Contacts of the strand formed by residues 123 - 135 (chain L) in PDB entry 1FPY
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 THR 123 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L GLU* 4.9 4.7 - - - +
115L LEU* 3.7 4.7 - - - +
116L ARG* 4.7 7.6 - - - +
121L ALA 3.7 1.4 - - - -
122L ASP* 1.3 98.6 + - - +
124L VAL* 1.3 65.8 + - - +
125L LEU* 4.8 10.0 - - - +
227L THR* 5.0 15.7 - - + -
274L LEU* 3.5 5.4 - - - +
275L ALA* 3.0 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L GLU* 4.0 19.5 + - + +
115L LEU* 3.8 29.6 - - + -
123L THR* 1.3 71.6 - - - +
125L LEU* 1.3 76.1 + - - +
126L PHE* 3.5 24.2 - - + -
227L THR* 3.3 2.9 - - - -
228L MET* 3.0 32.0 + - + -
272L MET* 5.4 0.9 - - + -
273L SER 4.3 2.9 - - - +
274L LEU* 3.6 15.3 - - + -
297L TYR* 4.3 5.6 - - + +
375L LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L THR* 4.8 9.9 - - - +
124L VAL* 1.3 90.2 - - - +
126L PHE* 1.3 61.9 + - - +
225L PHE* 3.5 30.7 - - + -
226L ASN 3.9 10.5 - - - +
227L THR* 4.0 11.0 - - + +
271L HIS 4.1 0.4 - - - -
272L MET* 3.0 32.9 - - - +
273L SER* 2.9 35.3 + - - +
275L ALA* 4.8 17.0 - - + -
4482L ADP 4.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L VAL* 3.5 18.8 - - + -
125L LEU* 1.3 78.1 - - - +
127L GLY* 1.3 57.7 + - - +
128L PRO* 3.8 2.7 - - + -
225L PHE* 3.1 23.7 - - - -
226L ASN 3.1 16.3 + - - +
228L MET* 3.4 36.3 - - + -
231L LYS* 3.5 22.0 - - + +
270L CYS* 4.7 8.1 - - + -
271L HIS 3.3 3.6 - - - -
272L MET* 3.5 33.9 - - + -
371L PHE* 3.3 61.2 - + + -
374L LEU* 4.0 8.3 - - + -
375L LEU* 4.4 3.6 - - + -
4482L ADP 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L PHE* 1.3 74.9 - - - +
128L PRO* 1.3 64.4 - - - +
129L GLU* 4.1 0.7 + - - +
225L PHE* 3.9 9.0 - - - -
269L HIS 3.7 1.2 - - - +
270L CYS* 4.7 0.2 - - - -
271L HIS* 2.9 44.2 + - - +
4482L ADP 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L PHE* 4.5 1.8 - - + -
127L GLY* 1.3 90.1 - - - +
129L GLU* 1.3 62.6 + - - +
130L PRO* 3.2 10.7 - - - +
222L ALA* 5.6 0.2 - - - -
223L THR* 4.3 12.6 + - - +
231L LYS* 3.3 33.9 - - + -
235L ILE* 4.1 8.2 - - + +
268L MET* 3.8 27.8 - - + -
269L HIS 3.1 8.3 - - - +
270L CYS* 4.3 8.1 - - - -
371L PHE* 3.6 26.7 - - + -
4482L ADP 4.3 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L GLY 4.7 2.5 - - - +
128L PRO* 1.3 73.2 - - + +
130L PRO* 1.3 58.3 - - - +
131L GLU* 3.4 3.3 + - - +
220L GLU* 3.5 20.0 - - - +
222L ALA* 5.8 3.4 - - + +
267L GLY 2.8 25.8 - - - +
268L MET* 3.2 8.0 - - - +
269L HIS* 2.9 22.0 + - + +
271L HIS* 3.4 13.7 + - - -
357L GLU* 2.8 6.6 - - - +
470L MN 1.9 33.3 + - - -
4482L ADP 2.6 55.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128L PRO 3.2 11.2 - - - +
129L GLU* 1.3 80.5 - - - +
131L GLU* 1.3 64.4 + - - +
132L PHE* 3.9 1.4 - - - -
220L GLU* 4.0 4.8 - - + +
221L VAL 4.1 15.5 - - - +
222L ALA* 5.7 0.2 - - - -
223L THR* 5.0 1.8 - - - +
235L ILE* 3.9 15.5 - - + -
238L TYR* 2.9 47.0 + - + -
239L LYS* 6.2 0.9 - - + -
255L PHE* 4.8 6.3 - - + -
267L GLY 3.9 2.5 - - - +
268L MET* 3.7 35.9 - - + -
363L PRO* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L GLU* 4.4 0.9 - - - +
130L PRO* 1.3 72.8 - - - +
132L PHE* 1.3 65.0 + - - +
212L GLU* 3.1 16.5 - - + +
218L GLN* 4.6 3.3 - - - +
219L ASN 3.8 5.6 - - - +
220L GLU* 3.0 25.8 - - + +
255L PHE* 3.4 15.1 - - - -
266L SER* 3.7 16.0 - - - -
267L GLY 3.0 28.4 + - - +
269L HIS* 4.8 1.5 - - - -
363L PRO* 3.5 11.7 - - - +
469L MN 2.3 30.2 + - - -
5911L PPQ 2.4 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L PRO 3.9 3.8 - - - -
131L GLU* 1.3 79.3 - - - +
133L PHE* 1.3 76.6 + - - +
134L LEU* 3.9 17.7 - - + -
192L ARG* 5.5 0.4 - - + -
195L MET* 4.0 21.1 - - - -
218L GLN* 3.2 5.4 - - - +
219L ASN* 2.7 67.2 + - + -
220L GLU* 4.2 2.5 - - - -
221L VAL* 4.3 8.1 - - + -
238L TYR* 3.5 19.1 - - - -
242L VAL* 3.9 24.9 - - + -
254L THR 3.5 16.2 - - - +
255L PHE* 3.7 25.8 - + + -
266L SER* 4.0 6.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L PHE* 1.3 77.8 - - - +
134L LEU* 1.3 64.5 + - - +
135L PHE* 3.3 21.5 - + + -
214L ALA* 3.6 9.0 - - + -
215L THR 3.6 2.9 - - - -
216L ALA 3.5 17.3 - - - -
217L GLY 3.3 4.7 - - - -
218L GLN* 3.4 32.3 - - + -
252L THR 3.9 0.2 - - - +
253L ALA* 3.3 6.8 - - - +
254L THR* 3.2 31.8 + - + +
256L MET 4.9 0.9 - - - -
259L PRO* 3.3 27.1 - - + -
260L MET* 3.1 31.9 - - + -
264L ASN 3.4 21.8 - - - -
266L SER* 3.3 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L PHE* 3.9 21.3 - - + -
133L PHE* 1.3 75.9 - - - +
135L PHE* 1.3 63.6 + - - +
153L ASP* 3.1 22.6 - - - +
188L ALA* 4.9 4.5 - - + -
191L ILE* 4.4 27.6 - - + -
192L ARG* 5.6 1.8 - - + -
195L MET* 4.5 6.7 - - + -
216L ALA 3.6 6.9 - - - +
217L GLY* 2.8 17.3 + - - +
219L ASN* 4.2 15.0 - - - +
246L ALA* 3.8 17.5 - - + -
251L LYS* 4.0 21.0 + - + -
252L THR 3.8 1.3 - - - +
253L ALA* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F PHE* 6.3 0.2 - + - -
466F TYR* 3.9 24.2 - + - -
133L PHE* 3.3 29.4 - + + -
134L LEU* 1.3 72.5 - - - +
136L ASP* 1.3 61.7 + - - +
137L ASP 4.1 6.3 - - - +
138L ILE* 5.0 3.6 - - + -
151L ILE* 3.6 31.0 - - + -
152L ASP 3.4 8.1 - - - +
153L ASP* 3.3 16.2 - - + -
216L ALA* 3.2 32.3 - - + -
251L LYS* 3.4 9.5 - - - +
252L THR* 3.0 39.2 + - + -
254L THR* 3.4 24.9 - - + -
259L PRO* 4.2 16.6 - - + -
260L MET* 4.2 3.8 - - + -
----------------------------------------------------------
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