Contacts of the helix formed by residues 311 - 325 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A GLU* 3.2 18.2 - - + +
294A ALA* 4.2 20.0 - - + -
297A VAL* 3.6 28.0 - - + -
298A LEU* 4.3 15.0 - - + -
307A GLN 3.6 8.3 - - - +
308A VAL* 3.1 24.2 + - + +
309A LYS 3.3 2.6 - - - -
310A GLN* 1.3 73.8 - - - +
312A LYS* 1.3 63.6 + - - +
314A VAL* 3.3 11.5 + - + -
315A GLY* 3.0 17.7 + - - -
411A THR* 3.7 34.7 - - + +
412A LEU* 5.1 0.9 - - - -
415A GLY* 4.2 13.2 - - - -
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.2 5.4 + - - +
309A LYS 5.1 3.1 - - - +
310A GLN 2.9 12.9 + - - +
311A LEU* 1.3 72.0 - - - +
313A TYR* 1.3 59.1 + - - +
315A GLY* 3.1 4.8 + - - +
316A MET* 2.6 70.4 + - + +
380A GLU* 3.6 23.0 + - - +
382A PRO* 6.1 1.1 - - - -
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Residues in contact with TYR 313 (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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286A VAL* 3.5 33.9 - - + +
289A LYS* 3.6 40.1 - - + +
290A ALA* 3.7 21.1 - - + -
293A GLU* 2.8 27.6 + - + +
296A ARG* 5.9 0.2 - - - +
312A LYS* 1.3 74.6 - - - +
314A VAL* 1.3 58.1 + - - +
316A MET* 3.1 20.6 + - + +
317A VAL* 2.8 48.1 + - + +
376A PRO* 3.8 18.4 - - + +
377A GLU* 2.8 35.6 + - + -
380A GLU* 5.7 0.9 - - - -
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Residues in contact with VAL 314 (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 ALA* 4.5 10.1 - - + +
293A GLU* 2.9 16.4 + - - +
294A ALA 5.2 1.1 - - - +
311A LEU* 3.6 24.5 - - + +
312A LYS 3.3 0.2 - - - -
313A TYR* 1.3 76.7 - - - +
315A GLY* 1.3 61.9 + - - +
317A VAL* 3.2 8.6 + - - +
318A LEU* 3.0 23.5 + - + +
411A THR* 3.9 29.8 - - + +
414A LEU* 4.0 27.1 - - + -
415A GLY* 4.3 6.7 - - - +
418A LEU* 4.2 21.8 - - + -
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU 3.0 13.6 + - - -
312A LYS* 3.1 5.6 + - - -
314A VAL* 1.3 78.3 - - - +
316A MET* 1.3 50.1 + - - +
318A LEU* 3.2 7.2 + - - +
319A ASN* 2.9 41.0 + - - -
411A THR* 4.6 11.1 - - - +
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Residues in contact with MET 316 (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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312A LYS* 2.6 69.5 + - + +
313A TYR* 3.1 26.9 + - + +
315A GLY* 1.3 71.2 - - - +
317A VAL* 1.3 67.9 + - - +
319A ASN* 3.2 3.0 + - - +
320A GLU* 2.9 26.7 + - - +
376A PRO* 3.4 25.5 - - + +
379A PHE* 3.8 24.3 - - + +
380A GLU* 4.0 29.8 - - + +
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Residues in contact with VAL 317 (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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276A ALA* 4.3 7.9 - - + +
280A LEU* 3.8 35.2 - - + -
290A ALA* 4.4 5.6 - - + -
313A TYR* 2.8 44.3 + - + +
314A VAL* 3.5 10.3 - - - +
316A MET* 1.3 76.9 - - - +
318A LEU* 1.3 64.2 + - - +
320A GLU* 3.3 1.7 + - - +
321A ALA* 3.0 21.8 + - - +
374A PHE* 3.9 11.2 - - + -
376A PRO* 3.8 17.7 - - + -
414A LEU* 4.2 15.7 - - + -
418A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 3.6 31.5 - - + +
273A LEU* 4.9 2.9 - - + -
276A ALA* 3.8 23.6 - - + -
314A VAL* 3.0 20.5 + - + +
315A GLY* 3.7 7.2 - - - +
316A MET 3.1 0.2 - - - -
317A VAL* 1.3 80.0 - - - +
319A ASN* 1.3 62.0 + - - +
321A ALA* 3.4 1.9 + - - -
322A LEU* 3.0 26.5 + - - +
407A LEU* 4.5 11.7 - - + +
410A ALA* 3.7 15.7 - - + +
411A THR* 3.4 46.0 - - - +
414A LEU* 4.0 10.8 - - + -
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Residues in contact with ASN 319 (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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315A GLY* 2.9 22.9 + - - +
316A MET* 3.2 1.5 + - - +
318A LEU* 1.3 77.6 - - - +
320A GLU* 1.3 56.4 + - - +
322A LEU* 3.2 10.2 + - - +
323A ARG* 2.8 24.9 + - - +
379A PHE* 3.7 38.2 - - + +
382A PRO* 5.5 6.3 - - - +
390A PHE* 3.5 30.9 - - + -
393A PHE* 5.5 0.9 - - - -
407A LEU* 4.7 15.2 - - - +
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Residues in contact with GLU 320 (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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316A MET 2.9 17.1 + - - +
317A VAL 3.9 2.9 - - - +
319A ASN* 1.3 79.1 - - - +
321A ALA* 1.3 61.9 + - - +
323A ARG* 2.8 47.9 + - - +
324A LEU* 3.1 23.8 + - - +
373A GLU 3.1 2.3 - - - +
374A PHE* 3.4 24.1 - - + -
375A ARG 2.7 36.2 + - - +
376A PRO* 3.8 11.4 - - + -
378A ARG* 3.0 12.6 + - - -
379A PHE* 3.4 10.0 - - + -
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Residues in contact with ALA 321 (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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272A LEU* 4.1 11.4 - - + -
275A PHE* 4.4 5.1 - - + +
276A ALA* 4.0 31.0 - - + +
279A PHE* 4.3 13.4 - - + -
317A VAL 3.0 17.5 + - - +
318A LEU 3.7 5.2 - - - +
320A GLU* 1.3 77.9 - - - +
322A LEU* 1.3 56.7 + - - +
324A LEU* 3.5 1.0 + - - +
325A TRP* 2.9 33.0 + - - +
374A PHE* 3.7 8.1 - - + -
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Residues in contact with LEU 322 (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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272A LEU* 3.5 30.3 - - + -
318A LEU 3.0 18.0 + - - +
319A ASN* 3.2 15.2 + - - +
321A ALA* 1.3 76.3 - - - +
323A ARG* 1.3 63.7 + - - +
325A TRP 4.4 2.2 - - - +
326A PRO* 3.2 26.8 - - + +
327A THR* 4.2 24.7 - - + +
361A HIS* 3.2 7.4 + - - -
390A PHE* 4.1 5.2 - - + -
392A PRO* 4.0 14.8 - - + -
393A PHE* 3.8 33.4 - - + -
407A LEU* 4.3 7.0 - - + -
500A HEM 4.3 14.8 - - + -
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Residues in contact with ARG 323 (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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319A ASN 2.8 16.7 + - - +
320A GLU* 2.8 47.9 + - - +
321A ALA 3.3 0.4 - - - -
322A LEU* 1.3 72.7 - - - +
324A LEU* 1.3 80.0 + - - +
326A PRO* 3.5 2.4 - - - +
361A HIS* 3.0 67.0 + - + +
362A ARG* 4.0 2.2 + - - +
367A TRP* 3.7 41.5 - - + -
371A VAL* 3.0 38.2 + - - +
373A GLU 3.1 11.5 + - - -
378A ARG* 3.3 13.6 - - - +
379A PHE* 4.2 1.8 - - + -
390A PHE* 3.7 7.8 - - + -
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Residues in contact with LEU 324 (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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279A PHE* 3.7 36.3 - - + -
320A GLU* 3.1 10.7 + - - +
321A ALA 4.3 0.2 - - - +
323A ARG* 1.3 100.3 - - - +
325A TRP* 1.4 68.5 + - + +
326A PRO* 3.5 2.5 - - - +
362A ARG* 2.7 47.9 + - - +
371A VAL 3.3 26.2 - - - +
372A GLU* 3.9 16.8 - - - +
373A GLU 4.2 0.4 - - - +
374A PHE* 3.8 29.6 - - + -
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Residues in contact with TRP 325 (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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26A VAL* 5.8 0.7 - - + -
27A GLN* 4.3 18.6 - - + -
30A MET* 3.8 39.7 - - + -
275A PHE* 3.8 35.7 - + + +
279A PHE* 3.6 33.4 - + - -
321A ALA 2.9 20.4 + - - +
322A LEU* 4.4 1.9 - - - +
324A LEU* 1.4 81.6 - - - +
326A PRO* 1.3 67.0 - - - +
327A THR* 3.1 16.6 + - - +
358A PRO* 4.5 4.9 - - + -
362A ARG* 3.5 17.3 - - - +
372A GLU* 5.4 1.8 - - - -
431A LEU* 4.0 10.7 - - + +
433A ILE* 3.3 25.7 - - + +
439A LEU* 3.8 20.6 - - + -
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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