Contacts of the strand formed by residues 235 - 243 (chain A) in PDB entry 2O3U
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 VAL 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ALA 3.3 31.0 - - - +
201A CYS* 4.0 0.4 - - - -
202A ASP 3.8 2.7 - - - +
204A VAL* 3.8 20.6 - - + -
230A LEU* 4.4 13.5 - - + -
231A GLN 2.8 30.8 + - - +
232A PRO 3.8 8.7 - - - +
234A LYS* 1.3 70.6 - - - +
236A GLN* 1.3 64.3 + - - +
237A THR 3.7 15.9 - - - +
238A LEU 4.6 0.2 - - - +
270A ASN 4.7 1.4 - - - +
271A ILE* 3.7 45.2 - - + +
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Residues in contact with GLN 236 (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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202A ASP* 2.8 22.0 + - - +
203A VAL* 4.0 11.8 - - - +
234A LYS 3.5 4.2 + - - +
235A VAL* 1.3 73.8 - - - +
237A THR* 1.3 71.2 + - - +
270A ASN 5.2 0.2 - - - +
271A ILE* 4.0 2.3 - - - -
272A GLN* 3.0 47.1 + - - +
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Residues in contact with THR 237 (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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202A ASP 3.2 3.5 + - - +
203A VAL* 3.5 17.2 - - + +
204A VAL 3.0 25.6 + - - -
235A VAL* 3.6 4.5 - - - +
236A GLN* 1.3 97.0 + - - +
238A LEU* 1.3 65.3 + - - +
239A GLU* 4.4 1.6 - - + +
271A ILE* 4.0 4.7 - - - -
272A GLN* 3.0 34.5 + - + +
273A PHE 4.5 0.2 - - - -
274A SER* 3.9 27.6 - - - -
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Residues in contact with LEU 238 (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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124A LEU* 4.9 0.7 - - + -
204A VAL* 3.4 31.0 - - + +
206A VAL* 3.7 28.3 - - + -
222A PHE* 4.0 25.1 - - + -
227A VAL* 4.9 0.4 - - + -
230A LEU* 4.5 15.3 - - + -
235A VAL* 5.3 0.2 - - + -
237A THR* 1.3 73.9 - - - +
239A GLU* 1.3 58.4 + - - +
262A LEU* 4.2 6.3 - - + -
266A ILE* 3.8 37.5 - - + -
271A ILE* 3.8 5.5 - - + +
272A GLN 2.9 11.9 + - - +
273A PHE* 3.4 16.9 - - + -
274A SER 2.9 21.7 + - - -
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Residues in contact with GLU 239 (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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203A VAL* 4.3 11.2 - - + +
204A VAL 2.8 10.8 + - - +
205A HIS* 3.2 26.9 + - + +
206A VAL* 2.9 26.5 + - - +
237A THR* 3.9 1.2 - - + +
238A LEU* 1.3 73.4 - - - +
240A ALA* 1.3 62.7 + - - +
241A TRP* 2.8 33.8 + - + +
274A SER* 3.0 33.0 + - - +
275A CYS 4.9 0.4 - - - +
276A LYS* 3.5 23.6 + - + +
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Residues in contact with ALA 240 (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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206A VAL* 3.3 20.0 - - + +
208A LEU* 4.1 18.2 - - + -
238A LEU 4.0 0.8 + - - -
239A GLU* 1.3 73.5 - - - +
241A TRP* 1.3 65.2 + - - +
242A VAL* 3.9 0.9 - - + -
259A ILE* 5.1 0.7 - - + -
262A LEU* 4.7 0.4 - - + -
273A PHE* 3.9 26.0 - - + -
274A SER 2.8 9.6 + - - +
275A CYS* 3.4 8.7 - - - -
276A LYS 2.9 27.0 + - - +
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Residues in contact with TRP 241 (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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123A LEU* 4.5 9.6 - - + -
135A PHE* 3.7 26.9 - + - -
142A MET* 3.6 24.5 - - + -
205A HIS* 3.4 24.7 - + + -
206A VAL 2.7 12.7 + - - +
207A MET* 3.4 30.5 - - + -
208A LEU* 2.9 27.1 + - - -
239A GLU* 2.8 29.6 + - + -
240A ALA* 1.3 80.2 - - - +
242A VAL* 1.3 62.4 + - - +
243A ILE* 3.6 5.3 + - + +
276A LYS* 3.4 18.2 - - + +
278A ILE* 3.8 27.6 - - + -
284A PHE* 3.9 15.3 - + - -
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Residues in contact with VAL 242 (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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208A LEU* 3.8 8.1 - - + -
210A GLY* 3.8 23.8 - - - +
215A ILE* 3.9 13.0 - - + -
240A ALA* 4.8 0.9 - - + -
241A TRP* 1.3 71.0 - - - +
243A ILE* 1.3 60.9 + - - +
244A HIS* 3.4 7.2 + - + -
253A LEU* 3.9 24.0 - - + +
254A CYS* 4.4 1.3 - - - -
259A ILE* 4.0 23.3 - - + -
275A CYS* 3.7 26.2 - - - -
276A LYS 2.8 13.3 + - - +
277A ASN* 3.6 7.1 - - - +
278A ILE 2.7 27.9 + - - +
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Residues in contact with ILE 243 (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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128A ILE* 4.2 26.7 - - + -
131A LEU* 3.9 16.6 - - + -
207A MET* 3.8 26.5 - - + -
208A LEU 2.9 21.5 + - - +
209A ASP* 4.2 2.6 - - - +
210A GLY* 2.8 27.5 + - - -
241A TRP 3.9 7.4 - - - +
242A VAL* 1.3 69.4 - - - +
244A HIS* 1.3 68.4 + - - +
245A GLY 3.5 1.0 + - - -
278A ILE* 3.5 35.7 - - + +
281A PRO* 3.9 27.4 - - + -
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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