Contacts of the helix formed by residues 287 - 299 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PHE 5.2 3.6 - - - -
283A GLN* 4.4 8.7 - - - +
284A HIS* 2.9 26.9 + - - +
285A LYS* 3.8 9.4 - - - +
286A ASP* 1.3 82.1 + - - +
288A GLN* 1.3 66.1 + - - +
289A GLN 3.4 2.5 - - - -
290A TYR* 3.0 59.1 + - + +
291A TRP* 2.9 33.5 + - - +
306A GLU* 2.9 33.8 + - - +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 5.9 2.2 - - - -
128A ASN* 3.1 49.2 + - + +
130A ILE* 3.5 15.1 + - + +
282A PHE 5.4 0.4 + - - -
284A HIS* 5.2 1.4 - - + +
286A ASP* 2.8 26.5 + - - +
287A ARG* 1.3 74.9 - - - +
289A GLN* 1.3 72.6 + - + +
291A TRP* 2.9 15.4 + - - +
292A ASN* 2.9 19.3 + - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 3.5 12.4 - - - +
262A SER* 2.6 53.0 + - - +
263A GLY* 3.6 26.3 - - - +
281A PRO* 3.9 2.2 - - + -
282A PHE* 2.9 49.2 + - + +
287A ARG 3.4 0.6 - - - -
288A GLN* 1.3 84.9 + - + +
290A TYR* 1.3 61.7 + - - +
292A ASN* 3.3 3.0 + - - +
293A ALA* 3.1 14.9 + - - +
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PRO* 3.8 14.7 - - + +
282A PHE 5.4 0.4 + - - -
287A ARG* 3.0 60.4 + - + +
289A GLN* 1.3 78.0 - - - +
291A TRP* 1.3 80.5 + + - +
293A ALA* 3.3 1.4 + - - -
294A LEU* 2.9 63.3 + - + +
297A GLU* 5.3 2.5 + - - -
304A ILE* 3.8 32.0 - - + +
306A GLU* 3.8 17.9 - - - +
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY* 3.7 17.8 - - - -
130A ILE* 3.3 37.4 - - + +
286A ASP 3.4 17.0 + - - -
287A ARG* 2.9 47.8 + - + +
288A GLN 2.9 6.8 + - - +
290A TYR* 1.3 87.1 - + - +
292A ASN* 1.3 57.8 + - - +
294A LEU* 3.4 34.5 - - + +
295A PRO* 2.9 25.1 - - - +
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Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 3.1 23.3 - - - +
129A GLY* 2.6 34.3 + - - +
149A PHE* 4.3 8.2 - - + -
262A SER 3.2 21.1 + - - +
263A GLY* 4.1 1.6 - - - -
264A ALA* 3.2 30.0 - - - +
267A VAL* 3.4 25.7 - - + +
288A GLN* 2.9 21.9 + - - +
289A GLN* 3.7 5.9 - - - +
290A TYR 3.2 0.4 - - - -
291A TRP* 1.3 76.5 - - - +
293A ALA* 1.3 58.8 + - - +
295A PRO* 3.1 16.0 - - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A SER* 3.8 10.1 - - - +
267A VAL* 4.2 7.0 - - - -
279A PHE* 3.5 31.0 - - + -
289A GLN 3.1 16.2 + - - +
290A TYR* 4.6 0.7 - - - -
292A ASN* 1.3 74.6 - - - +
294A LEU* 1.3 65.5 + - - +
295A PRO* 3.1 3.4 - - - -
296A LEU* 2.8 18.5 + - - +
297A GLU* 3.2 8.3 + - - +
304A ILE* 3.5 20.3 - - + +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A TYR* 2.9 41.3 + - + +
291A TRP* 3.4 39.0 - - + +
293A ALA* 1.3 74.4 - - - +
295A PRO* 1.3 62.7 - - + +
297A GLU* 3.3 19.4 + - + +
298A LYS* 2.9 38.8 + - + +
304A ILE* 3.3 8.2 - - + +
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Residues in contact with PRO 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY* 5.5 0.7 - - - -
149A PHE* 4.3 31.2 - - + -
150A PRO* 5.2 11.7 - - + +
291A TRP 2.9 22.0 - - - +
292A ASN 3.1 14.4 - - - +
293A ALA 2.9 0.4 - - - -
294A LEU* 1.3 93.1 - - + +
296A LEU* 1.3 62.5 + - + +
298A LYS* 3.6 9.1 + - + +
299A ALA* 3.3 20.8 + - - +
337A ALA* 5.7 1.5 - - - +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 6.2 0.2 - - + -
267A VAL* 3.6 34.8 - - + +
270A ILE* 4.4 11.2 - - + -
271A ALA* 4.1 19.5 - - + +
279A PHE* 3.5 34.1 - - + -
293A ALA 2.8 11.6 + - - +
295A PRO* 1.3 74.0 - - + +
297A GLU* 1.3 64.4 + - - +
299A ALA* 3.1 9.9 + - - +
300A GLY 3.2 0.2 + - - -
301A ALA* 2.9 40.5 + - + +
302A ALA* 4.1 7.6 - - + -
334A ALA* 4.4 4.7 - - + -
337A ALA* 4.2 21.5 - - + +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A TYR* 5.3 2.6 + - - -
293A ALA 3.2 3.0 + - - +
294A LEU* 3.7 21.1 - - - +
296A LEU* 1.3 78.2 - - - +
298A LYS* 1.3 58.9 + - - +
300A GLY* 2.8 21.0 + - - -
302A ALA* 3.5 24.5 - - + +
303A LYS* 3.6 10.1 + - - +
304A ILE* 2.7 58.4 + - + +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LEU* 2.9 26.7 + - + +
295A PRO* 3.7 8.1 - - + +
296A LEU 3.3 0.2 - - - -
297A GLU* 1.3 78.4 - - - +
299A ALA* 1.3 60.1 + - - +
300A GLY* 3.2 0.9 + - - -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PRO 3.3 11.5 + - - +
296A LEU* 3.1 12.7 + - - +
297A GLU 3.1 0.6 - - - -
298A LYS* 1.3 79.2 - - - +
300A GLY* 1.3 61.4 + - - +
301A ALA* 4.5 4.5 - - + +
333A ARG* 3.4 25.5 + - + +
337A ALA* 4.6 18.2 - - + -
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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