Contacts of the strand formed by residues 237 - 247 (chain B) in PDB entry 5NXR
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 VAL 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.5 16.3 - - + +
233B ASP* 3.5 4.5 - - - +
234B ALA 2.8 28.8 + - - +
235B ASN 3.5 13.9 - - - +
236B ASN* 1.3 81.5 - - - +
238B TYR* 1.3 65.4 + - - +
239B LEU* 3.4 28.3 - - + -
270B GLN 3.6 6.3 - - - +
271B TYR* 3.6 19.1 - - + -
402B LDA 3.9 28.5 - - + -
405B LDA 4.0 15.7 - - + -
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Residues in contact with TYR 238 (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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107B TRP* 2.6 41.9 + - - +
110B VAL* 3.9 22.0 - - + +
231B LYS* 3.6 25.4 + - + +
232B PHE 3.2 5.2 - - - -
233B ASP* 3.4 35.0 - - + +
237B VAL* 1.3 74.1 - - - +
239B LEU* 1.3 65.4 + - - +
240B ALA* 3.7 13.5 - - + -
268B VAL* 4.1 2.7 - - + -
269B ALA* 3.3 3.8 - - - -
270B GLN* 2.8 69.7 + - + +
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Residues in contact with LEU 239 (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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231B LYS* 3.1 5.6 - - - +
232B PHE* 2.8 49.1 + - + +
237B VAL* 3.4 29.4 - - + -
238B TYR* 1.3 78.7 - - - +
240B ALA* 1.3 63.2 + - - +
268B VAL 3.2 7.6 - - - +
269B ALA* 4.3 10.3 - - + -
270B GLN 5.7 0.2 - - - +
402B LDA 4.5 17.3 - - + -
403B LDA 4.8 15.0 - - + -
405B LDA 5.4 3.8 - - + -
413B LDA 3.8 28.3 - - + -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TRP* 3.3 32.3 - - + +
108B THR* 4.1 4.1 - - + +
230B GLY 3.3 12.6 - - - +
231B LYS* 3.9 6.1 - - + +
238B TYR* 3.7 8.5 - - + -
239B LEU* 1.3 78.4 - - - +
241B ALA* 1.3 61.0 + - - +
266B GLU 4.0 0.2 - - - +
267B LEU* 3.4 3.6 - - - +
268B VAL* 2.9 38.7 + - + +
403B LDA 4.7 2.9 - - - -
413B LDA 4.7 2.9 - - - +
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Residues in contact with ALA 241 (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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107B TRP* 5.3 1.7 - - - +
108B THR* 4.0 3.2 - - - +
229B GLY* 3.1 3.7 - - - -
230B GLY 3.0 33.1 + - - +
240B ALA* 1.3 75.0 - - - +
242B MET* 1.3 62.2 + - - +
266B GLU 3.3 5.4 - - - -
267B LEU* 3.6 20.6 - - + -
403B LDA 4.2 16.7 - - + +
413B LDA 5.3 3.4 - - + -
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Residues in contact with MET 242 (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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104B THR* 4.7 6.7 - - + +
105B ASN* 3.6 37.5 - - - +
108B THR* 3.8 14.1 - - + +
118B THR* 3.9 17.9 - - - +
119B MET* 3.8 24.0 - - + -
227B ASN* 3.6 26.2 - - + +
228B VAL 3.3 14.1 - - - +
229B GLY* 4.7 1.3 - - - -
241B ALA* 1.3 76.1 - - - +
243B TYR* 1.3 61.7 + - - +
244B GLY 4.4 7.2 - - - +
264B ASN* 3.9 3.3 - - + +
265B VAL* 3.4 6.4 - - - +
266B GLU* 2.8 47.1 + - + +
267B LEU* 5.8 0.2 - - - -
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Residues in contact with TYR 243 (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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226B TRP* 3.7 29.8 - + - -
227B ASN* 3.1 4.5 - - - +
228B VAL* 2.8 46.7 + - + +
242B MET* 1.3 75.9 - - - +
244B GLY* 1.3 60.6 + - - +
245B GLN* 2.7 36.5 + - + +
263B GLU* 3.6 15.8 - - + +
264B ASN 3.1 28.3 - - - -
265B VAL* 4.5 11.7 - - + -
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Residues in contact with GLY 244 (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 MET* 4.0 7.6 - - - -
226B TRP* 3.2 14.6 - - - -
227B ASN* 3.8 6.3 - - - -
242B MET* 4.4 1.6 - - - +
243B TYR* 1.3 80.4 - - - +
245B GLN* 1.3 66.5 + - - +
264B ASN* 2.8 48.2 + - - +
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Residues in contact with GLN 245 (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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225B ALA* 3.4 2.3 - - - -
226B TRP* 2.9 73.6 + - + +
243B TYR* 2.7 26.6 + - + +
244B GLY* 1.3 79.2 - - - +
246B THR* 1.3 68.0 + - - +
247B GLN* 6.0 2.2 - - - +
262B THR 3.3 12.3 - - - +
263B GLU* 3.8 13.2 - - + +
264B ASN* 4.3 0.2 - - - +
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Residues in contact with THR 246 (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 MET* 3.7 24.7 - - + -
127B THR* 5.2 1.3 - - + -
224B GLN 3.3 7.2 - - - -
225B ALA* 4.2 7.9 - - + -
245B GLN* 1.3 81.3 - - - +
247B GLN* 1.3 64.0 + - - +
249B THR* 4.1 11.5 + - + -
250B SER* 3.6 21.9 + - - +
259B ALA 5.1 1.0 + - - -
261B LYS* 3.1 8.8 - - - +
262B THR* 2.5 62.8 + - - +
264B ASN* 4.1 3.6 - - - +
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Residues in contact with GLN 247 (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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222B ARG 4.8 3.5 - - - +
223B ALA* 3.3 0.5 - - - -
224B GLN* 2.7 58.9 + - + +
226B TRP* 6.1 0.6 - - - +
245B GLN* 6.0 2.2 - - - +
246B THR* 1.3 74.7 - - - +
248B ASN* 1.3 79.1 + - - +
249B THR* 2.9 12.8 + - - -
260B ASN 3.3 11.2 - - - +
261B LYS* 4.0 20.0 - - + +
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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