Contacts of the strand formed by residues 277 - 282 (chain B) in PDB entry 5FJH
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 TYR 277 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TRP* 3.6 9.1 - - + -
190B HIS* 3.4 26.2 - - - -
191B THR* 3.6 28.7 + - + +
212B ALA* 3.2 4.7 - - - +
213B ILE* 2.9 37.9 + - + -
218B GLY* 3.8 28.9 - - - -
221B LEU* 3.4 26.7 - - + -
222B GLU* 2.6 38.9 + - + +
240B LEU* 3.8 27.6 - - + +
275B TYR* 3.5 15.2 + + - -
276B GLY* 1.3 73.7 - - - +
278B HIS* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 6.1 0.7 - - - +
46B LEU* 5.3 2.0 - - + -
187B PHE* 4.2 2.0 - + - -
188B ALA 3.3 3.8 - - - +
189B TRP* 3.5 3.6 - - - -
190B HIS* 3.0 50.9 + + - -
191B THR* 4.6 1.1 - - - -
192B GLU* 2.9 22.2 - - + -
210B TRP* 3.8 20.0 - + + -
211B TYR 3.0 15.5 - - - +
212B ALA* 4.6 4.7 - - + -
272B THR* 3.7 25.7 - - + +
276B GLY 3.0 22.7 + - - +
277B TYR* 1.3 75.7 - - - +
279B ALA* 1.3 63.4 + - - +
1348B NI 2.2 33.6 - - + +
1349B MMK 3.6 13.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.2 27.6 - - - +
188B ALA* 4.4 0.9 - - - -
189B TRP* 3.6 40.5 - - + +
210B TRP* 3.4 4.3 - - - +
211B TYR* 2.7 38.5 + - + +
278B HIS* 1.3 76.6 - - - +
280B GLY* 1.3 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 4.1 1.7 + - - -
186B THR* 3.5 7.6 - - - +
187B PHE* 3.0 38.9 + - - +
209B SER 3.1 15.0 - - - -
211B TYR* 4.2 11.2 - - - -
279B ALA* 1.3 76.9 - - - +
281B PHE* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR 5.6 0.7 - - - -
119B LEU* 4.8 2.5 - - + -
120B GLU* 4.0 28.0 - - + -
123B TYR* 3.3 59.0 - + + +
183B TRP* 4.5 8.3 - + - -
185B THR 3.1 11.4 - - - +
186B THR* 4.4 0.2 - - - +
187B PHE* 3.7 3.4 - - - -
208B LYS* 3.7 3.5 - - - -
209B SER* 2.9 51.9 + - - -
211B TYR* 3.7 25.8 - + - -
280B GLY* 1.3 78.8 - - - +
282B ASN* 1.3 72.6 + - - +
283B HIS* 3.8 21.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 3.1 32.3 + - - -
181B GLY* 3.8 0.8 - - - -
182B MET 3.6 5.2 - - - +
183B TRP* 3.6 3.5 - - - -
184B LYS 3.0 25.6 + - - -
185B THR* 2.8 36.7 + - - +
187B PHE* 5.4 2.2 - - - -
207B PRO 3.8 1.8 - - - -
208B LYS* 2.7 30.2 + - - +
281B PHE* 1.3 77.5 - - - +
283B HIS* 1.3 62.4 + - - +
284B GLY 3.3 5.6 - - - +
286B ASN* 2.9 26.2 + - - +
----------------------------------------------------------
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