Contacts of the helix formed by residues 287 - 299 (chain B) in PDB entry 1F0K
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 ARG 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PHE 5.1 3.6 - - - -
283B GLN* 3.8 12.3 - - - +
284B HIS* 2.6 33.4 + - - +
285B LYS* 3.9 7.9 - - - +
286B ASP* 1.3 74.2 - - - +
288B GLN* 1.3 66.0 + - - +
289B GLN 3.3 2.9 - - - -
290B TYR* 2.9 49.1 + - + +
291B TRP* 3.0 33.6 + - - +
306B GLU* 2.5 43.4 + - - +
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Residues in contact with GLN 288 (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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17B GLY* 5.9 4.1 + - - -
19B HIS* 5.8 1.4 + - - -
128B ASN* 3.2 45.1 + - + +
130B ILE* 4.0 18.7 + - + +
132B GLY* 6.0 3.8 - - - -
282B PHE 5.5 0.2 + - - -
284B HIS* 5.2 3.3 - - + +
286B ASP* 3.1 22.3 + - + +
287B ARG* 1.3 75.4 - - - +
289B GLN* 1.3 64.1 + - + +
291B TRP* 3.0 5.9 + - - +
292B ASN* 2.9 31.5 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 3.5 12.3 - - - +
262B SER* 2.8 60.4 + - - +
263B GLY* 3.8 13.9 - - - +
281B PRO* 4.0 1.3 - - + -
282B PHE* 3.0 50.7 + - + +
287B ARG 3.3 0.4 - - - -
288B GLN* 1.3 83.1 - - + +
290B TYR* 1.3 67.0 + - - +
292B ASN* 3.2 5.9 + - - +
293B ALA* 3.1 13.9 + - - +
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Residues in contact with TYR 290 (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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281B PRO* 3.7 16.3 - - + +
282B PHE 5.3 0.4 + - - -
287B ARG* 2.9 47.2 + - + +
289B GLN* 1.3 79.6 - - - +
291B TRP* 1.3 98.2 + + - +
293B ALA* 3.2 4.0 + - - +
294B LEU* 3.0 44.9 + - + +
297B GLU* 5.0 3.2 + - - -
304B ILE* 3.9 25.6 - - + -
306B GLU* 3.2 34.8 - - + +
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Residues in contact with TRP 291 (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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129B GLY* 3.7 29.0 - - - -
130B ILE* 4.0 25.4 - - + +
286B ASP 3.5 18.6 + - - -
287B ARG* 3.0 49.7 + - - +
288B GLN 3.5 4.9 - - - +
290B TYR* 1.3 89.6 - + - +
292B ASN* 1.3 63.1 + - - +
294B LEU* 3.4 36.4 - - + +
295B PRO* 3.1 18.5 - - - +
298B LYS* 5.7 0.7 - - - -
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Residues in contact with ASN 292 (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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128B ASN* 3.2 30.2 - - - +
129B GLY* 2.7 34.8 + - - +
149B PHE* 4.2 7.6 - - + -
262B SER 3.3 20.7 + - - +
263B GLY* 3.8 1.8 - - - -
264B ALA* 3.3 24.8 - - - +
267B VAL* 3.4 25.4 - - + +
288B GLN* 2.9 20.2 + - - +
289B GLN* 3.6 7.3 - - - +
290B TYR 3.2 0.2 - - - -
291B TRP* 1.3 78.4 - - - +
293B ALA* 1.3 56.8 + - - +
295B PRO* 3.3 13.5 - - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B SER* 3.7 16.8 - - - +
267B VAL* 4.3 6.5 - - - -
279B PHE* 3.6 30.3 - - + -
281B PRO* 4.9 1.6 - - + -
289B GLN 3.1 9.5 + - - +
290B TYR 3.2 0.4 + - - +
292B ASN* 1.3 75.8 - - - +
294B LEU* 1.3 65.3 + - - +
295B PRO* 3.2 3.6 - - - -
296B LEU* 3.0 16.8 + - - +
297B GLU* 3.1 8.8 + - - +
304B ILE* 3.6 20.4 - - + +
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Residues in contact with LEU 294 (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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290B TYR* 3.0 40.1 + - + +
291B TRP* 3.4 39.9 - - + +
293B ALA* 1.3 75.2 - - - +
295B PRO* 1.3 63.8 - - + +
297B GLU* 3.1 18.9 + - - +
298B LYS* 2.8 72.8 + - + +
304B ILE* 3.4 6.2 - - + +
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Residues in contact with PRO 295 (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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129B GLY* 5.5 0.9 - - - -
149B PHE* 4.0 32.3 - - + -
150B PRO* 4.8 16.4 - - + +
291B TRP 3.1 18.8 - - - +
292B ASN 3.3 13.7 - - - +
293B ALA 3.3 0.7 - - - -
294B LEU* 1.3 92.2 - - + +
296B LEU* 1.3 63.4 + - + +
298B LYS* 3.4 11.3 + - + +
299B ALA* 3.1 23.0 + - - +
337B ALA* 5.7 1.3 - - - +
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Residues in contact with LEU 296 (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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149B PHE* 6.3 0.2 - - + -
267B VAL* 3.7 39.3 - - + +
270B ILE* 4.4 11.9 - - + -
271B ALA* 4.3 13.9 - - + -
275B LEU 5.7 0.2 - - - +
279B PHE* 3.8 18.2 - - + -
293B ALA 3.0 9.8 + - - +
295B PRO* 1.3 79.5 - - + +
297B GLU* 1.3 63.5 + - - +
299B ALA* 3.3 6.1 + - + +
301B ALA* 2.9 44.1 + - + +
302B ALA* 4.1 14.1 - - + -
334B ALA* 4.4 4.3 - - + -
337B ALA* 3.7 29.6 - - + +
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Residues in contact with GLU 297 (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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290B TYR* 5.0 3.1 + - - -
293B ALA 3.1 4.6 + - - -
294B LEU* 3.1 19.8 + - + +
296B LEU* 1.3 75.9 - - - +
298B LYS* 1.3 59.0 + - - +
300B GLY* 3.0 19.2 + - - -
302B ALA* 3.4 23.3 - - + +
303B LYS* 3.6 6.2 - - - +
304B ILE* 2.7 61.0 + - + +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 5.7 0.6 - - - -
294B LEU* 2.8 56.5 + - + +
295B PRO* 3.6 9.6 - - + +
297B GLU* 1.3 76.5 - - - +
299B ALA* 1.3 60.0 + - - +
300B GLY 3.1 1.3 + - - -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO 3.1 15.6 + - - +
296B LEU* 3.7 8.5 - - - +
297B GLU 3.2 0.6 - - - -
298B LYS* 1.3 77.0 - - - +
300B GLY* 1.3 62.4 + - - +
301B ALA* 3.5 5.1 + - + +
333B ARG* 3.2 25.7 + - + +
337B ALA* 4.7 17.7 - - + -
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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