Contacts of the strand formed by residues 268 - 276 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B PRO* 3.8 20.9 - - + -
129B GLU 3.2 4.3 - - - +
130B PRO* 3.7 23.8 - - + -
235B ILE* 3.4 48.7 - - + -
239B LYS* 6.1 0.9 - - + -
267B GLY* 1.3 73.2 - - - -
269B HIS* 1.3 63.4 + - - +
270B CYS* 3.7 3.9 - - - -
361B PRO* 2.9 35.8 + - - +
362B ASP 3.7 15.3 - - - +
363B PRO* 3.2 25.4 - - + +
365B ALA* 5.3 7.2 - - - +
367B PRO* 5.4 3.4 - - + -
370B CYS* 6.0 1.1 - - - -
371B PHE* 4.9 11.9 - - + -
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Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLY 3.7 1.3 - - - +
128B PRO* 3.1 6.8 - - - +
129B GLU* 2.9 45.0 + - + +
131B GLU* 4.8 4.2 + - - -
220B GLU* 5.9 0.2 - - - -
267B GLY 4.6 2.2 - - - -
268B MET* 1.3 73.7 - - - +
270B CYS* 1.3 59.5 + - - +
271B HIS* 4.1 0.7 - - - -
321B ARG* 4.5 0.9 - - - -
357B GLU* 3.3 16.1 + - + +
358B VAL 3.6 5.6 - - - -
359B ARG* 3.2 41.7 + - + +
470B MN 2.4 24.9 + - - -
5901B PPQ 2.9 64.8 + - + +
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 4.7 8.5 - - + -
127B GLY 3.9 1.8 - - - -
128B PRO* 4.3 9.4 - - - -
268B MET* 3.7 12.8 - - - -
269B HIS* 1.3 77.6 - - - +
271B HIS* 1.3 63.0 + - - +
272B MET* 3.6 12.3 - - + +
357B GLU* 3.3 1.0 - - - -
358B VAL* 2.7 42.5 + - + +
361B PRO* 4.4 7.6 - - + -
370B CYS* 5.1 0.7 - - - -
371B PHE* 4.1 26.5 - - - -
374B LEU* 4.3 25.6 - - + -
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU 3.4 0.2 - - - +
126B PHE* 3.3 3.3 - - - +
127B GLY 2.9 42.1 + - - +
129B GLU* 3.4 17.9 + - - -
270B CYS* 1.3 74.1 - - - +
272B MET* 1.3 66.4 + - - +
344B ARG* 5.2 0.9 - - - -
346B PRO* 5.0 6.3 - - + -
355B ARG* 3.0 28.5 + - - -
356B ILE 3.1 3.8 - - - -
357B GLU* 2.7 52.0 + - + +
4472B ADP 2.7 52.5 + - + -
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Residues in contact with MET 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 5.4 1.3 - - + -
125B LEU 3.0 13.2 - - - +
126B PHE* 3.5 39.7 - - + -
270B CYS* 3.6 11.4 - - + +
271B HIS* 1.3 80.2 - - - +
273B SER* 1.3 62.9 + - - +
282B PHE* 4.4 0.7 - - + -
297B TYR* 3.7 25.4 - - + +
301B VAL* 5.4 0.2 - - + -
355B ARG* 3.0 6.0 - - - +
356B ILE* 2.8 51.3 + - + +
358B VAL* 3.2 37.0 - - + -
374B LEU* 3.8 17.3 - - + -
4472B ADP 4.4 1.8 - - - -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 4.0 0.9 - - - +
125B LEU* 2.9 36.4 + - - +
272B MET* 1.3 79.0 - - - +
274B LEU* 1.3 65.6 + - - +
280B ASN* 4.1 10.9 + - - -
282B PHE* 3.7 15.5 - - - -
297B TYR* 6.0 0.4 - - - -
354B ARG 3.7 16.6 - - - -
355B ARG* 3.8 1.1 - - - -
4472B ADP 2.5 33.1 + - - -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.8 19.3 - - + -
120B ILE* 5.0 2.9 - - + -
121B ALA* 3.9 12.8 - - + -
123B THR 3.5 15.5 - - - +
124B VAL* 3.6 27.1 - - + -
273B SER* 1.3 76.5 - - - +
275B ALA* 1.3 61.8 + - - +
280B ASN* 3.4 8.8 - - - +
281B LEU* 3.1 28.0 + - + +
282B PHE* 3.3 25.6 - - + -
293B GLN* 5.4 1.8 - - + +
297B TYR* 3.7 28.5 - - + -
375B LEU* 4.4 1.6 - - + -
379B LEU* 4.3 15.5 - - + -
382B ILE* 4.4 9.2 - - + -
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 3.2 5.5 - - - +
122B ASP* 2.8 33.8 + - - +
123B THR* 3.0 26.0 + - - +
125B LEU* 4.8 14.1 - - + -
274B LEU* 1.3 76.4 - - - +
276B LYS* 1.3 56.3 + - - +
278B GLY* 5.4 5.2 - - - +
279B THR 3.3 16.8 - - - +
280B ASN* 4.9 1.8 - - - -
281B LEU* 3.7 3.6 - - - -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY* 3.0 31.1 + - - -
120B ILE 4.2 13.7 - - - +
121B ALA* 4.5 6.1 - - - +
122B ASP* 3.2 17.5 + - - +
275B ALA* 1.3 78.2 - - - +
277B ASN* 1.3 93.5 + - - +
278B GLY 3.4 0.4 - - - -
279B THR* 3.0 21.0 + - - -
281B 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