Contacts of the strand formed by residues 267 - 277 (chain B) in PDB entry 1U5U
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 267 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA* 3.6 20.4 - - + -
218B ASP* 3.5 8.1 - - - +
258B TYR* 4.0 11.2 - - + +
261B ARG* 3.5 34.1 - - + -
262B LEU* 3.3 25.4 - - + -
265B GLY 4.2 0.4 - - - +
266B PRO* 1.3 74.1 - - - +
268B ASN* 1.3 65.7 + - - +
269B TYR* 3.5 32.2 - - + +
306B VAL 3.6 1.4 - - - +
307B SER* 3.6 0.9 - - - -
308B ILE* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA 5.1 1.4 - - - +
216B PRO* 4.3 1.0 - - - +
217B GLY* 2.8 26.4 + - - +
218B ASP* 2.8 34.9 + - - +
266B PRO* 3.9 17.4 + - - +
267B VAL* 1.3 74.7 - - - +
269B TYR* 1.3 69.0 + - - +
305B LYS* 3.4 27.1 + - - +
306B VAL 3.1 4.5 - - - +
307B SER* 2.8 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.7 14.8 - - + -
103B HIS* 2.6 40.0 - + - -
119B PHE* 3.5 26.2 - + + -
187B PHE 4.3 2.0 - - - -
188B ALA* 4.1 22.1 - - - -
190B LEU 5.7 0.4 - - - -
192B TYR* 4.8 4.5 - + - -
214B ALA* 4.8 4.0 - - + -
215B LEU 3.3 16.2 - - - +
217B GLY* 3.7 2.5 - - - +
258B TYR* 2.7 24.4 + - - -
267B VAL* 3.5 23.9 - - + +
268B ASN* 1.3 78.2 - - - +
270B ARG* 1.3 67.2 + - - +
271B LEU 3.9 0.2 - - - -
305B LYS* 3.7 8.1 - - - +
306B VAL* 2.8 52.0 + - + -
308B ILE* 3.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 3.4 1.9 - - - -
215B LEU* 2.7 63.1 + - + +
216B PRO 4.0 13.2 + - - +
217B GLY* 4.1 12.8 - - - -
220B ASP* 5.4 5.9 + - - -
269B TYR* 1.3 75.0 - - - +
271B LEU* 1.3 61.2 + - - +
272B GLN* 3.5 13.6 - - - +
302B ASP* 3.1 39.3 + - - +
304B ALA 3.9 3.6 - - - -
305B LYS* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 5.0 0.7 - - + -
119B PHE* 4.9 0.4 - - + -
121B ILE* 4.2 17.3 - - + -
123B PHE* 4.2 11.2 - - + -
134B ILE* 4.1 19.1 - - + -
136B MET* 3.7 24.2 - - + -
212B TYR* 4.7 2.2 - - + -
213B ARG 3.5 15.7 - - - +
214B ALA* 4.5 5.6 - - + +
269B TYR 3.8 1.8 + - - -
270B ARG* 1.3 72.6 - - - +
272B GLN* 1.3 57.5 + - - +
302B ASP* 3.7 1.9 - - - +
303B LEU* 2.7 58.0 + - + -
304B ALA* 2.8 29.1 + - + +
306B VAL* 4.1 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 3.4 9.9 - - - +
213B ARG* 2.7 71.4 + - + +
215B LEU* 3.3 24.2 - - + +
270B ARG* 3.5 19.9 - - - +
271B LEU* 1.3 79.6 - - - +
273B ILE* 1.3 64.6 + - - +
300B TRP* 3.5 23.9 + - + +
301B PHE 3.2 11.6 - - - +
302B ASP* 3.0 29.0 + - - +
303B LEU* 3.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.0 30.5 - - + -
91B PHE* 4.4 4.9 - - + -
200B PHE* 3.8 25.1 - - + -
210B CYS* 3.7 23.1 - - + -
211B ARG 3.5 13.7 - - - +
212B TYR* 3.6 27.4 - - + -
272B GLN* 1.3 77.3 - - - +
274B GLN* 1.3 62.9 + - - +
275B ILE* 3.9 4.5 - - + -
300B TRP* 3.4 5.2 - - - -
301B PHE* 2.8 41.8 + - + +
303B LEU* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 5.9 0.2 - - - -
210B CYS* 3.3 26.3 - - - +
211B ARG* 3.1 36.0 + - + +
273B ILE* 1.3 73.0 - - - +
275B ILE* 1.3 63.7 + - - +
292B LEU* 5.7 5.9 - - - +
293B TRP* 3.5 31.5 - - + +
295B LYS* 5.8 0.7 - - - -
298B HIS* 3.1 34.1 - - - +
299B PRO 3.8 7.9 - - - +
300B TRP* 3.5 42.1 + - + -
301B PHE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.4 0.9 - - + -
86B PRO* 4.1 13.9 - - + -
200B PHE* 4.0 19.5 - - + -
208B ARG* 3.5 33.9 - - + +
209B TYR 3.5 6.3 - - - +
210B CYS* 3.9 17.0 - - + -
273B ILE* 3.9 17.9 - - + -
274B GLN* 1.3 85.8 - - - +
276B HIS* 1.3 65.8 + - - +
277B GLU 4.7 0.4 - - - +
293B TRP* 3.8 2.9 - - - -
297B THR 4.4 2.4 - - - +
298B HIS* 3.0 23.1 + - - +
299B PRO 4.6 1.0 + - - -
301B PHE* 3.8 30.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 3.2 3.8 - - - -
209B TYR* 2.9 52.2 + + + +
275B ILE* 1.3 79.0 - - - +
277B GLU* 1.3 75.8 + - - +
278B ALA 3.5 0.2 + - - -
279B SER* 5.6 0.7 - - - -
282B ASP* 3.0 37.2 + - - -
286B ILE* 4.1 17.9 - - + +
293B TRP* 3.8 24.8 - + + -
298B HIS* 2.8 33.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LYS* 3.7 32.1 + - + +
207B VAL 3.8 10.3 - - - +
208B ARG* 3.9 24.6 + - + +
275B ILE* 4.3 1.6 - - - +
276B HIS* 1.3 87.3 + - - +
278B ALA* 1.3 74.0 + - - +
279B SER* 3.4 5.2 + - - -
----------------------------------------------------------
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