Contacts of the strand formed by residues 171 - 177 (chain J) in PDB entry 3FFC
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 171 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J TYR* 4.3 5.1 + - - -
139J PRO* 4.6 0.7 - - + -
166J PHE* 3.6 47.8 - - + -
169J ASP* 3.5 11.8 + - - +
170J HIS* 1.3 82.3 - - - +
172J GLU* 1.3 68.6 + - - +
173J LEU 5.2 0.2 - - - +
206J LEU* 4.0 21.7 - - + +
228J VAL* 3.8 20.6 - - + -
229J GLN 3.1 6.7 - - - +
230J PHE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I SER* 5.6 8.2 + - - +
9J ARG* 4.6 6.6 - - - +
10J TYR* 3.5 26.6 + - - +
171J VAL* 1.3 78.3 - - - +
173J LEU* 1.3 63.0 + - - +
174J SER* 3.8 3.9 + - - -
227J GLN* 3.6 2.8 + - - +
228J VAL* 4.4 1.1 - - - -
229J GLN* 2.9 40.8 + - + +
231J TYR* 2.9 28.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J CYS* 4.3 7.9 - - + -
163J ALA* 4.1 20.9 - - + -
171J VAL 4.1 1.4 + - - -
172J GLU* 1.3 70.9 - - - +
174J SER* 1.3 73.4 + - - +
175J TRP* 4.2 6.1 - - + +
188J THR* 4.2 15.9 + - + +
206J LEU* 3.9 37.5 - - + +
208J SER* 3.7 33.2 - - - +
226J CYS* 3.3 26.0 - - - -
227J GLN 3.3 4.3 - - - -
228J VAL* 3.8 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J GLU 4.5 3.7 + - - -
173J LEU* 1.3 79.2 - - - +
175J TRP* 1.3 66.9 + - - +
176J TRP* 2.9 22.5 + - - -
181J GLU* 3.4 24.5 - - - -
186J VAL* 6.0 1.3 - - - -
226J CYS* 3.9 0.5 - - - -
227J GLN* 2.8 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 175 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J VAL* 4.4 7.4 - - + -
159J LEU* 3.6 41.3 - - + -
160J VAL 4.3 1.1 - - - -
161J CYS* 3.3 34.1 - - + -
173J LEU* 4.2 4.1 - - + +
174J SER* 1.3 74.7 - - - +
176J TRP* 1.3 67.9 + - - +
181J GLU* 3.4 4.3 + - - +
182J VAL* 2.9 48.2 + - + -
186J VAL* 3.5 28.4 - - + +
188J THR* 5.4 0.2 - - - -
208J SER* 3.1 32.3 + - - -
209J ARG 4.0 4.9 - - - -
210J LEU* 3.5 31.2 - - + -
224J PHE* 4.7 2.5 - - + -
225J ARG 3.6 15.9 - - - -
226J CYS* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 176 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J SER* 2.9 32.8 + - - -
175J TRP* 1.3 78.6 + - - +
177J VAL* 1.3 62.9 + - - +
178J ASN 4.0 1.0 + - - -
179J GLY* 4.0 21.3 - - - +
180J LYS 3.3 7.4 - - - +
181J GLU* 3.4 43.1 - - + -
223J HIS* 3.4 4.3 - - - +
224J PHE* 3.7 0.5 - - - -
225J ARG* 2.7 71.1 + - + +
227J GLN* 3.6 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J TRP* 1.3 73.0 - - - +
178J ASN* 1.3 89.7 + - - +
179J GLY 3.4 0.4 - - - -
180J LYS* 2.8 26.7 + - - +
182J VAL* 3.8 24.5 - - + -
210J LEU* 3.7 30.3 - - + -
212J VAL* 5.3 2.2 - - + -
216J PHE* 3.6 26.0 - - + -
223J HIS 3.4 3.6 - - - -
224J PHE* 3.9 13.2 - - + -
----------------------------------------------------------
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