Contacts of the strand formed by residues 268 - 276 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PRO* 3.8 20.9 - - + -
129C GLU 3.2 3.8 - - - +
130C PRO* 3.7 23.3 - - + -
235C ILE* 3.4 49.1 - - + -
239C LYS* 6.1 0.7 - - + -
267C GLY* 1.3 72.4 - - - -
269C HIS* 1.3 64.5 + - - +
270C CYS* 3.7 3.6 - - - -
321C ARG* 4.5 0.2 - - - +
361C PRO* 2.9 34.4 + - - +
362C ASP 3.7 16.8 - - - +
363C PRO* 3.2 26.3 - - + +
365C ALA* 5.3 6.3 - - - +
367C PRO* 5.4 4.0 - - + -
370C CYS* 6.0 1.3 - - - -
371C PHE* 4.9 12.1 - - + -
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Residues in contact with HIS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C GLY 3.7 1.3 - - - +
128C PRO* 3.1 6.8 - - - +
129C GLU* 2.9 45.2 + - + +
131C GLU* 4.8 4.0 + - - -
220C GLU* 5.9 0.4 - - - -
267C GLY 4.6 2.2 - - - -
268C MET* 1.3 74.3 - - - +
270C CYS* 1.3 59.9 + - - +
271C HIS* 4.1 0.9 - - - -
321C ARG* 4.5 0.7 - - - -
357C GLU* 3.3 16.5 + - + +
358C VAL 3.6 5.6 - - - -
359C ARG* 3.2 43.7 + - + +
470C MN 2.4 24.9 + - - -
5902C PPQ 2.9 64.8 + - + +
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Residues in contact with CYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 4.7 8.3 - - + -
127C GLY 3.9 1.6 - - - -
128C PRO* 4.3 9.4 - - - -
268C MET* 3.7 12.3 - - - -
269C HIS* 1.3 78.3 - - - +
271C HIS* 1.3 63.9 + - - +
272C MET* 3.6 12.2 - - + +
357C GLU* 3.3 1.0 - - - -
358C VAL* 2.7 41.5 + - + +
361C PRO* 4.4 7.9 - - + -
370C CYS* 5.1 1.1 - - - -
371C PHE* 4.1 26.2 - - - -
374C LEU* 4.3 24.9 - - + -
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Residues in contact with HIS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU 3.4 0.2 - - - +
126C PHE* 3.3 3.3 - - - +
127C GLY 2.9 42.0 + - - +
129C GLU* 3.4 17.0 + - - -
270C CYS* 1.3 74.1 - - - +
272C MET* 1.3 64.2 + - - +
344C ARG* 5.2 1.1 - - - -
346C PRO* 5.0 6.1 - - + -
355C ARG* 3.0 28.4 + - - -
356C ILE 3.1 4.5 - - - -
357C GLU* 2.7 52.7 + - + +
4473C ADP 2.7 53.8 + - + -
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Residues in contact with MET 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C VAL* 5.4 1.3 - - + -
125C LEU 3.0 13.2 - - - +
126C PHE* 3.5 39.7 - - + -
270C CYS* 3.6 12.5 + - + +
271C HIS* 1.3 79.6 - - - +
273C SER* 1.3 61.9 + - - +
282C PHE* 4.0 0.4 - - - -
297C TYR* 3.7 26.0 - - + +
301C VAL* 5.4 0.7 - - + -
355C ARG* 3.0 7.0 - - - +
356C ILE* 2.8 51.9 + - + +
358C VAL* 3.2 35.9 - - + -
374C LEU* 3.8 16.8 - - + -
4473C ADP 4.4 1.5 + - - -
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Residues in contact with SER 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 4.3 0.8 - - - +
125C LEU* 2.9 36.6 + - - +
272C MET* 1.3 79.4 - - - +
274C LEU* 1.3 65.3 + - - +
275C ALA 4.3 0.2 + - - -
280C ASN* 4.1 10.8 + - - -
282C PHE* 3.7 14.8 - - - -
297C TYR* 6.0 0.4 - - - -
354C ARG 3.7 16.8 - - - -
355C ARG* 3.8 0.9 - - - -
4473C ADP 2.5 33.0 + - - -
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU* 3.8 19.3 - - + -
120C ILE* 5.0 2.9 - - + -
121C ALA* 3.9 14.1 - - + -
123C THR 3.5 15.9 - - - +
124C VAL* 3.6 26.7 - - + -
273C SER* 1.3 75.8 - - - +
275C ALA* 1.3 61.0 + - - +
280C ASN* 3.4 8.5 - - - +
281C LEU* 3.1 28.9 + - + +
282C PHE* 3.3 25.4 - - + -
293C GLN* 5.4 1.6 - - + +
297C TYR* 3.7 28.5 - - + -
375C LEU* 4.4 1.8 - - + -
379C LEU* 4.3 14.6 - - + -
382C ILE* 4.4 9.0 - - + -
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ALA* 3.2 5.1 - - - +
122C ASP* 2.8 34.2 + - - +
123C THR* 3.0 26.5 + - - +
125C LEU* 4.8 14.4 - - + -
274C LEU* 1.3 75.5 - - - +
276C LYS* 1.3 55.9 + - - +
278C GLY* 5.4 4.9 - - - +
279C THR 3.3 17.0 - - - +
280C ASN* 4.9 1.8 - - - -
281C LEU* 3.7 3.8 - - - -
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY* 3.0 31.3 + - - -
120C ILE 4.2 13.0 - - - +
121C ALA* 4.5 6.1 + - - +
122C ASP* 3.2 17.3 + - - +
275C ALA* 1.3 76.6 - - - +
277C ASN* 1.3 92.9 + - - +
278C GLY 3.4 0.2 - - - -
279C THR* 3.0 21.0 + - - -
281C LEU* 3.4 18.4 - - + +
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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