Contacts of the strand formed by residues 243 - 251 (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 SER 243 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181Q THR 3.5 13.2 - - - -
182Q HIS* 3.2 23.4 - - - -
183Q SER 3.2 8.0 + - - -
242Q VAL* 1.3 71.2 - - - +
244Q VAL* 1.3 62.5 + - - +
315Q TRP* 3.3 10.0 - - - +
316Q TYR* 2.8 62.1 + - - -
318Q ASN* 3.1 14.0 + - - -
208R ILE* 5.0 1.3 - - - -
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Residues in contact with VAL 244 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Q THR 3.9 0.3 - - - +
180Q THR* 3.4 2.8 + - - -
181Q THR* 2.9 52.8 + - + +
243Q SER* 1.3 80.7 - - - +
245Q VAL* 1.3 67.1 + - - +
246Q ASP 4.2 0.2 + - - -
313Q ILE* 3.3 34.1 - - + -
314Q ALA 3.3 14.4 - - - +
315Q TRP* 3.7 28.7 - - + +
316Q TYR* 3.7 1.3 - - - -
208R ILE* 4.6 4.3 - - + -
235R LEU* 4.4 14.8 - - + -
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Residues in contact with VAL 245 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Q THR* 3.8 27.1 - - + +
159Q CYS* 3.3 28.5 - - + -
160Q LEU* 4.9 15.9 - - + +
163Q VAL* 6.0 1.8 - - + -
178Q MET* 4.7 8.3 - - - -
179Q THR 3.5 4.7 - - - +
180Q THR* 4.2 4.0 - - - -
244Q VAL* 1.3 78.5 - - - +
246Q ASP* 1.3 61.3 + - - +
247Q LEU* 5.2 4.0 - - + +
312Q VAL 3.6 1.8 - - - +
313Q ILE* 3.4 6.1 - - - +
314Q ALA* 2.8 38.7 + - + +
316Q TYR* 3.6 21.3 - - + +
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Residues in contact with ASP 246 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177Q THR 4.0 0.2 - - - +
178Q MET* 3.2 6.8 - - - -
179Q THR* 2.7 42.1 + - - +
181Q THR* 6.1 0.9 - - - +
244Q VAL* 5.6 0.4 - - + +
245Q VAL* 1.3 71.2 - - - +
247Q LEU* 1.3 60.3 + - - +
248Q VAL* 3.9 6.0 + - - +
311Q LYS* 3.1 32.7 + - - +
313Q ILE* 3.5 14.7 - - + +
179R THR* 2.5 37.3 + - + +
235R LEU* 5.8 5.8 - - + -
246R ASP* 4.7 5.9 - - - +
311R LYS* 5.3 0.5 + - - -
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Residues in contact with LEU 247 (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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160Q LEU* 3.8 27.8 - - + -
163Q VAL* 4.2 14.8 - - + -
164Q ALA* 4.6 11.9 - - + -
167Q LEU* 4.1 21.7 - - + +
173Q ILE* 6.1 0.2 - - + -
177Q THR 3.4 18.4 - - - +
178Q MET* 3.8 12.1 - - + -
230Q LEU* 4.3 11.0 - - + -
245Q VAL* 3.8 4.6 - - + -
246Q ASP* 1.3 73.5 - - - +
248Q VAL* 1.3 59.6 + - - +
249Q VAL* 3.5 29.1 - - + +
310Q VAL 3.6 0.9 - - - +
311Q LYS* 3.0 5.5 - - - +
312Q VAL* 2.9 45.7 + - + +
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Residues in contact with VAL 248 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Q GLY* 3.1 2.3 - - - -
177Q THR* 2.8 50.2 + - + +
246Q ASP* 4.0 6.1 - - - +
247Q LEU* 1.3 77.8 - - - +
249Q VAL* 1.3 63.5 + - - +
309Q LEU* 3.8 24.0 - - + -
310Q VAL 3.3 4.5 - - - +
311Q LYS* 3.9 19.5 - - + +
177R THR* 3.7 28.9 - - + -
248R VAL* 3.7 30.1 - - + -
309R LEU* 5.5 2.4 - - + +
311R LYS* 5.7 0.7 - - - +
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Residues in contact with VAL 249 (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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164Q ALA* 6.5 0.4 - - + -
167Q LEU* 4.0 9.0 - - + -
173Q ILE* 3.6 32.3 - - + -
175Q LYS 3.5 8.5 - - - +
176Q GLY* 3.8 9.6 - - - -
230Q LEU* 4.1 8.5 - - + -
247Q LEU* 3.5 28.5 - - + -
248Q VAL* 1.3 80.6 - - - +
250Q GLN* 1.3 61.4 + - - +
251Q VAL* 3.9 4.0 - - + -
308Q ASP 3.5 0.7 - - - +
309Q LEU* 4.0 4.5 - - - -
310Q VAL* 2.8 55.8 + - + +
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Residues in contact with GLN 250 (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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173Q ILE* 3.9 1.7 - - - -
174Q ILE* 2.9 54.9 + - + +
175Q LYS* 2.7 54.0 + - + +
176Q GLY* 4.7 0.4 - - - -
249Q VAL* 1.3 72.8 - - - +
251Q VAL* 1.3 63.8 + - - +
308Q ASP* 3.1 19.9 - - - +
309Q LEU* 4.1 12.9 - - + +
250R GLN* 2.4 32.2 - - + +
308R ASP* 4.8 1.4 + - - +
309R LEU* 5.6 6.3 - - + +
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Residues in contact with VAL 251 (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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167Q LEU* 5.1 0.7 - - + +
171Q PHE* 3.6 23.6 - - + +
172Q GLY 3.1 12.1 - - - +
173Q ILE* 4.1 8.5 - - + -
174Q ILE* 3.6 12.4 - - - +
249Q VAL* 3.9 23.6 - - + +
250Q GLN* 1.3 78.1 - - - +
252Q GLU* 1.3 63.3 + - - +
253Q LYS 3.6 21.1 - - - +
255Q THR* 4.6 6.7 - - + -
307Q GLY 4.5 2.0 - - - +
308Q ASP* 2.8 48.9 + - - +
310Q VAL* 4.2 9.4 - - + -
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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