Contacts of the strand formed by residues 265 - 272 (chain B) in PDB entry 1NU6
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 THR 265 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 3.3 6.3 - - - +
229B ASN* 2.9 48.3 + - - +
263B ASN 3.8 5.1 + - - +
264B PRO* 1.3 78.3 - - - +
266B VAL* 1.3 65.0 + - - +
267B LYS* 6.5 0.2 - - - -
297B ASP* 6.0 2.2 - - - +
298B HIS* 5.8 4.0 - - - -
796B NAG 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 3.6 17.9 - - - +
226B ALA* 4.3 5.2 - - + -
227B GLN 3.2 10.5 - - - +
228B PHE* 3.6 26.2 - - + -
264B PRO 5.5 0.2 - - - +
265B THR* 1.3 81.3 - - - +
267B LYS* 1.3 86.6 + - - +
298B HIS* 4.5 23.5 - - + +
300B LEU* 4.2 24.7 - - + +
315B TRP* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA* 3.3 4.7 - - - -
227B GLN* 2.9 44.4 + - + +
266B VAL* 1.3 85.4 - - - +
268B PHE* 1.3 60.8 + - - +
269B PHE* 3.7 22.9 - - + -
286B GLN* 2.5 41.1 + - - +
287B ILE 5.9 0.2 - - - +
288B THR* 4.8 9.3 + - - +
294B LEU* 6.1 3.0 - - - +
315B TRP* 5.5 2.0 - - - -
796B NAG 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 3.6 14.6 - + - -
224B ALA* 3.6 20.2 - - + -
225B TYR 3.6 11.7 - - - -
226B ALA* 4.6 0.4 - - - -
267B LYS* 1.3 76.9 - - - +
269B PHE* 1.3 65.8 + - - +
270B VAL* 3.9 20.2 - - + -
286B GLN* 3.4 6.8 - - - +
287B ILE* 2.9 50.7 + - + +
300B LEU* 3.8 20.4 - - + -
303B VAL* 3.6 27.6 - - + -
311B ILE* 4.6 4.5 - - + -
313B LEU* 3.4 35.2 - - + -
315B TRP* 4.5 15.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.2 1.7 - - - +
225B TYR* 2.9 73.1 + + + +
227B GLN* 4.4 20.2 - - + -
267B LYS* 3.7 25.4 - - + -
268B PHE* 1.3 79.0 - - - +
270B VAL* 1.3 71.3 + - - +
284B SER* 3.9 17.5 - - - -
285B ILE 3.1 9.4 - - - -
286B GLN* 3.5 48.2 - - + -
287B ILE 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.9 36.6 - - + -
223B LEU 3.5 9.6 - - - +
224B ALA* 4.0 5.4 - - + -
268B PHE* 3.9 19.3 - - + -
269B PHE* 1.3 82.6 - - - +
271B VAL* 1.3 64.5 + - - +
285B ILE* 2.7 40.4 + - - +
287B ILE* 4.0 12.8 - - + -
305B TRP* 4.4 2.5 - - + -
311B ILE* 3.9 13.9 - - + -
337B TRP* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.8 17.3 - - + -
222B PHE* 3.4 6.6 - - - -
223B LEU* 2.9 40.4 + - + +
225B TYR* 3.8 16.2 - - + -
270B VAL* 1.3 77.6 - - - +
272B ASN* 1.3 75.2 + - - +
273B THR* 3.5 2.8 + - - +
276B LEU* 4.6 4.3 - - + -
282B ALA* 4.5 16.4 - - + -
283B THR 3.4 17.5 - - - +
284B SER* 3.1 30.5 - - - +
285B ILE* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B THR* 3.7 16.9 - - - +
222B PHE* 4.1 23.4 - - + -
271B VAL* 1.3 81.6 - - - +
273B THR* 1.3 60.3 + - - +
274B ASP* 2.8 39.4 + - - +
275B SER* 3.5 31.8 + - - +
276B LEU* 3.9 3.1 - - - +
283B THR 4.6 2.2 + - - -
285B ILE* 5.5 5.6 - - + +
330B TYR* 4.9 7.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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