Contacts of the strand formed by residues 268 - 276 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D PRO* 3.8 20.6 - - + -
129D GLU 3.2 4.0 - - - +
130D PRO* 3.7 23.3 - - + -
235D ILE* 3.4 48.9 - - + -
239D LYS* 6.1 0.9 - - + -
267D GLY* 1.3 73.5 - - - -
269D HIS* 1.3 63.6 + - - +
270D CYS* 3.6 3.4 + - - -
361D PRO* 2.9 35.4 + - - +
362D ASP 3.7 15.9 - - - +
363D PRO* 3.2 25.8 - - + +
365D ALA* 5.3 7.6 - - - +
367D PRO* 5.3 3.4 - - + -
370D CYS* 6.0 1.1 - - - -
371D PHE* 4.9 11.9 - - + -
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Residues in contact with HIS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLY 3.7 1.6 - - - +
128D PRO* 3.1 6.9 - - - +
129D GLU* 2.9 44.2 + - + +
131D GLU* 4.8 4.0 - - - -
220D GLU* 5.9 0.2 - - - -
267D GLY 4.6 1.9 - - - -
268D MET* 1.3 75.3 - - - +
270D CYS* 1.3 59.7 + - - +
271D HIS* 4.1 0.7 - - - -
321D ARG* 4.5 0.7 - - - -
357D GLU* 3.3 16.0 + - + +
358D VAL 3.6 5.6 - - - -
359D ARG* 3.2 42.3 + - + +
470D MN 2.4 24.5 + - - -
5903D PPQ 2.9 64.2 + - + +
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Residues in contact with CYS 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.7 8.3 - - + -
127D GLY 3.9 1.8 - - - -
128D PRO* 4.3 9.6 - - - -
268D MET* 3.7 13.2 - - - -
269D HIS* 1.3 78.2 - - - +
271D HIS* 1.3 63.7 + - - +
272D MET* 3.6 12.8 - - + +
357D GLU* 3.3 0.9 - - - -
358D VAL* 2.7 41.3 + - + +
361D PRO* 4.4 8.3 - - + -
370D CYS* 5.1 0.9 - - - -
371D PHE* 4.1 26.0 - - - -
374D LEU* 4.3 24.0 - - + -
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Residues in contact with HIS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU 3.4 0.2 - - - +
126D PHE* 3.3 2.9 - - - -
127D GLY 2.9 41.6 + - - +
129D GLU* 3.4 17.4 + - - -
270D CYS* 1.3 73.3 - - - +
272D MET* 1.3 66.3 + - - +
344D ARG* 5.2 1.1 - - - -
346D PRO* 5.0 6.3 - - + -
355D ARG* 3.0 29.3 + - - -
356D ILE 3.1 3.6 - - - -
357D GLU* 2.7 51.6 + - + +
4474D ADP 2.7 54.2 + - + -
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Residues in contact with MET 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D VAL* 5.4 1.1 - - + -
125D LEU 3.0 12.6 - - - +
126D PHE* 3.5 39.9 - - + -
270D CYS* 3.6 12.3 + - + +
271D HIS* 1.3 79.6 - - - +
273D SER* 1.3 62.4 + - - +
282D PHE* 4.0 0.4 - - - -
297D TYR* 3.7 25.4 - - + +
301D VAL* 5.4 0.2 - - + -
355D ARG* 3.0 6.7 - - - +
356D ILE* 2.8 50.0 + - + +
358D VAL* 3.2 37.0 - - + -
374D LEU* 3.8 17.0 - - + -
4474D ADP 4.4 2.2 + - - -
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Residues in contact with SER 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D VAL* 3.9 1.9 - - - +
125D LEU* 2.9 38.1 + - - +
272D MET* 1.3 79.7 - - - +
274D LEU* 1.3 66.2 + - - +
280D ASN* 4.0 10.3 + - - -
282D PHE* 3.7 15.0 - - - -
297D TYR* 6.0 0.2 - - - -
354D ARG 3.7 17.3 - - - -
355D ARG* 3.8 0.7 - - - -
4474D ADP 2.5 32.2 + - - -
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.8 19.3 - - + -
120D ILE* 5.0 3.1 - - + -
121D ALA* 3.9 13.7 - - + -
123D THR 3.5 15.3 - - - +
124D VAL* 3.6 26.5 - - + -
273D SER* 1.3 78.0 - - - +
275D ALA* 1.3 62.2 + - - +
280D ASN* 3.4 8.3 - - - +
281D LEU* 3.1 29.2 + - + +
282D PHE* 3.3 25.2 - - + -
293D GLN* 5.4 1.3 - - + -
297D TYR* 3.7 28.3 - - + -
375D LEU* 4.4 1.8 - - + -
379D LEU* 4.3 15.5 - - + -
382D ILE* 4.4 8.7 - - + -
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA* 3.2 5.1 - - - +
122D ASP* 2.8 34.1 + - - +
123D THR* 3.0 24.7 + - - +
125D LEU* 4.8 14.6 - - + -
274D LEU* 1.3 75.4 - - - +
276D LYS* 1.3 56.7 + - - +
278D GLY* 5.4 4.9 - - - +
279D THR 3.3 16.4 - - - +
280D ASN* 4.9 2.2 - - - -
281D LEU* 3.7 3.4 - - - -
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Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLY* 3.0 30.1 + - - -
120D ILE 4.2 12.8 - - - +
121D ALA* 4.5 6.1 - - - +
122D ASP* 3.2 18.0 + - - +
275D ALA* 1.3 78.2 - - - +
277D ASN* 1.3 93.3 + - - +
278D GLY 3.4 0.2 - - - -
279D THR* 3.0 21.0 + - - -
281D LEU* 3.4 18.1 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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