Contacts of the strand formed by residues 277 - 289 (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 LEU 277 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.5 2.1 - - - +
273B PHE* 2.8 53.2 + - + +
275B PHE* 3.5 28.2 + - + -
276B GLY* 1.3 77.7 - - - +
278B LYS* 1.3 61.8 + - - +
279B PRO* 3.9 16.6 - - + -
308B SER* 3.4 20.6 - - - +
309B TYR 3.6 7.2 - - - +
310B TYR* 4.0 5.5 - - + -
407B LDA 5.8 6.7 - - + -
409B LDA 6.4 0.9 - - + -
417B LDA 3.8 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 6.5 0.4 - - + -
270B GLN* 3.4 31.4 - - + +
271B TYR 3.2 19.1 - - - +
272B LEU* 3.8 28.0 - - + +
277B LEU* 1.3 76.9 - - - +
279B PRO* 1.4 74.2 - - - +
280B SER* 4.3 0.2 - - - -
308B SER* 3.3 3.8 - - - -
309B TYR* 3.0 46.1 + - + -
311B TYR* 3.2 39.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLN* 3.1 18.4 - - - +
271B TYR* 3.2 21.8 + - + +
273B PHE* 3.7 28.7 - - + -
277B LEU* 3.9 14.1 - - + -
278B LYS* 1.4 90.9 - - - +
280B SER* 1.3 58.4 + - - +
307B GLY 3.3 10.3 - - - +
308B SER* 3.3 6.3 - - - +
409B LDA 5.5 6.1 - - + -
414B LDA 4.3 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 4.5 2.8 - - - -
112B PRO* 3.9 28.6 - - - +
268B VAL* 3.7 12.5 - - - +
269B ALA 3.4 5.2 - - - -
270B GLN* 2.8 27.3 + - - -
278B LYS 4.3 4.3 - - - -
279B PRO* 1.3 75.7 - - - +
281B ILE* 1.3 62.7 + - - +
305B SER* 3.7 5.1 + - - +
306B VAL* 3.7 0.3 - - - -
307B GLY* 2.7 35.9 + - - +
309B TYR* 4.6 2.0 - - - -
414B LDA 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.4 4.5 - - - +
269B ALA* 2.8 50.1 + - + +
280B SER* 1.3 76.2 - - - +
282B GLY* 1.3 62.2 + - - +
304B ILE* 4.6 11.2 - - + -
305B SER* 3.2 9.9 - - - +
306B VAL* 3.6 22.9 - - + -
412B LDA 6.2 3.8 - - + -
413B LDA 4.2 20.2 - - + +
414B LDA 3.9 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.8 19.1 - - - -
267B LEU 3.3 9.4 - - - -
268B VAL* 4.3 1.1 - - - -
281B ILE* 1.3 78.4 - - - +
283B TYR* 1.3 61.6 + - - +
304B ILE* 3.3 11.0 - - - +
305B SER* 2.7 41.3 + - - -
413B LDA 4.5 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.7 1.8 - - - -
265B VAL* 3.9 14.6 - - + -
266B GLU* 3.4 1.7 - - - -
267B LEU* 2.8 48.8 + - + +
282B GLY* 1.3 75.1 - - - +
284B ASN* 1.3 74.5 + - - +
285B GLN* 2.6 48.8 + - + -
302B LYS* 3.5 9.1 - - + +
303B TYR 3.4 15.3 - - - -
304B ILE* 3.7 7.6 - - + -
326B LEU* 3.8 19.7 - - + -
413B LDA 3.5 66.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.2 28.9 - - - -
115B GLY* 4.0 3.6 - - - -
116B ALA 3.6 0.4 + - - -
117B ASP* 3.1 18.0 + - - -
118B THR* 3.4 7.2 - - + +
265B VAL 3.6 2.5 - - - -
266B GLU* 3.0 34.3 - - - +
283B TYR* 1.3 92.6 + - - +
285B GLN* 1.3 60.7 + - - +
301B VAL* 4.4 3.6 - - + -
302B LYS* 3.2 4.5 + - - -
303B TYR* 2.9 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.3 8.9 - - - +
263B GLU 3.9 1.1 - - - +
264B ASN* 3.3 1.9 - - - -
265B VAL* 2.9 46.4 + - + +
283B TYR* 2.6 40.5 + - + +
284B ASN* 1.3 76.3 - - - +
286B SER* 1.3 69.4 + - - +
287B LYS* 3.4 26.5 - - + +
299B ASP* 3.8 2.4 - - - +
301B VAL 3.1 10.3 - - - +
302B LYS* 3.0 32.9 + - + +
413B LDA 4.4 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.7 13.7 + - - -
262B THR* 4.1 3.6 - - - +
263B GLU 3.4 4.3 - - - -
264B ASN* 2.8 21.4 + - - -
285B GLN* 1.3 73.0 - - - +
287B LYS* 1.3 58.1 + - - +
299B ASP* 3.6 2.6 - - - +
300B LEU* 2.7 51.1 + - - +
301B VAL* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR* 3.1 7.3 - - - -
263B GLU* 2.8 53.7 + - + +
285B GLN* 3.4 26.2 - - + +
286B SER* 1.3 71.2 + - - +
288B GLY* 1.3 61.4 + - - +
289B LYS* 4.1 25.0 + - - +
297B ASN* 5.6 8.5 - - - +
298B GLN* 3.8 4.7 - - - +
299B ASP* 3.3 22.9 - - - +
300B LEU* 4.4 1.8 - - - -
302B LYS* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LYS 3.5 6.3 - - - -
287B LYS* 1.3 74.7 - - - +
289B LYS* 1.3 63.7 + - - +
291B LEU* 3.9 19.3 - - - -
297B ASN* 3.2 5.5 - - - +
298B GLN 2.7 39.2 + - - +
300B LEU* 3.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASN* 3.6 1.0 - - - +
261B LYS* 2.8 51.7 + - + +
263B GLU* 3.5 37.4 + - + +
287B LYS* 4.3 28.7 - - - +
288B GLY* 1.3 76.3 - - - +
290B ASN* 1.3 73.4 + - - +
291B LEU* 3.3 7.0 + - - +
296B ASP 3.7 2.9 - - - -
297B ASN* 3.1 31.9 + - - +
----------------------------------------------------------
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