Contacts of the strand formed by residues 230 - 237 (chain O) in PDB entry 2D2I
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 230 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O LEU* 5.2 7.9 - - + -
164O ALA* 4.7 7.9 - - + -
173O ILE* 4.5 8.3 - - + -
176O GLY* 3.6 23.6 - - - +
177O THR* 4.5 1.3 - - - +
178O MET* 6.1 1.1 - - + -
216O ALA* 3.6 37.8 - - + +
217O LYS* 3.7 6.6 + - - +
219O VAL* 4.1 27.1 - - + -
226O LEU* 4.1 19.5 + - + +
228O GLY* 3.6 4.1 - - - +
229O LYS* 1.3 91.6 - - + +
231O ASN* 1.3 69.9 + - - +
247O LEU* 4.5 7.6 - - + -
249O VAL* 4.3 14.6 - - + -
305P MET* 4.3 2.0 - - - -
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Residues in contact with ASN 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O GLY 3.4 6.8 + - - +
177O THR* 3.2 6.3 - - - -
178O MET* 3.0 20.8 + - - +
216O ALA* 3.4 11.7 - - - +
217O LYS* 3.5 33.4 - - - +
230O LEU* 1.3 78.2 + - - +
232O GLY* 1.3 61.1 + - - +
303P LEU* 3.4 35.6 - - + +
305P MET* 3.5 22.1 - - + +
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Residues in contact with GLY 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O THR* 4.6 2.9 - - - -
178O MET* 2.9 22.4 - - - -
212O THR* 5.8 0.3 - - - -
213O THR* 3.7 16.3 + - - +
216O ALA* 3.7 5.1 - - - +
231O ASN* 1.3 82.1 + - - +
233O ILE* 1.3 72.1 + - - +
303P LEU* 5.2 3.0 - - - +
311P LYS* 5.4 1.6 - - - -
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Residues in contact with ILE 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O MET* 3.0 11.0 + - - +
179O THR* 3.3 26.5 - - + +
180O THR* 3.0 21.8 + - - +
210O PRO* 6.1 0.2 - - + -
211O THR 4.3 4.0 - - - +
212O THR* 5.7 2.2 - - - -
213O THR* 3.5 12.4 - - - +
232O GLY* 1.3 85.1 - - - +
234O ALA* 1.3 63.2 + - - +
235O LEU* 4.9 9.6 - - + -
301P LEU* 4.5 35.9 - - + +
303P LEU* 6.0 3.6 - - + -
311P LYS* 4.1 12.8 - - + -
313P ILE* 3.6 38.1 - - + -
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Residues in contact with ALA 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180O THR* 3.3 24.2 - - + +
182O HIS* 5.2 1.3 - - + -
210O PRO* 3.3 5.4 - - - +
211O THR* 2.9 54.6 + - + +
213O THR* 4.0 9.8 - - - +
233O ILE* 1.3 77.8 - - - +
235O LEU* 1.3 67.6 + - - +
236O ARG* 4.0 6.3 - - - +
3339O SO4 5.9 0.7 - - - +
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Residues in contact with LEU 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O THR* 4.0 20.6 - - + -
180O THR 2.7 12.1 + - - +
181O THR* 3.3 9.1 - - - +
182O HIS 2.8 25.6 + - - -
208O ILE* 4.5 15.7 - - + -
209O VAL 3.5 1.8 - - - -
210O PRO* 3.9 28.3 - - + -
233O ILE* 4.9 10.1 - - + -
234O ALA* 1.3 81.8 - - - +
236O ARG* 1.3 63.4 + - - +
237O VAL* 3.6 4.9 + - + +
181P THR* 3.9 22.7 - - + +
244P VAL* 4.1 20.4 - - + -
246P ASP* 5.8 6.7 - - + -
301P LEU* 5.4 2.5 - - + -
313P ILE* 5.4 7.0 - - + -
315P TRP* 5.2 0.9 - - + -
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Residues in contact with ARG 236 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O HIS* 3.3 36.6 + - - +
183O SER 3.4 13.7 + - - -
184O TYR* 5.2 0.7 - - - -
185O THR* 3.1 26.4 + - - +
188O GLN* 2.7 61.0 + - + +
200O ARG* 3.6 25.3 - - - +
204O ALA 5.9 0.2 - - - -
207O ASN 3.6 2.1 - - - +
208O ILE* 3.3 7.1 - - - -
209O VAL* 2.6 43.0 + - + +
211O THR* 3.8 23.5 - - + +
234O ALA* 5.1 2.6 - - - +
235O LEU* 1.3 71.4 - - - +
237O VAL* 1.3 61.0 + - - +
3339O SO4 5.6 4.0 + - - -
3340O SO4 3.2 24.7 + - - -
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Residues in contact with VAL 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O THR* 3.8 33.9 - - + -
182O HIS 2.7 23.4 + - - +
184O TYR* 3.6 15.6 + - - +
204O ALA 4.6 1.3 - - - -
207O ASN 4.1 0.7 - - - -
208O ILE* 4.2 19.5 - - + -
235O LEU* 3.9 6.1 - - + +
236O ARG* 1.3 81.2 - - - +
238O PRO* 1.3 62.1 - - + +
239O THR* 2.7 32.5 + - + +
181P THR* 4.3 11.2 - - + -
208P ILE* 3.8 13.0 - - + -
237P VAL* 4.3 9.0 - - + -
238P PRO* 5.5 0.4 - - + -
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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