Contacts of the strand formed by residues 286 - 291 (chain B) in PDB entry 4ZCH
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 PHE 286 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 5.8 0.4 - - - -
86B PHE* 3.9 14.6 - - + -
105B SER* 3.7 12.8 - - - -
106B ALA 3.3 27.4 - - - -
107B GLY* 4.8 1.3 - - - -
109B PHE* 6.1 0.7 - + - -
156B GLN* 4.6 10.5 - - - +
157B LEU 3.2 15.0 - - - +
158B ILE* 4.0 6.3 - - + -
176B TRP* 3.6 7.4 - - - -
204B TYR* 4.0 23.1 - + - -
205B GLY* 3.5 0.5 - - - -
206B GLN* 2.9 68.4 + - + +
254B TYR* 4.5 3.4 - + - -
269B LEU* 4.2 0.3 - - - +
282B GLY 3.8 20.2 - - - +
283B ASP 3.7 11.2 - - - -
284B VAL 3.8 4.9 - - - -
285B THR* 1.3 75.8 - - - +
287B PHE* 1.4 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLN* 3.7 1.2 - - - -
157B LEU* 2.7 52.4 + - + +
176B TRP* 3.6 30.3 - + + -
192B LYS* 5.5 1.1 - - - -
193B ILE* 3.6 31.6 - - + -
203B ILE* 4.1 19.5 - - + -
204B TYR* 3.2 25.1 - - - -
205B GLY* 4.1 0.9 - - - -
220B ILE* 4.3 13.5 - - + -
267B LEU* 3.8 32.8 - - + -
268B GLN* 3.9 8.7 - - - -
269B LEU* 4.0 24.7 - - + -
286B PHE* 1.4 78.0 - - - +
288B GLY* 1.3 56.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
155B LEU 3.2 13.2 - - - -
156B GLN* 4.2 0.2 - - - -
193B ILE* 3.8 10.3 - - - +
203B ILE* 3.5 8.8 - - - +
204B TYR* 2.8 53.4 + - - +
287B PHE* 1.3 75.5 - - - +
289B ALA* 1.3 59.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 5.9 0.3 - - - +
154B CYS* 3.4 2.6 - - - +
155B LEU 3.0 31.0 + - - +
186B LEU* 3.8 31.0 - - + -
193B ILE* 4.1 5.3 - - + +
201B PHE* 4.6 4.9 - - + -
202B PHE 3.3 9.2 - - - +
203B ILE* 4.3 5.4 - - + +
204B TYR* 4.1 5.1 + - - -
267B LEU* 4.2 18.8 - - + -
288B GLY* 1.3 74.0 - - - +
290B LEU* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.7 8.1 - - + -
108B VAL* 3.8 20.4 - - + -
142B LEU* 3.8 38.6 - - + -
152B GLN* 3.8 17.9 - - + +
153B ASP 3.5 9.4 - - - +
154B CYS* 4.3 4.5 - - + +
201B PHE* 3.2 4.8 - - - -
202B PHE* 2.8 57.5 + - + +
204B TYR* 5.2 0.7 - - + -
289B ALA* 1.3 76.8 - - - +
291B LYS* 1.3 62.5 + - - +
292B LEU* 3.8 24.0 - - + -
303B GLN* 6.0 0.7 - - - +
441B LEU* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.2 27.0 - - - +
153B ASP* 2.8 30.6 + - + +
185B ALA* 3.7 20.4 - - + -
186B LEU* 4.5 0.4 - - - +
197B GLU* 3.6 21.9 + - - +
198B THR 3.8 23.3 + - - -
199B GLY* 4.5 6.3 - - - -
200B TYR 3.9 4.7 - - - +
201B PHE* 3.6 29.8 - - + -
290B LEU* 1.3 72.0 - - - +
292B LEU* 1.3 76.4 + - - +
294B GLY 4.9 12.9 + - - -
----------------------------------------------------------
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