Contacts of the helix formed by residues 285 - 299 (chain B) in PDB entry 3WF4
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 LYS 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B THR* 6.0 1.3 - - - +
284B ILE* 1.3 78.2 - - - +
286B THR* 1.3 65.7 + - - +
287B GLU* 3.2 7.4 - - + +
288B ALA* 3.2 19.7 + - + +
289B VAL* 3.3 13.6 + - - +
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Residues in contact with THR 286 (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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284B ILE 3.6 1.8 + - - -
285B LYS* 1.3 72.2 - - - +
287B GLU* 1.3 55.0 - - - +
289B VAL* 3.2 3.3 + - - +
290B ALA* 2.8 33.0 + - + +
345B GLU* 4.5 7.2 - - + +
346B LYS* 3.6 41.9 + - + +
349B ALA* 3.4 33.2 - - + -
350B LEU* 4.8 1.3 - - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 3.2 4.8 - - + +
286B THR* 1.3 77.7 - - - +
288B ALA* 1.3 61.2 + - - +
290B ALA* 4.5 6.1 - - - -
291B SER* 2.7 60.3 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B THR* 3.5 20.3 - - + +
284B ILE* 4.5 6.5 - - + -
285B LYS* 3.2 17.6 + - + +
287B GLU* 1.3 78.0 - - - +
289B VAL* 1.3 64.2 + - - +
291B SER* 4.0 3.3 - - - -
292B SER* 3.1 27.5 + - - -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B THR* 3.7 10.3 - - + +
269B PHE* 3.5 21.8 - - + -
271B THR* 3.7 36.3 - - + +
284B ILE* 3.7 13.9 - - + -
285B LYS 3.3 13.9 + - - +
286B THR* 3.2 7.3 + - - +
288B ALA* 1.3 76.6 - - - +
290B ALA* 1.3 58.7 + - - +
292B SER 3.4 0.3 + - - -
293B LEU* 3.0 25.6 + - - +
346B LYS* 4.3 8.7 - - + -
350B LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 2.8 18.6 + - + +
287B GLU* 4.1 6.3 - - - +
289B VAL* 1.3 73.6 - - - +
291B SER* 1.3 66.6 + - - +
293B LEU* 3.3 1.6 + - - +
294B TYR* 3.1 22.9 + - - +
349B ALA* 4.6 12.1 - - + +
350B LEU* 3.9 17.5 - - + +
353B ILE* 3.8 27.4 - - + +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 2.7 39.9 + - - +
288B ALA* 4.1 3.8 - - - -
290B ALA* 1.3 74.6 - - - +
292B SER* 1.3 65.3 + - - +
294B TYR* 3.2 9.1 + - - +
295B ASP* 3.0 26.9 + - - +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY 5.3 0.4 - - - -
244B THR* 3.8 21.9 + - - -
248B ILE* 4.4 18.4 - - - +
269B PHE* 3.5 28.3 - - - -
288B ALA 3.1 14.4 + - - -
291B SER* 1.3 76.5 - - - +
293B LEU* 1.3 59.3 + - - +
295B ASP* 3.1 5.2 + - - +
296B ILE* 2.9 30.9 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 5.0 2.2 - - + -
269B PHE* 3.8 11.4 - - + -
289B VAL 3.0 17.5 + - - +
290B ALA* 3.9 4.7 - - - +
291B SER 3.2 0.2 - - - -
292B SER* 1.3 76.3 - - - +
294B TYR* 1.3 62.6 + - - +
296B ILE* 4.4 4.0 - - + -
297B LEU* 3.0 49.7 + - + +
303B VAL* 3.9 21.1 - - + -
305B LEU* 3.8 41.5 - - + -
350B LEU* 4.3 27.6 - - + +
353B ILE* 4.2 12.3 - - + -
354B ILE* 4.6 8.1 - - + -
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Residues in contact with TYR 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 ALA 3.1 12.9 + - - +
291B SER* 3.4 11.7 - - - +
293B LEU* 1.3 75.6 - - - +
295B ASP* 1.3 76.5 + - - +
297B LEU* 3.1 4.2 + - - +
298B ALA* 3.0 36.6 + - + +
353B ILE* 3.8 28.1 - - + +
356B LYS* 4.2 21.3 - - + -
357B PHE* 3.8 28.0 - + - -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.7 19.5 - - + +
291B SER* 3.0 17.5 + - - +
292B SER* 3.6 6.9 - - - +
294B TYR* 1.3 88.1 - - - +
296B ILE* 1.3 63.7 + - - +
298B ALA* 3.3 11.9 + - - +
299B ARG* 3.4 32.1 + - - +
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Residues in contact with ILE 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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242B PHE* 3.8 24.7 - - + -
248B ILE* 4.0 15.3 - - + -
252B PHE* 4.6 6.5 - - + -
266B ASN* 3.9 7.4 - - + +
269B PHE* 3.6 36.8 - - + -
292B SER 2.9 23.3 + - - +
293B LEU* 3.9 4.5 - - - +
295B ASP* 1.3 74.5 - - - +
297B LEU* 1.3 61.4 + - - +
299B ARG* 3.3 20.7 + - - +
301B ALA* 3.7 22.2 - - + +
303B VAL* 3.6 33.0 - - + -
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Residues in contact with LEU 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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49B ARG* 3.0 36.1 + - - +
51B THR* 3.7 23.3 - - + +
293B LEU* 3.0 45.7 + - + +
296B ILE* 1.3 75.1 - - - +
298B ALA* 1.3 58.5 + - - +
300B GLY* 2.9 17.0 + - - -
301B ALA 4.3 2.0 - - - +
303B VAL* 3.7 19.3 - - + -
353B ILE* 4.1 6.5 - - + -
354B ILE* 4.6 12.3 - - + -
357B PHE* 3.6 40.5 - - + -
358B GLU* 5.6 0.2 - - - +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B TYR* 3.0 29.3 + - + +
295B ASP* 3.8 7.4 - - - +
296B ILE 3.3 0.2 - - - -
297B LEU* 1.3 77.0 - - - +
299B ARG* 1.3 59.2 + - + +
300B GLY 3.2 0.6 + - - -
357B PHE* 3.8 16.1 - - + -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.5 34.0 - - - +
249B THR* 3.1 40.2 + - - +
252B PHE* 4.2 13.0 - - - +
264B LEU* 4.5 20.5 - - + +
295B ASP* 3.4 31.1 + - - +
296B ILE 3.3 8.2 + - - +
297B LEU 3.2 0.8 - - - -
298B ALA* 1.3 78.5 - - - +
300B GLY* 1.3 59.3 + - - +
301B ALA* 3.4 3.9 + - + +
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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
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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