Contacts of the helix formed by residues 283 - 298 (chain B) in PDB entry 4DUB
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 ASN 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B PHE* 2.9 27.5 + - - +
280B LEU 3.0 7.2 + - - +
282B LYS* 1.3 91.6 + - - +
284B PRO* 1.3 60.5 - - - +
285B HIS 3.2 3.6 - - - -
286B VAL* 2.8 38.1 + - + +
287B LEU 3.0 9.2 + - - -
374B PHE* 3.9 32.7 + - + +
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Residues in contact with PRO 284 (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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280B LEU 3.6 1.5 - - - +
281B VAL* 4.1 8.7 - - - +
282B LYS 3.5 8.7 - - - +
283B ASN* 1.3 87.3 - - - +
285B HIS* 1.3 60.5 + - + +
287B LEU* 3.3 12.7 + - + +
288B GLN* 2.9 29.3 + - - +
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Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ASN 3.0 1.4 + - - -
284B PRO* 1.3 77.5 - - + +
286B VAL* 1.3 64.6 + - + +
288B GLN* 3.5 17.4 + - - +
289B LYS* 3.1 27.0 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.5 20.2 - - + -
283B ASN* 2.8 25.8 + - + +
285B HIS* 1.3 77.9 - - + +
287B LEU* 1.3 66.3 + - - +
289B LYS* 3.2 3.3 + - - +
290B ALA* 2.9 22.5 + - - +
313B TYR* 3.3 30.7 - - + +
317B VAL* 3.9 1.3 - - + -
374B PHE* 3.9 11.0 - - + +
376B PRO* 3.5 30.1 - - + -
377B GLU* 5.2 3.1 - - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 5.7 0.4 - - + -
280B LEU* 3.5 46.9 - - + +
281B VAL* 4.1 17.0 - - + +
283B ASN 3.0 5.5 + - - -
284B PRO* 3.6 12.8 - - + +
285B HIS 3.3 0.2 - - - -
286B VAL* 1.3 74.7 - - - +
288B GLN* 1.3 50.8 + - - +
290B ALA* 3.2 2.6 + - - -
291B ALA* 2.6 41.8 + - + +
418B LEU* 3.1 34.8 - - + -
423B PHE* 4.5 24.7 - - + +
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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
----------------------------------------------------------
284B PRO 2.9 17.1 + - - +
285B HIS* 3.8 18.7 - - - +
286B VAL 3.2 0.2 - - - -
287B LEU* 1.3 75.6 - - - +
289B LYS* 1.3 59.1 + - - +
291B ALA* 3.3 6.4 + - - +
292B GLU* 2.9 59.6 + - + +
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Residues in contact with LYS 289 (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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285B HIS 3.1 15.6 + - - +
286B VAL* 3.6 6.5 - - - +
288B GLN* 1.3 78.6 - - - +
290B ALA* 1.3 61.5 + - - +
292B GLU* 3.4 13.8 + - - +
293B GLU* 3.1 22.0 + - - +
313B TYR* 3.5 41.0 - - + +
316B MET* 5.7 0.6 - - - +
377B GLU* 3.2 28.5 + - - +
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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
----------------------------------------------------------
280B LEU* 4.7 6.5 - - + -
286B VAL 2.9 18.6 + - - +
287B LEU* 3.7 3.1 - - - +
289B LYS* 1.3 72.7 - - - +
291B ALA* 1.4 57.1 + - - +
293B GLU* 3.2 7.1 + - - +
294B ALA* 3.0 27.9 + - - +
313B TYR* 3.6 18.9 - - + -
314B VAL* 4.5 9.3 - - + +
317B VAL* 4.5 11.2 - - + -
418B LEU* 3.6 24.3 - - + +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 2.6 26.0 + - + +
288B GLN* 3.7 7.2 - - - +
290B ALA* 1.4 71.7 - - - +
292B GLU* 1.3 59.2 + - + +
294B ALA* 3.3 2.1 + - - +
295B ALA* 2.9 30.7 + - - +
418B LEU* 4.1 33.6 - - + +
451B LYS* 4.2 13.1 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLN* 2.9 48.1 + - + +
289B LYS* 3.7 12.2 - - + +
291B ALA* 1.3 78.1 - - + +
293B GLU* 1.3 61.9 + - - +
295B ALA* 3.5 6.0 + - - +
296B ARG* 3.0 24.2 + - - +
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Residues in contact with GLU 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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289B LYS 3.1 13.3 + - - +
290B ALA* 3.2 8.9 + - - +
292B GLU* 1.3 77.4 - - - +
294B ALA* 1.4 57.3 + - - +
296B ARG* 3.1 29.6 + - - +
297B VAL* 2.9 33.9 + - + +
310B GLN 4.0 2.5 - - - +
311B LEU* 3.1 19.1 - - + -
312B LYS* 3.2 14.9 + - - +
313B TYR* 2.6 32.9 + - + +
314B VAL* 2.9 31.9 + - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.0 15.9 + - - +
291B ALA 3.3 4.2 + - - +
293B GLU* 1.4 74.8 - - - +
295B ALA* 1.3 56.3 + - - +
298B LEU* 2.8 39.9 + - + +
311B LEU* 4.0 13.4 - - + +
314B VAL* 5.3 0.4 - - + -
415B GLY* 3.6 30.3 - - - +
418B LEU* 4.0 14.1 - - + -
419B LYS* 4.0 8.9 - - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA 2.9 17.1 + - - +
292B GLU* 3.8 7.4 - - - +
294B ALA* 1.3 76.1 - - - +
296B ARG* 1.3 63.8 + - - +
298B LEU 4.2 8.1 + - - +
299B VAL* 4.5 5.9 - - - +
419B LYS* 5.1 11.1 - - - +
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Residues in contact with ARG 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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292B GLU 3.0 16.8 + - - +
293B GLU* 3.6 34.9 + - - +
295B ALA* 1.3 80.0 - - - +
297B VAL* 1.3 75.4 + - - +
299B VAL* 3.2 20.1 - - - +
310B GLN 5.3 2.0 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 2.9 28.3 + - + +
296B ARG* 1.3 96.8 - - - +
298B LEU* 1.3 63.2 + - + +
299B VAL* 3.0 11.9 + - - +
307B GLN* 3.2 45.8 + - + +
310B GLN* 3.9 38.9 - - + +
311B LEU* 3.7 15.0 - - + -
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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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294B ALA* 2.8 26.0 + - + +
295B ALA 4.5 4.5 - - - +
296B ARG 3.6 0.2 - - - -
297B VAL* 1.3 74.4 - - + +
299B VAL* 1.3 55.7 + - - +
300B ASP 3.3 6.1 - - - +
303B PRO* 3.9 34.1 - - + -
307B GLN* 3.9 22.9 - - + +
308B VAL* 5.3 0.7 - - + -
311B LEU* 4.3 16.8 - - + -
412B LEU 5.4 0.4 - - - +
415B GLY* 3.6 38.1 - - - +
416B MET* 4.0 4.5 - - + +
419B LYS* 2.9 41.5 + - + +
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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