Contacts of the helix formed by residues 289 - 298 (chain B) in PDB entry 4IF8
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 VAL 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ARG* 3.9 39.5 + - + +
53B MET* 4.7 8.6 - - + +
54B ASP* 3.5 44.1 + - + +
288B GLN* 1.3 71.5 - - + +
290B ASP* 1.3 69.6 + - - +
291B THR 3.2 2.4 + - - -
292B PHE* 3.9 9.9 + - - +
293B SER* 3.9 8.0 + - - -
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Residues in contact with ASP 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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50B ARG* 4.8 9.7 + - - -
288B GLN* 3.5 9.9 - - + +
289B VAL* 1.3 80.9 - - - +
291B THR* 1.4 57.4 + - - +
293B SER* 2.8 22.8 + - - +
294B ARG* 3.0 27.4 + - + +
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Residues in contact with THR 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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57B PHE* 4.7 3.4 - - + -
255B LEU* 3.7 28.0 - - + +
286B GLY 3.4 9.4 + - - +
287B LEU* 4.6 6.3 - - + -
288B GLN* 2.9 42.7 + - - +
289B VAL 3.2 0.4 - - - -
290B ASP* 1.4 76.5 - - - +
292B PHE* 1.3 58.5 + - - +
294B ARG* 3.6 12.9 + - - +
295B TRP* 3.0 54.6 + - + -
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Residues in contact with PHE 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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53B MET* 3.5 39.5 - - + -
57B PHE* 5.0 3.5 - - + -
259B ILE* 6.2 0.9 - - + -
261B GLU* 5.3 1.6 - - - -
271B ILE* 3.7 28.0 - - + -
288B GLN 4.4 1.0 + - - -
289B VAL 3.9 7.6 + - - +
290B ASP 3.4 0.6 - - - -
291B THR* 1.3 74.3 - - - +
293B SER* 1.4 67.7 + - - +
295B TRP* 3.2 20.8 + + + +
296B LYS* 3.1 64.9 + - + +
393B LEU* 4.5 10.8 - - + -
395B TYR* 3.9 31.6 - + + -
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Residues in contact with SER 293 (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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50B ARG* 5.6 7.1 + - - -
289B VAL 3.9 4.1 + - - -
290B ASP* 2.8 30.3 + - - +
292B PHE* 1.4 79.3 - - - +
294B ARG* 1.4 58.4 + - - +
296B LYS* 3.6 17.2 + - - +
297B THR* 3.7 18.2 + - - +
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Residues in contact with ARG 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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252B ASP* 2.8 43.2 + - - -
254B LYS* 3.7 24.9 - - - +
255B LEU* 3.8 12.3 - - - +
290B ASP* 3.0 23.0 + - + +
291B THR* 3.6 12.1 + - - +
293B SER* 1.4 74.6 + - - +
295B TRP* 1.4 66.9 + - - +
297B THR* 2.7 25.7 + - - +
298B LEU* 3.4 29.8 - - + +
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Residues in contact with TRP 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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57B PHE* 4.7 6.7 - + - -
252B ASP* 2.8 40.0 + - + +
255B LEU* 3.7 19.6 - - + +
257B CYS* 4.3 4.2 - - - -
259B ILE* 3.6 34.4 - - + +
271B ILE* 4.9 2.0 - - + -
273B ILE* 3.7 45.8 - - + -
283B LEU* 4.0 5.2 - - + -
287B LEU* 4.3 14.4 - - + -
291B THR* 3.0 32.4 + - + -
292B PHE* 3.2 24.8 + + + +
294B ARG* 1.4 78.5 - - - +
296B LYS* 1.4 60.8 + - - +
298B LEU* 3.3 17.6 + - + +
299B LEU* 3.4 19.0 + - - +
391B LEU* 5.5 1.1 - - + -
393B LEU* 4.6 13.5 - - + -
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Residues in contact with LYS 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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261B GLU* 4.9 6.3 - - - +
292B PHE* 3.1 49.5 + - + +
293B SER* 3.7 13.2 - - - +
294B ARG 3.3 0.4 - - - -
295B TRP* 1.4 75.8 - - - +
297B THR* 1.3 60.3 + - + +
298B LEU 3.5 0.7 + - - -
299B LEU* 3.6 32.5 + - + +
395B TYR* 4.1 6.3 + - - -
397B GLU* 3.7 25.3 + - - -
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Residues in contact with THR 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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293B SER 3.7 13.0 + - - +
294B ARG* 2.7 24.8 + - - +
296B LYS* 1.3 76.1 - - + +
298B LEU* 1.4 67.2 + - - +
299B LEU 3.5 4.8 - - - +
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Residues in contact with LEU 298 (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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249B VAL 4.2 0.2 - - - +
250B GLY* 3.4 16.0 - - - -
251B TYR 3.4 31.1 + - - +
252B ASP* 5.1 5.6 - - + +
253B ASP* 6.1 0.9 - - - +
259B ILE* 5.3 3.6 - - + -
294B ARG* 3.4 35.0 - - - +
295B TRP* 3.3 15.0 + - + +
297B THR* 1.4 83.5 - - - +
299B LEU* 1.3 60.5 + - - +
300B SER* 4.0 3.3 + - - -
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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