Contacts of the strand formed by residues 268 - 276 (chain H) 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 MET 268 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 3.8 20.9 - - + -
129H GLU 3.2 3.6 - - - +
130H PRO* 3.7 23.1 - - + -
235H ILE* 3.4 48.7 - - + -
239H LYS* 6.1 0.9 - - + -
267H GLY* 1.3 74.9 - - - -
269H HIS* 1.3 63.6 + - - +
270H CYS* 3.7 3.7 - - - -
361H PRO* 2.9 35.1 + - - +
362H ASP 3.7 15.5 - - - +
363H PRO* 3.2 24.5 - - + +
365H ALA* 5.3 7.6 - - - +
367H PRO* 5.4 3.6 - - + -
370H CYS* 6.0 1.3 - - - -
371H PHE* 4.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H GLY 3.7 1.0 - - - +
128H PRO* 3.1 7.1 - - - +
129H GLU* 2.9 44.5 + - + +
131H GLU* 4.8 3.6 - - - -
220H GLU* 5.9 0.2 - - - -
267H GLY 4.6 1.7 - - - -
268H MET* 1.3 74.2 - - - +
270H CYS* 1.3 59.5 + - - +
271H HIS* 4.1 0.9 - - - -
321H ARG* 4.5 0.7 - - - -
357H GLU* 3.3 15.8 + - + +
358H VAL 3.6 5.8 - - - -
359H ARG* 3.2 41.8 + - + +
470H MN 2.4 24.7 + - - -
5907H PPQ 2.9 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 270 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PHE* 4.7 8.1 - - + -
127H GLY 3.9 2.0 - - - -
128H PRO* 4.3 9.4 - - - -
268H MET* 3.7 12.3 - - - -
269H HIS* 1.3 78.2 - - - +
271H HIS* 1.3 63.9 + - - +
272H MET* 3.6 12.2 - - + +
357H GLU* 3.3 1.0 - - - -
358H VAL* 2.7 42.2 + - + +
361H PRO* 4.4 8.5 - - + -
370H CYS* 5.1 1.1 - - - -
371H PHE* 4.1 25.8 - - - -
374H LEU* 4.3 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 271 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H LEU 3.4 0.2 - - - +
126H PHE* 3.3 3.6 - - - +
127H GLY 2.9 41.8 + - - +
129H GLU* 3.4 17.2 + - - -
270H CYS* 1.3 74.3 - - - +
272H MET* 1.3 65.6 + - - +
344H ARG* 5.2 1.1 - - - -
346H PRO* 5.0 5.8 - - + -
355H ARG* 3.0 29.4 + - - -
356H ILE 3.1 3.8 - - - -
357H GLU* 2.7 52.0 + - + +
4478H ADP 2.7 54.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 272 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H VAL* 5.4 1.1 - - + -
125H LEU 3.0 12.3 - - - +
126H PHE* 3.5 39.9 - - + -
270H CYS* 3.6 11.4 + - + +
271H HIS* 1.3 80.5 - - - +
273H SER* 1.3 62.7 + - - +
282H PHE* 4.0 0.3 - - - -
297H TYR* 3.7 25.1 - - + +
301H VAL* 5.4 0.4 - - + -
355H ARG* 3.0 6.5 - - - +
356H ILE* 2.8 51.9 + - + +
358H VAL* 3.2 36.6 - - + -
374H LEU* 3.8 16.8 - - + -
4478H ADP 4.4 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 273 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H VAL* 3.9 1.1 - - - +
125H LEU* 2.9 36.4 + - - +
272H MET* 1.3 78.1 - - - +
274H LEU* 1.3 66.2 + - - +
280H ASN* 4.1 10.8 + - - -
282H PHE* 3.7 15.2 - - - -
354H ARG 3.7 17.5 - - - -
355H ARG* 3.8 0.7 - - - -
4478H ADP 2.5 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H LEU* 3.8 18.6 - - + -
120H ILE* 5.0 2.5 - - + -
121H ALA* 3.9 13.7 - - + -
123H THR 3.5 15.0 - - - +
124H VAL* 3.6 26.9 - - + -
273H SER* 1.3 75.8 - - - +
275H ALA* 1.3 61.8 + - - +
280H ASN* 3.4 8.8 - - - +
281H LEU* 3.1 29.5 + - + +
282H PHE* 3.3 25.4 - - + -
293H GLN* 5.4 1.3 - - + +
297H TYR* 3.7 28.9 - - + -
375H LEU* 4.4 1.8 - - + -
379H LEU* 4.3 14.8 - - + -
382H ILE* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H ALA* 3.2 4.9 - - - +
122H ASP* 2.8 35.2 + - - +
123H THR* 3.0 25.2 + - - +
125H LEU* 4.8 14.6 - - + -
274H LEU* 1.3 75.8 - - - +
276H LYS* 1.3 55.3 + - - +
278H GLY* 5.4 4.0 - - - +
279H THR 3.3 16.8 - - - +
280H ASN* 4.9 2.0 - - - -
281H LEU* 3.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H GLY* 3.0 30.9 + - - -
120H ILE 4.2 13.2 - - - +
121H ALA* 4.4 6.8 - - - +
122H ASP* 3.2 17.3 + - - +
275H ALA* 1.3 77.7 - - - +
277H ASN* 1.3 92.2 + - - +
279H THR* 3.0 21.2 + - - -
281H LEU* 3.4 18.8 - - + +
----------------------------------------------------------
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