Contacts of the strand formed by residues 230 - 237 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Q LEU* 5.2 8.1 - - + -
164Q ALA* 4.5 9.4 - - + -
173Q ILE* 4.4 7.0 - - + -
176Q GLY* 3.4 24.9 - - - +
177Q THR* 5.2 0.7 - - - -
178Q MET* 6.2 1.1 - - + -
216Q ALA* 3.5 29.6 - - + +
217Q LYS* 3.6 6.1 + - - +
219Q VAL* 4.1 34.1 - - + -
226Q LEU* 4.1 19.8 + - + +
228Q GLY* 3.7 2.9 - - - +
229Q LYS* 1.3 89.5 - - + +
231Q ASN* 1.3 71.3 + - - +
247Q LEU* 4.3 9.9 - - + -
249Q VAL* 4.1 14.6 - - + -
305R MET* 4.4 1.3 - - - -
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Residues in contact with ASN 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176Q GLY 3.3 6.0 + - - +
177Q THR* 3.2 6.7 - - - -
178Q MET* 2.9 22.3 + - - +
216Q ALA* 3.3 10.7 - - - +
217Q LYS* 3.5 32.7 - - - +
230Q LEU* 1.3 81.4 + - - +
232Q GLY* 1.3 60.2 + - - +
303R LEU* 3.1 47.7 - - + +
305R MET* 3.8 12.7 - - + +
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Residues in contact with GLY 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177Q THR* 4.6 2.9 - - - -
178Q MET* 2.8 23.3 - - - -
212Q THR* 5.5 0.7 - - - -
213Q THR* 3.7 18.7 + - - +
216Q ALA* 3.6 4.9 - - - +
231Q ASN* 1.3 79.1 - - - +
233Q ILE* 1.3 71.3 + - - +
303R LEU* 5.5 1.2 - - - +
311R LYS* 5.4 1.6 - - - -
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Residues in contact with ILE 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q MET* 3.1 7.0 + - - +
179Q THR* 3.2 24.6 - - + +
180Q THR 3.0 22.2 + - - -
210Q PRO* 6.1 0.4 - - + -
211Q THR 4.3 4.0 - - - +
212Q THR* 5.1 2.7 - - + +
213Q THR* 3.5 10.5 - - - +
232Q GLY* 1.3 81.1 - - - +
234Q ALA* 1.3 62.8 + - - +
235Q LEU* 4.9 10.5 - - + -
301R LEU* 4.4 37.9 - - + +
303R LEU* 6.1 2.2 - - + -
311R LYS* 4.2 9.9 - - + -
313R ILE* 3.5 39.5 - - + -
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Residues in contact with ALA 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Q THR* 3.1 24.2 - - + -
182Q HIS* 5.1 6.1 - - + -
210Q PRO* 3.4 5.2 - - - +
211Q THR* 2.9 53.7 + - + +
212Q THR 4.6 0.2 - - - +
213Q THR* 3.9 10.1 - - - +
233Q ILE* 1.3 76.8 - - - +
235Q LEU* 1.3 66.1 - - - +
236Q ARG* 4.0 2.9 - - - +
5339Q SO4 5.5 1.6 - - - +
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Residues in contact with LEU 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Q THR* 4.1 20.6 - - + -
180Q THR 2.6 11.5 + - - +
181Q THR* 3.3 9.5 - - - +
182Q HIS 2.8 25.1 + - - -
208Q ILE* 4.4 15.3 - - + -
209Q VAL 3.5 1.8 - - - -
210Q PRO* 3.9 28.7 - - + -
233Q ILE* 4.9 10.8 - - + -
234Q ALA* 1.3 80.3 - - - +
236Q ARG* 1.3 65.2 + - - +
237Q VAL* 3.5 4.9 + - + +
181R THR* 3.8 25.1 - - + +
244R VAL* 4.1 19.7 - - + -
246R ASP* 5.8 5.8 - - + -
313R ILE* 5.4 8.3 - - + -
315R TRP* 5.0 1.1 - - + -
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Residues in contact with ARG 236 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Q HIS* 3.2 34.6 + - - +
183Q SER 3.4 15.0 - - - -
184Q TYR* 5.1 0.7 - - - -
185Q THR* 3.2 29.9 + - - +
188Q GLN* 2.7 63.8 + - + +
200Q ARG* 3.6 19.1 - - - +
204Q ALA 5.7 0.4 - - - -
207Q ASN 3.5 2.8 - - - +
208Q ILE* 3.2 6.4 - - - -
209Q VAL* 2.7 48.3 + - + +
211Q THR* 4.1 16.5 - - + +
234Q ALA* 4.0 2.0 - - - +
235Q LEU* 1.3 72.0 - - - +
237Q VAL* 1.3 59.6 + - - +
5339Q SO4 5.8 2.0 + - - -
5340Q SO4 2.8 27.3 + - - -
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Residues in contact with VAL 237 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181Q THR* 3.8 32.1 - - + -
182Q HIS 2.7 19.7 + - - +
184Q TYR* 3.6 15.4 + - - -
204Q ALA 4.5 0.9 - - - -
207Q ASN 4.3 1.1 - - - -
208Q ILE* 4.2 20.2 - - + -
235Q LEU* 3.8 4.7 - - + +
236Q ARG* 1.3 78.8 - - - +
238Q PRO* 1.3 62.9 - - + +
239Q THR* 2.7 38.2 + - + +
181R THR* 4.4 3.4 - - + -
208R ILE* 4.0 14.1 - - + -
237R VAL* 4.1 17.0 - - + -
238R PRO* 5.4 0.2 - - + -
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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