Contacts of the strand formed by residues 208 - 219 (chain B) in PDB entry 2NXJ
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B PRO* 4.2 5.0 - - - +
185B PHE* 3.4 18.2 - - + +
187B LEU* 3.9 19.1 - - - +
188B LEU* 4.0 10.8 - - + +
204B TYR* 3.2 13.9 + - + +
205B ARG 3.2 2.2 + - - +
206B GLU 4.4 1.6 - - - -
207B ALA* 1.3 81.9 - - + +
209B VAL* 1.3 66.9 + - - +
212B GLY* 4.2 1.3 - - - -
213B ARG 3.4 38.6 - - - +
214B ALA* 4.2 5.8 - - + -
236B PHE* 3.4 32.5 - - + -
254B ARG* 3.0 39.4 + - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 5.8 1.6 - - - +
184B PRO* 3.3 38.8 - - + +
185B PHE 3.0 19.7 + - - +
186B ASP* 3.4 25.8 - - - +
208B LEU* 1.3 76.5 - - - +
210B PRO* 1.4 81.2 - - + +
211B GLY 4.8 0.4 - - - -
212B GLY 2.9 26.2 + - - +
254B ARG* 3.2 9.4 - - - +
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Residues in contact with PRO 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B VAL* 1.4 95.2 - - + +
211B GLY* 1.3 58.6 + - - +
254B ARG* 3.6 30.5 - - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 4.3 13.4 + - - -
209B VAL* 4.8 1.3 - - - -
210B PRO* 1.3 72.3 - - - +
212B GLY* 1.3 65.5 + - - +
213B ARG* 4.1 9.4 + - - +
253B GLY* 5.7 0.4 - - - -
254B ARG* 2.5 19.1 + - - -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 5.2 0.4 - - - -
186B ASP* 3.5 17.7 - - - -
208B LEU* 4.2 11.9 - - - -
209B VAL* 2.9 24.0 + - - +
210B PRO 3.3 1.4 + - - -
211B GLY* 1.3 79.5 - - - +
213B ARG* 1.3 61.2 + - - +
253B GLY* 3.4 4.3 - - - -
254B ARG* 3.0 25.3 + - - -
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG 4.6 2.0 + - - -
117B HIS* 3.3 58.7 + - - +
119B ARG* 4.0 20.5 - - - +
186B ASP 3.2 4.8 + - - -
187B LEU* 3.3 17.4 - - + -
188B LEU 3.0 23.7 + - - -
208B LEU* 3.4 9.0 - - - +
211B GLY 4.1 5.3 + - - +
212B GLY* 1.3 79.0 - - - +
214B ALA* 1.3 60.5 + - - +
215B LEU* 4.7 6.1 - - + -
239B LEU* 4.0 26.3 - - + +
252B TYR 3.1 11.2 - - - +
253B GLY* 4.5 0.4 - - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 3.5 10.5 - - + +
204B TYR* 5.2 2.5 - - + -
208B LEU* 4.2 14.5 - - + +
213B ARG* 1.3 73.9 - - - +
215B LEU* 1.3 62.7 + - - +
216B LEU* 3.7 20.4 - - + -
231B MET* 4.1 20.9 - - + -
236B PHE* 4.3 2.0 - - + -
250B LEU 3.7 1.0 - - - +
251B ALA* 3.2 6.1 - - - -
252B TYR* 2.9 32.7 + - + +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA* 3.6 34.8 - - + +
114B LEU* 3.8 23.1 - - + +
117B HIS* 4.0 19.7 - - + +
187B LEU* 3.9 23.3 - - + -
188B LEU 2.7 12.4 + - - +
189B VAL* 3.3 13.4 - - + +
190B ALA 2.8 31.7 + - - +
213B ARG* 4.7 2.7 - - + -
214B ALA* 1.3 81.5 - - - +
216B LEU* 1.3 58.7 + - - +
217B THR* 5.3 0.3 - - - +
249B LEU* 4.3 13.5 - - + -
250B LEU 3.8 2.7 - - - -
251B ALA* 3.8 19.5 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.2 10.1 - - + -
190B ALA* 3.7 3.6 - - + -
197B HIS* 3.6 17.5 - - + +
204B TYR* 3.9 20.4 - - + -
214B ALA* 3.7 23.1 - - + -
215B LEU* 1.3 79.8 - - - +
217B THR* 1.3 60.8 + - - +
219B ILE* 3.3 15.0 - - + +
227B VAL* 3.5 28.0 - - + -
231B MET* 3.7 26.9 - - + -
249B LEU* 3.3 3.6 - - - +
250B LEU* 2.8 37.7 + - + +
252B TYR* 4.2 6.1 - - + -
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.6 33.2 + - - +
109B LEU* 4.1 2.8 - - - +
110B ALA* 4.0 14.4 - - + -
189B VAL* 5.5 0.7 - - + -
190B ALA 2.9 11.0 + - - +
191B ASN* 3.8 23.6 - - + +
192B LEU 3.1 9.4 + - - -
197B HIS* 2.8 22.6 + - - -
215B LEU 5.3 1.1 - - - +
216B LEU* 1.3 74.2 - - - +
218B GLY* 1.3 65.6 + - - +
219B ILE* 3.0 7.0 - - - +
248B VAL 3.0 21.6 + - - -
249B LEU* 3.8 15.7 - - + -
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Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.8 12.2 - - - +
191B ASN* 3.2 19.7 + - - -
192B LEU 3.5 17.7 - - - +
193B TYR* 3.7 10.0 - - - +
194B ALA 4.5 0.3 + - - -
217B THR* 1.3 83.4 + - - +
219B ILE* 1.3 60.2 + - - +
220B LEU* 3.7 1.9 + - - +
247B TRP* 3.5 18.3 - - - -
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA* 4.3 14.1 - - + +
197B HIS* 3.5 33.9 - - + +
216B LEU* 3.3 31.0 - - + +
217B THR* 3.0 0.8 - - - +
218B GLY* 1.3 79.2 - - - +
220B LEU* 1.3 73.8 + - - +
223B ARG 4.2 3.6 - - - -
224B ALA* 3.8 23.8 - - - +
227B VAL* 3.9 13.5 - - + -
247B TRP* 3.4 5.5 - - - -
248B VAL* 2.8 44.0 + - + +
250B LEU* 4.0 14.4 - - + -
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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