Contacts of the strand formed by residues 164 - 169 (chain B) in PDB entry 3FN3
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 GLU 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 1.3 74.6 - - - +
165B VAL* 1.3 62.3 + - - +
166B ILE* 4.0 18.9 - - + +
179B THR* 5.4 3.4 - - - -
210B THR 3.6 0.3 - - - +
211B PHE* 3.4 3.1 - - - -
212B ARG* 2.7 66.5 + - + +
214B LEU* 4.7 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 1.3 78.5 - - - +
166B ILE* 1.3 66.9 + - - +
167B TRP* 3.7 24.4 + - + +
179B THR* 4.2 13.6 + - + +
193B VAL* 3.9 11.9 - - + -
195B SER* 3.6 37.0 - - - +
209B CYS* 4.2 15.3 - - + -
210B THR 3.0 8.3 - - - +
211B PHE* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 4.0 19.5 - - + +
165B VAL* 1.3 76.9 - - - +
167B TRP* 1.3 68.5 + - - +
168B THR* 4.2 12.9 + - + +
208B TYR 3.4 2.4 - - - +
210B THR* 2.6 49.9 + - + +
212B ARG* 3.5 60.1 - - + +
219B ASN* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.5 39.7 - - + -
154B THR 4.0 4.5 - - - -
155B CYS* 4.1 7.9 - - + -
165B VAL* 3.7 18.2 - - + +
166B ILE* 1.3 76.2 - - - +
168B THR* 1.3 67.1 + - - +
173B GLN 4.7 1.4 - - - +
175B LEU* 3.8 35.9 + - + +
176B SER* 5.3 0.9 - - - -
177B GLY* 4.3 21.8 - - - -
195B SER* 2.9 46.9 + - - -
196B THR 3.8 3.6 - - - +
197B LEU* 3.7 28.0 - - + -
207B PHE* 5.2 2.5 - - + -
208B TYR 3.3 11.9 - - - -
209B CYS* 3.8 27.1 - - + -
224B LEU* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.6 15.1 + - + +
167B TRP* 1.3 79.5 - - - +
169B SER* 1.3 64.3 + - - +
172B HIS* 4.7 17.5 - - + +
173B GLN 4.7 5.8 - - - +
175B LEU* 3.8 7.4 - - - +
207B PHE* 3.3 5.9 - - - +
208B TYR* 2.9 55.0 + - - +
210B THR* 5.2 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR* 1.3 76.8 - - - +
170B SER* 1.3 55.3 + - - +
171B ASP* 2.6 23.2 + - - -
172B HIS* 2.7 26.8 + - - +
173B GLN* 3.0 33.3 + - - +
175B LEU* 3.8 9.6 - - - +
206B ILE 3.4 5.8 - - - -
207B PHE* 3.8 23.8 - - - +
208B TYR* 4.2 7.6 - - - -
----------------------------------------------------------
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