Contacts of the helix formed by residues 267 - 281 (chain F) in PDB entry 1P8J
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 ALA 267 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F ASP* 3.4 31.1 + - + +
236F GLU* 4.9 1.0 + - - -
265F GLY 3.5 3.2 + - - +
266F PRO* 1.3 74.6 - - - +
268F ARG* 1.3 62.1 + - - +
269F LEU 3.5 1.3 - - - -
270F ALA* 3.5 1.4 + - - +
271F GLU* 2.9 29.3 + - - +
308F TYR* 4.7 0.8 + - - -
530G ASP* 5.9 0.7 - - - +
802P ARG* 5.7 0.2 - - - +
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Residues in contact with ARG 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ASP* 4.0 0.2 - - - +
267F ALA* 1.3 79.1 - - - +
269F LEU* 1.3 58.0 + - - +
271F GLU* 3.4 5.8 + - - +
272F GLU* 3.1 32.2 + - - +
266G PRO 5.1 10.9 + - - -
267G ALA 6.2 1.8 - - - -
271G GLU* 5.5 10.7 + - - +
490G ARG* 3.9 16.1 - - - +
529G ASN 4.9 4.2 + - - -
530G ASP* 3.4 40.3 + - - +
531G TRP* 5.3 12.9 - - - -
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ASP* 2.8 23.9 + - + +
234F ALA* 4.1 13.7 - - + +
237F ALA* 3.6 14.5 - - + +
268F ARG* 1.3 72.6 - - - +
270F ALA* 1.3 59.9 + - - +
272F GLU* 3.3 24.6 + - - +
273F ALA* 2.9 27.5 + - - +
449G LYS* 4.3 11.6 + - - +
451G ILE* 4.0 29.2 - - + -
488G GLN* 5.2 0.4 - - - +
490G ARG* 3.5 32.3 - - - +
530G ASP* 5.7 0.4 - - - +
567G THR* 4.2 14.4 - - + +
569G VAL* 4.4 9.2 - - + -
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Residues in contact with ALA 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ASP* 2.9 17.8 + - - +
236F GLU* 3.8 27.4 - - + +
237F ALA* 4.0 5.3 - - - +
240F LEU* 4.0 8.3 - - + +
266F PRO* 3.7 22.0 - - + -
267F ALA 4.0 2.0 - - - +
268F ARG 3.4 0.2 - - - -
269F LEU* 1.3 72.3 - - - +
271F GLU* 1.3 66.4 + - - +
273F ALA* 3.1 8.6 + - - +
274F PHE* 3.0 26.0 + - - -
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F PRO* 3.2 30.0 - - - +
267F ALA 2.9 20.1 + - - +
268F ARG* 3.6 5.4 - - - +
270F ALA* 1.3 75.6 - - - +
272F GLU* 1.3 62.3 + - + +
274F PHE* 3.4 7.9 + - - +
275F PHE* 3.2 22.6 + - + +
311F SER* 5.1 1.4 + - - -
313F TYR* 3.7 24.8 + - - -
4070F SO4 3.0 35.7 + - - +
272G GLU* 4.4 4.7 - - + +
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Residues in contact with GLU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ARG* 3.1 16.1 + - - +
269F LEU* 3.4 21.6 - - - +
271F GLU* 1.3 77.0 - - + +
273F ALA* 1.3 51.5 + - - +
275F PHE* 3.2 5.7 + - - +
276F ARG* 2.7 39.3 + - + +
271G GLU* 4.4 16.0 - - + +
275G PHE* 5.4 1.8 - - + -
313G TYR* 4.2 17.6 + - - +
449G LYS* 2.7 34.8 + - - +
488G GLN* 5.1 4.9 + - - +
490G ARG* 4.0 17.0 + - - -
571G TYR* 3.9 8.3 + - - -
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Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F ALA* 3.8 29.8 - - + +
240F LEU* 4.1 17.2 - - + +
241F GLY* 4.6 6.3 - - - +
269F LEU 2.9 14.0 + - - +
270F ALA 3.4 9.2 - - - +
272F GLU* 1.3 76.9 - - - +
274F PHE* 1.3 57.1 + - - +
276F ARG* 3.6 9.5 - - - +
277F GLY* 2.8 29.3 + - - -
289F PHE* 4.5 2.6 - - - -
449G LYS* 4.9 2.2 - - - +
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Residues in contact with PHE 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU* 3.7 30.5 - - + -
266F PRO* 4.2 21.1 - - + -
270F ALA 3.0 18.8 + - - -
271F GLU* 3.6 8.7 - - - +
272F GLU 3.2 0.2 - - - -
273F ALA* 1.3 77.0 - - - +
275F PHE* 1.3 62.4 + - - +
278F VAL* 3.1 25.3 + - - +
289F PHE* 3.7 29.8 - + - -
291F TRP* 3.6 26.2 - + - -
308F TYR* 4.0 20.4 - + + -
311F SER* 4.7 5.2 - - - -
313F TYR* 3.5 28.3 - + + -
314F THR* 3.6 24.2 - - + -
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Residues in contact with PHE 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F GLU* 3.2 9.2 + - + +
272F GLU* 3.2 8.3 + - - +
274F PHE* 1.3 77.4 - - - +
276F ARG* 1.3 65.4 + - - +
278F VAL* 3.3 9.7 + - + -
279F SER* 2.8 45.5 + - - -
313F TYR* 3.8 34.2 - + + +
390F TRP* 6.2 0.4 - + - -
447F GLN* 5.8 1.1 - - - -
449F LYS* 6.1 0.7 - - - -
272G GLU* 3.9 32.8 - - + -
275G PHE* 3.3 30.1 - + + -
276G ARG* 4.0 30.5 - - + -
279G SER* 5.7 0.4 - - - -
280G GLN* 4.2 15.0 - - - -
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Residues in contact with ARG 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F GLY* 6.4 1.8 - - - -
244F PRO* 6.3 3.2 - - + +
272F GLU* 2.7 22.4 + - + +
273F ALA* 3.6 7.4 - - - +
275F PHE* 1.3 73.1 - - - +
277F GLY* 1.3 57.2 + - - +
279F SER* 3.3 0.5 + - - -
280F GLN* 2.8 61.6 + - + +
275G PHE* 4.0 24.8 - - + -
447G GLN* 2.9 55.1 + - - -
448G ARG* 4.2 0.2 - - - +
449G LYS* 3.7 49.7 - - - +
479G ASN* 5.0 3.0 + - - -
571G TYR* 4.4 4.2 - - - -
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Residues in contact with GLY 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU 5.7 1.8 - - - -
241F GLY* 6.3 2.0 - - - -
244F PRO* 5.5 5.6 - - - -
273F ALA 2.8 19.4 + - - -
274F PHE 3.9 1.1 - - - -
276F ARG* 1.3 74.8 - - - +
278F VAL* 1.3 53.4 + - - +
281F GLY* 2.9 20.8 + - - -
287F SER* 2.7 43.0 + - - -
289F PHE* 4.4 4.7 - - - -
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Residues in contact with VAL 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PHE 3.1 18.0 + - - +
275F PHE* 3.8 10.5 - - + +
276F ARG 3.3 0.2 - - - -
277F GLY* 1.3 76.5 - - - +
279F SER* 1.3 62.8 + - - +
284F GLY 4.8 1.4 - - - +
285F LEU 4.4 0.5 - - - -
286F GLY* 3.2 20.0 + - - -
287F SER 4.0 11.7 - - - +
289F PHE* 4.4 3.4 - - + -
313F TYR* 3.9 31.6 - - + +
390F TRP* 3.2 64.6 + - + +
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Residues in contact with SER 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F PHE* 2.8 42.2 + - - -
276F ARG 3.8 2.2 - - - -
278F VAL* 1.3 81.8 - - - +
280F GLN* 1.3 68.1 + - - +
284F GLY* 3.4 22.0 - - - +
275G PHE* 3.8 11.5 - - - -
279G SER* 4.4 13.5 + - - -
280G GLN* 4.6 5.1 + - - -
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Residues in contact with GLN 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F PRO* 5.1 3.5 - - + +
245F ASN* 3.8 6.4 + - - +
276F ARG* 2.8 52.9 + - + +
279F SER* 1.3 78.6 - - - +
281F GLY* 1.3 67.4 + - - +
283F GLY* 3.6 5.4 + - - -
284F GLY* 3.1 12.5 + - - +
275G PHE* 3.7 27.9 - - - -
278G VAL* 6.4 0.2 - - - +
279G SER* 4.6 5.2 + - - -
447G GLN* 4.6 9.0 + - - +
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Residues in contact with GLY 281 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F PRO* 3.7 16.7 - - - +
276F ARG 3.8 0.4 + - - -
277F GLY* 2.9 22.4 + - - -
279F SER 3.8 0.2 - - - -
280F GLN* 1.3 78.0 - - - +
282F ARG* 1.3 68.5 + - - -
284F GLY 2.8 11.1 + - - -
286F GLY* 2.9 16.7 + - - -
287F SER* 3.7 11.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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