with TRP 237 (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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7B PRO* 4.5 6.3 - - + +
161B LEU* 4.8 2.5 - - + -
162B ILE* 3.3 4.0 - - - -
163B TYR* 2.7 52.8 + + + +
165B LEU* 4.1 19.1 - - + -
172B LEU* 3.6 27.9 - - + +
174B VAL* 4.7 4.9 - - + -
183B CYS* 3.6 27.4 - - + -
184B GLY 3.5 14.1 - - - -
185B LEU* 3.5 34.8 - - + -
200B LEU* 4.3 5.8 - - + -
221B TYR* 3.4 31.0 - + - -
227B VAL* 4.3 18.8 - - + -
229B VAL* 5.1 0.7 - - + -
235B LEU 3.6 2.0 + - - -
236B LEU* 1.3 74.0 - - - +
238B THR* 1.4 67.9 + - - +
239B MET* 3.4 28.9 - - + +
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Residues in contact with THR 238 (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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132A PHE* 3.7 30.5 - - + +
133A ASP* 4.0 13.7 - - + -
161B LEU 3.1 15.2 + - - -
162B ILE* 4.2 1.6 - - - -
182B TRP* 3.5 20.8 - - + -
183B CYS* 3.2 4.7 - - - +
184B GLY* 2.8 54.0 + - - +
186B ILE* 4.7 6.7 - - + -
236B LEU* 5.1 1.1 - - - -
237B TRP* 1.4 79.4 - - - +
239B MET* 1.4 61.4 + - - +
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Residues in contact with MET 239 (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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7B PRO* 3.6 28.3 - - + -
8B LEU* 3.7 20.6 - - + -
160B SER* 3.6 3.6 - - - -
161B LEU* 3.1 44.5 + - + +
173B HIS 6.0 0.2 - - - +
174B VAL* 4.6 8.5 - - + -
179B GLU* 3.4 34.8 - - + +
182B TRP* 3.6 12.5 - - - -
183B CYS* 4.0 0.2 - - - +
221B TYR* 3.6 22.4 - - - +
237B TRP* 3.4 22.4 - - + +
238B THR* 1.4 77.8 + - - +
240B ALA* 1.4 67.2 + - - +
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Residues in contact with ALA 240 (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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8B LEU* 4.3 0.2 - - - +
159B GLU* 3.5 6.5 - - + +
179B GLU* 3.8 5.2 - - - -
180B GLY* 2.8 34.6 + - - +
181B ASP 3.8 0.4 - - - +
182B TRP* 2.8 56.2 + - + +
221B TYR* 5.4 0.2 + - - -
239B MET* 1.4 81.9 - - - +
241B ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 241 (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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8B LEU* 4.0 14.1 - - + -
11B LEU* 3.6 27.8 - - + -
31B TYR* 6.2 0.7 - - + -
156B ILE* 3.3 35.2 - - + -
158B GLU 4.3 6.1 - - - +
159B GLU* 2.7 34.4 + - - +
160B SER 3.8 12.8 - - - +
161B LEU* 4.2 7.2 - - + -
178B MET* 3.8 12.1 - - + +
179B GLU* 4.8 0.2 - - - +
180B GLY* 3.9 3.3 - - - -
239B MET 4.5 4.3 - - - +
240B ALA* 1.3 78.8 - - - +
242B LYS* 1.3 79.3 + - - +
243B SER* 3.4 2.3 + - - -
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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