Contacts of the strand formed by residues 268 - 276 (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 MET 268 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128L PRO* 3.8 20.9 - - + -
129L GLU 3.2 4.0 - - - +
130L PRO* 3.7 22.4 - - + -
235L ILE* 3.4 49.1 - - + -
239L LYS* 6.1 0.7 - - + -
267L GLY* 1.3 73.5 - - - -
269L HIS* 1.3 62.8 + - - +
270L CYS* 3.7 3.6 - - - -
321L ARG* 4.5 0.2 - - - +
361L PRO* 2.9 35.1 + - - +
362L ASP 3.7 15.9 - - - +
363L PRO* 3.2 26.1 - - + +
365L ALA* 5.3 7.4 - - - +
367L PRO* 5.3 3.4 - - + -
370L CYS* 6.0 0.9 - - - -
371L PHE* 4.9 11.7 - - + -
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Residues in contact with HIS 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L GLY 3.7 1.4 - - - +
128L PRO* 3.1 7.1 - - - +
129L GLU* 2.9 44.9 + - + +
131L GLU* 4.8 4.0 - - - -
220L GLU* 5.9 0.2 - - - -
267L GLY 4.6 2.1 - - - -
268L MET* 1.3 74.4 - - - +
270L CYS* 1.3 59.0 + - - +
271L HIS* 4.1 0.9 - - - -
321L ARG* 4.5 0.9 - - - -
357L GLU* 3.3 15.6 + - + +
358L VAL 3.6 5.8 - - - -
359L ARG* 3.2 41.7 + - + +
470L MN 2.4 24.0 + - - -
5911L PPQ 2.9 65.6 + - + +
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Residues in contact with CYS 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L PHE* 4.7 8.5 - - + -
127L GLY 3.9 1.8 - - - -
128L PRO* 4.3 9.9 - - - -
268L MET* 3.7 12.6 - - - -
269L HIS* 1.3 78.2 - - - +
271L HIS* 1.3 63.9 + - - +
272L MET* 3.6 12.3 - - + +
357L GLU* 3.3 0.7 - - - -
358L VAL* 2.7 42.8 + - + +
361L PRO* 4.4 8.3 - - + -
370L CYS* 5.1 1.1 - - - -
371L PHE* 4.1 25.1 - - - -
374L LEU* 4.2 24.2 - - + -
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Residues in contact with HIS 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L PHE* 3.3 3.5 - - - +
127L GLY 2.9 42.5 + - - +
129L GLU* 3.4 17.2 + - - -
270L CYS* 1.3 73.3 - - - +
272L MET* 1.3 65.6 + - - +
344L ARG* 5.2 0.9 - - - -
346L PRO* 5.0 5.8 - - + -
355L ARG* 3.0 29.4 + - - -
356L ILE 3.1 3.8 - - - -
357L GLU* 2.7 52.3 + - + +
4482L ADP 2.7 52.7 + - + -
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Residues in contact with MET 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L VAL* 5.4 1.3 - - + -
125L LEU 3.0 13.2 - - - +
126L PHE* 3.5 40.8 - - + -
270L CYS* 3.6 11.2 - - + +
271L HIS* 1.3 80.3 - - - +
273L SER* 1.3 62.8 + - - +
282L PHE* 4.0 0.4 - - + -
297L TYR* 3.7 24.9 - - + +
301L VAL* 5.4 0.9 - - + -
355L ARG* 3.0 6.2 - - - +
356L ILE* 2.8 52.3 + - + +
358L VAL* 3.2 36.3 - - + -
374L LEU* 3.8 17.0 - - + -
4482L ADP 4.4 1.6 - - - -
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Residues in contact with SER 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L VAL* 4.0 1.1 - - - +
125L LEU* 2.9 37.1 + - - +
272L MET* 1.3 80.3 - - - +
274L LEU* 1.3 64.5 + - - +
275L ALA 4.3 0.2 + - - -
280L ASN* 4.0 10.7 + - - -
282L PHE* 3.7 14.1 - - - -
354L ARG 3.7 17.0 - - - -
355L ARG* 3.8 0.7 - - - -
4482L ADP 2.5 32.7 + - - -
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Residues in contact with LEU 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L LEU* 3.8 19.1 - - + -
120L ILE* 5.0 2.9 - - + -
121L ALA* 3.9 13.2 - - + -
123L THR 3.5 15.3 - - - +
124L VAL* 3.6 26.7 - - + -
273L SER* 1.3 78.2 - - - +
275L ALA* 1.3 62.6 + - - +
280L ASN* 3.4 8.1 - - - +
281L LEU* 3.1 29.0 + - + +
282L PHE* 3.3 26.0 - - + -
293L GLN* 5.4 1.3 - - + -
297L TYR* 3.7 28.7 - - + -
375L LEU* 4.4 2.0 - - + -
379L LEU* 4.3 15.3 - - + -
382L ILE* 4.4 9.0 - - + -
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Residues in contact with ALA 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ALA* 3.2 5.8 - - - +
122L ASP* 2.8 34.4 + - - +
123L THR* 3.0 25.5 + - - +
125L LEU* 4.8 14.6 - - + -
273L SER 4.3 0.2 + - - -
274L LEU* 1.3 76.7 - - - +
276L LYS* 1.3 54.7 + - - +
278L GLY* 5.4 5.2 - - - +
279L THR 3.3 16.4 - - - +
280L ASN* 4.9 1.8 - - - -
281L LEU* 3.7 3.1 - - - -
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Residues in contact with LYS 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L GLY* 3.0 30.9 + - - -
120L ILE 4.2 13.2 - - - +
121L ALA* 4.4 7.0 + - - +
122L ASP* 3.2 17.5 + - - +
275L ALA* 1.3 77.5 - - - +
277L ASN* 1.3 90.8 + - - +
278L GLY 3.4 0.2 - - - -
279L THR* 3.0 21.2 + - - -
281L LEU* 3.4 19.1 - - + -
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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