Contacts of the strand formed by residues 242 - 247 (chain J) in PDB entry 2ABJ
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 GLN 242 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173G VAL 5.8 1.6 + - - -
200J VAL* 4.8 3.8 - - + -
201J SER 3.4 3.0 + - - -
202J LEU* 3.3 22.2 - - + -
203J TRP 3.0 15.2 + - - -
232J GLN* 3.6 17.8 + - - +
235J ASP* 2.6 22.2 + - - +
241J GLN* 1.3 95.9 + - + +
243J VAL* 1.3 59.7 + - - +
256J VAL* 4.3 6.7 - - + -
257J GLY* 3.3 23.4 - - - -
258J THR* 3.7 8.3 + - - +
259J MET* 4.2 9.1 - - + +
4401J CBC 3.5 43.0 - - + +
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Residues in contact with VAL 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J LEU* 4.7 2.0 - - - -
203J TRP* 3.5 15.7 - - + +
205J ASN 5.8 2.9 - - - +
208J TYR* 5.9 2.2 - - + -
231J ALA* 3.6 38.6 - - + +
232J GLN* 3.7 19.8 + - + +
235J ASP* 3.8 5.2 - - + -
242J GLN* 1.3 75.2 - - - +
244J LEU* 1.3 70.7 + - - +
245J TRP* 3.7 40.5 + - + +
256J VAL* 3.6 3.0 - - - +
257J GLY* 2.7 33.5 + - - +
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Residues in contact with LEU 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J LEU* 3.9 27.1 - - + +
203J TRP 2.9 13.9 + - - +
204J ALA* 3.9 14.2 - - + -
205J ASN 4.7 3.1 + - - +
242J GLN 4.0 1.2 + - - -
243J VAL* 1.3 75.6 - - - +
245J TRP* 1.3 62.8 + - - +
246J LEU* 3.5 17.0 + - + +
253J ILE* 4.0 22.2 - - + -
254J THR 4.9 0.9 - - - +
255J GLU 3.7 14.1 - - - +
256J VAL* 4.2 8.1 - - + -
261J LEU* 4.9 1.6 - - + -
311J MET* 3.9 20.9 - - - -
326J MET* 4.8 6.5 - - + -
341J ILE* 3.8 39.0 - - + -
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Residues in contact with TRP 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J TYR* 4.0 28.0 - - + -
209J VAL 4.1 2.7 - - - -
210J ARG* 3.4 52.5 - - + +
227J SER 5.2 1.1 - - - -
228J SER* 3.5 39.0 - - - -
231J ALA* 3.8 17.7 - - + -
232J GLN* 6.2 0.2 - - + -
243J VAL* 3.8 26.3 + - + -
244J LEU* 1.3 69.2 - - - +
246J LEU* 1.3 62.3 + - - +
252J GLN 3.6 0.2 - - - +
253J ILE* 3.9 1.7 - - - -
254J THR* 2.9 47.9 + - - +
255J GLU 3.0 26.4 + - - +
257J GLY* 3.1 39.6 + - - -
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Residues in contact with LEU 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204J ALA* 4.0 11.2 - - + -
205J ASN 4.3 2.6 + - - +
206J PRO* 3.8 38.8 - - + +
208J TYR 3.7 18.5 + - - +
209J VAL* 4.3 9.9 - - - +
210J ARG 5.0 1.2 + - - -
244J LEU* 3.5 15.4 + - + +
245J TRP* 1.3 77.3 - - - +
247J TYR* 1.3 63.3 + - - +
251J HIS* 4.2 11.2 - - + +
252J GLN 3.2 11.9 - - - +
253J ILE* 3.8 23.1 - - + -
311J MET* 3.8 16.6 - - + -
343J TYR* 3.8 28.3 - - + -
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Residues in contact with TYR 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G TRP* 3.2 44.0 - + - -
209J VAL* 3.4 13.7 - - + -
211J ALA 3.4 27.1 - - - -
212J TRP* 3.7 4.5 - - - -
213J LYS* 3.2 45.1 + - + +
246J LEU* 1.3 75.6 - - - +
248J GLY* 1.3 71.3 + - - +
251J HIS* 3.7 0.6 + - - +
252J GLN* 2.9 48.3 + - + +
254J THR* 3.7 19.7 - - + -
282J ILE* 3.6 20.4 - - + -
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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