Contacts of the strand formed by residues 218 - 226 (chain A) in PDB entry 1O94
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 ALA 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.4 45.3 - - + +
17A PRO* 3.7 7.4 - - + +
18A LYS* 4.1 5.3 - - + +
164A ASP 2.9 12.8 + - - +
165A ILE* 3.5 6.0 - - + -
166A VAL 2.9 26.3 + - - -
217A CYS* 1.3 73.2 - - - +
219A ILE* 1.3 62.0 + - - +
220A ALA* 3.8 1.3 + - + -
252A ASP* 3.5 11.0 - - + +
253A MET* 6.3 0.9 - - + -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 3.4 9.6 - - + +
168A VAL* 5.3 1.8 - - + -
206A LEU* 3.8 33.0 - - + +
209A VAL* 4.1 19.1 - - + -
210A LYS* 3.9 25.6 - - + -
213A VAL* 3.8 28.0 - - + -
214A GLY* 4.1 6.3 - - - -
217A CYS 3.7 14.1 - - - +
218A ALA* 1.3 74.9 - - - +
220A ALA* 1.3 63.1 + - - +
250A LEU 4.1 11.4 - - - +
251A VAL* 3.9 1.0 - - - -
252A ASP* 2.7 51.2 + - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 5.0 1.3 - - - +
165A ILE* 3.9 21.3 - - + -
166A VAL 2.9 7.8 + - - +
167A TYR* 3.2 26.7 - - + -
168A VAL 3.1 21.0 + - - -
206A LEU* 4.5 0.8 - - - +
218A ALA* 3.8 1.5 + - + -
219A ILE* 1.3 81.9 - - - +
221A THR* 1.3 61.9 + - - +
251A VAL* 5.2 1.1 - - - -
253A MET* 3.4 24.9 - - + +
255A ASP* 5.8 0.2 - - + -
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.8 4.9 - - - -
168A VAL* 2.6 20.9 + - - +
202A TRP* 3.0 31.4 + - + +
206A LEU* 4.2 11.4 - - + -
220A ALA* 1.3 75.7 - - - +
222A ARG* 1.3 57.6 + - - +
223A PHE 4.0 0.2 + - - -
251A VAL* 4.0 10.7 - - + +
253A MET 3.2 8.7 + - - +
254A TRP* 3.3 39.4 - - + -
255A ASP* 3.1 24.8 + - - +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.5 18.8 - - - +
28A PRO* 3.9 5.5 + - - -
103A GLU* 3.7 14.1 - - - -
167A TYR* 3.6 14.1 - - + -
168A VAL 3.4 4.9 + - - -
169A TYR* 4.1 14.8 - - + -
170A GLY* 2.8 31.3 + - - +
171A ALA* 3.9 11.4 - - + -
172A HIS* 3.8 5.9 - - - -
202A TRP* 3.6 4.6 - - - -
221A THR* 1.3 75.1 + - - +
223A PHE* 1.3 59.3 + - - +
255A ASP* 2.7 39.8 + - - +
257A THR* 3.3 18.4 - - + +
297A VAL* 3.6 9.9 - - - +
1730A FMN 2.7 75.7 + - - -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY 3.5 2.9 - - - -
171A ALA* 4.2 0.2 - - - -
177A LEU* 3.8 3.8 - - + -
180A LEU* 3.5 31.9 - - + -
202A TRP* 3.4 22.9 - + + -
222A ARG* 1.3 75.7 - - - +
224A GLY* 1.3 74.4 + - - +
225A VAL* 3.0 28.8 + - + -
234A ILE* 4.3 4.0 - - + -
240A GLY* 3.4 38.8 - - - -
243A PHE* 3.7 11.2 - + + -
244A VAL* 4.0 7.0 - - + -
254A TRP* 3.9 30.5 - + + -
255A ASP 2.9 8.7 + - - -
256A ILE* 3.5 12.8 - - + +
257A THR* 3.0 25.1 + - - -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY 3.3 12.8 + - - -
171A ALA* 3.8 6.7 - - - +
177A LEU* 3.9 10.8 - - - +
223A PHE* 1.3 80.7 - - - +
225A VAL* 1.3 62.3 + - - -
226A ASP* 3.1 10.8 + - - -
227A THR* 5.0 1.0 + - - -
234A ILE* 4.0 6.2 - - - +
257A THR* 3.3 20.2 + - - -
258A ILE* 4.8 2.7 - - - -
259A GLY 4.8 8.9 - - - +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.0 35.1 + - + -
224A GLY* 1.3 71.6 - - - -
226A ASP* 1.3 58.9 + - + +
234A ILE* 3.4 12.0 - - - +
236A ALA* 3.3 26.5 + - + -
240A GLY* 3.8 15.2 - - - +
241A GLN* 4.8 2.0 - - + +
256A ILE* 3.4 28.5 - - + -
257A THR 3.1 9.5 + - - +
258A ILE* 4.3 10.1 - - + -
282A TRP* 4.2 18.6 - - + +
285A LEU* 6.0 0.4 - - + -
286A VAL* 3.9 20.6 - - + -
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY 3.1 4.3 - - - -
225A VAL* 1.3 80.5 - - - +
227A THR* 1.3 60.7 + - - +
228A VAL* 2.7 34.3 + - + +
229A TYR 4.3 1.2 + - - -
230A GLY 5.3 0.7 + - - -
234A ILE 3.3 13.8 - - - +
235A GLU* 3.4 8.8 - - - +
236A ALA* 2.9 21.7 + - + +
258A ILE* 3.3 10.4 - - + +
259A GLY 2.9 20.6 + - - +
282A TRP* 3.4 37.7 + - + -
616B TYR* 4.4 5.7 - - - -
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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