Contacts of the helix formed by residues 311 - 325 (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 LEU 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLU* 3.1 19.1 - - + +
294B ALA* 4.0 21.1 - - - -
297B VAL* 3.7 26.2 - - + -
298B LEU* 4.3 13.2 - - + -
307B GLN 3.6 10.3 - - - +
308B VAL* 3.1 24.6 + - + +
309B LYS 3.2 2.2 - - - -
310B GLN* 1.3 73.7 - - - +
312B LYS* 1.3 58.0 + - - +
314B VAL* 3.3 9.0 + - + +
315B GLY* 2.9 25.1 + - - -
411B THR* 3.7 37.3 - - + +
412B LEU* 5.1 1.1 - - - -
415B GLY* 4.0 13.2 - - - -
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 3.2 5.8 + - - +
309B LYS 4.6 3.6 + - - +
310B GLN 3.0 9.4 + - - +
311B LEU* 1.3 76.2 - - - +
313B TYR* 1.3 62.5 + - - +
315B GLY* 3.1 4.8 + - - -
316B MET* 3.0 39.0 + - + +
379B PHE 4.9 2.2 + - - -
380B GLU* 3.3 32.7 + - - -
382B PRO* 5.0 6.9 - - - +
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Residues in contact with TYR 313 (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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286B VAL* 3.3 34.8 - - + +
289B LYS* 3.5 44.8 - - + +
290B ALA* 3.6 26.5 - - + -
293B GLU* 2.6 29.7 + - + +
312B LYS* 1.3 71.0 - - - +
314B VAL* 1.3 66.3 + - - +
316B MET* 3.1 25.8 + - + +
317B VAL* 2.8 26.8 + - + +
376B PRO* 3.7 18.0 - - + +
377B GLU* 2.7 32.3 + - - -
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA* 4.5 11.4 - - + +
293B GLU* 2.9 20.3 + - - +
294B ALA* 5.3 0.7 - - + -
311B LEU* 3.6 25.4 - - + +
312B LYS 3.3 0.2 - - - -
313B TYR* 1.3 76.9 - - - +
315B GLY* 1.4 62.4 + - - +
317B VAL* 3.1 8.7 + - - +
318B LEU* 3.0 21.9 + - + +
411B THR* 4.0 22.4 - - + +
414B LEU* 3.9 34.8 - - + -
415B GLY* 4.4 4.3 - - - +
418B LEU* 4.2 21.3 - - + -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU 2.9 14.3 + - - -
312B LYS* 3.1 6.0 + - - -
314B VAL* 1.4 76.8 - - - +
316B MET* 1.4 54.9 + - - +
318B LEU* 3.3 12.4 + - - +
319B ASN* 3.0 36.6 + - - -
411B THR* 4.6 7.3 - - - +
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS* 5.7 0.2 - - - +
312B LYS* 3.0 33.7 + - + +
313B TYR* 3.4 30.1 - - + +
315B GLY* 1.4 71.9 - - - +
317B VAL* 1.4 66.6 + - - +
319B ASN* 3.3 4.1 + - - +
320B GLU* 3.0 24.3 + - - +
376B PRO* 3.3 30.7 - - + +
377B GLU* 3.7 17.3 - - + -
379B PHE* 3.8 24.2 - - + +
380B GLU* 3.9 29.2 - - + -
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ALA* 4.4 7.9 - - + +
280B LEU* 4.0 32.5 - - + -
286B VAL* 3.9 8.1 - - + -
290B ALA* 4.5 5.8 - - + -
313B TYR* 2.8 36.2 + - + +
314B VAL* 3.1 9.8 + - - +
316B MET* 1.4 77.3 - - - +
318B LEU* 1.3 57.3 + - - +
320B GLU* 3.3 2.8 + - - +
321B ALA* 2.9 26.3 + - - +
374B PHE* 3.9 10.9 - - + -
376B PRO* 3.8 24.7 - - + -
414B LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.7 28.8 - - + +
273B LEU* 5.0 2.9 - - + -
276B ALA* 3.8 24.2 - - + -
314B VAL* 3.0 19.7 + - + +
315B GLY* 3.6 8.7 - - - +
317B VAL* 1.3 76.1 - - - +
319B ASN* 1.4 64.2 + - - +
321B ALA* 3.2 3.8 + - - +
322B LEU* 2.9 29.0 + - - +
407B LEU* 4.5 11.9 - - + +
410B ALA* 3.7 16.4 - - + +
411B THR* 3.3 44.6 - - - +
414B LEU* 3.9 13.0 - - + -
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Residues in contact with ASN 319 (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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315B GLY 3.0 23.0 + - - +
316B MET* 3.8 3.2 - - - +
317B VAL 3.3 0.2 - - - -
318B LEU* 1.4 78.4 - - - +
320B GLU* 1.3 57.6 - - - +
322B LEU* 3.3 11.9 + - - +
323B ARG* 2.9 22.5 + - - +
379B PHE* 3.8 34.2 - - + +
382B PRO* 6.0 4.0 - - - +
390B PHE* 3.4 32.4 - - + -
393B PHE* 5.4 1.0 - - - -
407B LEU* 4.8 13.2 - - - +
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Residues in contact with GLU 320 (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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316B MET 3.0 17.1 + - - +
317B VAL 3.9 1.1 - - - +
319B ASN* 1.3 76.0 - - - +
321B ALA* 1.4 62.3 + - - +
323B ARG* 2.7 39.2 + - - +
324B LEU* 3.2 22.3 + - - +
373B GLU 3.1 1.4 - - - +
374B PHE* 3.5 28.1 - - + -
375B ARG 2.7 37.5 + - - +
376B PRO* 3.9 9.9 - - + -
378B ARG* 2.8 23.3 + - - -
379B PHE* 3.4 10.6 - - + -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.9 12.1 - - + -
275B PHE* 4.3 5.2 - - + +
276B ALA* 3.9 32.5 - - + +
279B PHE* 4.2 14.3 - - + -
317B VAL 2.9 16.4 + - - +
318B LEU 3.2 5.1 + - - +
320B GLU* 1.4 76.0 - - - +
322B LEU* 1.4 51.7 + - - +
324B LEU* 3.4 1.9 + - - +
325B TRP* 2.9 37.4 + - - +
374B PHE* 3.7 6.6 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.7 26.5 - - + -
318B LEU 2.9 18.3 + - - +
319B ASN* 3.5 20.6 - - - +
321B ALA* 1.4 72.4 - - - +
323B ARG* 1.4 64.4 + - - +
325B TRP 4.2 4.9 - - - +
326B PRO* 3.2 27.2 - - + +
327B THR* 4.4 4.0 - - + +
361B HIS* 3.2 11.0 + - - -
390B PHE* 4.1 4.5 - - + -
392B PRO* 3.9 15.9 - - + -
393B PHE* 3.8 31.9 - - + -
407B LEU* 4.1 10.8 - - + -
500B HEM 4.3 24.7 - - + -
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Residues in contact with ARG 323 (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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319B ASN 2.9 12.4 + - - +
320B GLU* 2.7 48.1 + - - +
321B ALA 3.2 0.8 - - - -
322B LEU* 1.4 76.7 - - - +
324B LEU* 1.3 81.1 + - - +
326B PRO* 3.6 2.3 - - - +
361B HIS* 2.9 68.2 + - + +
362B ARG* 4.1 2.2 + - - +
367B TRP* 3.7 39.6 - - + -
371B VAL* 3.0 38.0 + - - +
373B GLU 3.0 12.7 + - - -
378B ARG* 3.4 14.1 - - - +
379B PHE* 4.2 1.6 - - + -
390B PHE* 3.8 8.3 - - + -
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Residues in contact with LEU 324 (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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279B PHE* 3.7 28.0 - - + -
320B GLU 3.2 8.0 + - - +
321B ALA 4.1 1.3 - - - +
323B ARG* 1.3 103.5 - - - +
325B TRP* 1.3 75.9 + - + +
326B PRO* 3.5 2.0 - - - +
362B ARG* 2.8 48.6 + - - +
371B VAL 3.3 25.8 - - - +
372B GLU* 4.1 16.2 - - - +
373B GLU 4.1 1.8 - - - +
374B PHE* 4.1 25.6 - - + -
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Residues in contact with TRP 325 (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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27B GLN* 4.6 13.2 - - + -
30B MET* 3.8 39.7 - - + -
275B PHE* 3.8 40.2 - + + -
279B PHE* 3.8 28.8 - + - -
321B ALA 2.9 19.2 + - - +
322B LEU* 4.2 2.8 - - - +
324B LEU* 1.3 81.0 + - + +
326B PRO* 1.3 67.6 - - - +
327B THR* 3.1 14.9 + - - +
358B PRO* 4.7 3.4 - - + -
362B ARG* 3.6 17.1 - - - +
372B GLU* 5.8 0.4 - - - -
431B LEU* 4.0 12.2 - - + +
433B ILE* 3.3 30.2 - - + +
439B LEU* 3.7 20.9 - - + -
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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