Contacts of the helix formed by residues 334 - 352 (chain D) in PDB entry 3EBL
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 THR 334 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D PRO* 3.5 28.5 - - + -
20D THR* 5.2 0.9 - - - +
328D PHE* 4.3 13.3 + - + +
332D PRO 3.8 0.6 + - - -
333D ASN* 1.3 92.3 + - - +
335D VAL* 1.3 65.4 + - - +
336D HIS* 3.6 12.6 + - + +
337D TYR* 3.1 28.8 + - - +
338D HIS* 3.2 21.2 - - - -
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Residues in contact with VAL 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 4.9 10.3 - - + +
338A HIS* 3.5 31.6 - - + +
339A GLU* 4.0 22.2 - - + +
342A GLU* 3.6 37.6 + - + +
334D THR* 1.3 74.5 - - - +
336D HIS* 1.3 67.2 + - + +
338D HIS* 2.9 11.4 + - - +
339D GLU* 2.9 27.9 + - - +
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Residues in contact with HIS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D GLN 4.8 0.2 - - - -
321D CYS* 3.5 29.5 - - + +
322D GLU* 3.8 17.7 - - - -
323D ASN* 3.1 39.5 + - + +
324D ALA* 3.6 22.9 - - + -
328D PHE* 3.7 18.4 - - + -
334D THR* 3.2 11.1 + - - +
335D VAL* 1.3 81.0 - - + +
337D TYR* 1.3 64.2 + - - +
339D GLU* 3.1 21.8 + - - +
340D VAL* 2.9 29.3 + - - +
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Residues in contact with TYR 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ARG* 2.8 45.9 + - + +
328D PHE* 3.8 17.8 - - - +
329D TYR* 3.6 26.9 - - - +
330D LEU 5.0 0.9 - - - -
331D LEU 3.3 23.3 - - - +
332D PRO* 3.7 34.5 - - + +
334D THR* 3.1 24.5 + - - +
336D HIS* 1.3 78.4 - - - +
338D HIS* 1.3 84.1 + + - +
340D VAL* 3.3 2.4 + - - +
341D MET* 3.0 44.3 + - + +
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Residues in contact with HIS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.3 22.6 - - + +
338A HIS* 3.7 51.9 + + + -
140D ARG* 5.1 3.9 + - - -
332D PRO* 4.2 16.1 + - + -
333D ASN* 5.6 0.4 - - - -
334D THR 3.2 25.3 + - - -
335D VAL* 2.9 7.3 + - - +
337D TYR* 1.3 96.5 - + - +
339D GLU* 1.3 66.8 + - - +
341D MET* 3.4 4.8 + - - +
342D GLU* 3.1 18.7 + - - +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A VAL* 3.8 23.2 - - + +
319D VAL* 3.9 24.2 - - + +
320D GLN 4.8 4.4 - - - +
321D CYS* 4.7 3.1 - - - -
335D VAL* 2.9 19.8 + - + +
336D HIS* 3.1 32.7 + - - +
338D HIS* 1.3 76.9 - - - +
340D VAL* 1.3 58.4 + - + +
342D GLU* 3.3 5.6 + - - +
343D GLU* 2.9 40.2 + - + +
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Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 4.0 11.2 - - + -
291D ILE* 3.7 33.2 - - + -
319D VAL* 4.2 8.7 - - + -
321D CYS* 3.6 27.1 - - - -
328D PHE* 3.6 16.2 - - + -
329D TYR* 5.1 0.4 - - + -
336D HIS 2.9 20.1 + - - +
337D TYR* 3.9 2.9 - - - +
339D GLU* 1.3 74.6 - - + +
341D MET* 1.3 71.6 + - + +
343D GLU* 3.2 5.8 + - - +
344D ILE* 2.9 33.8 + - + +
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Residues in contact with MET 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.9 17.5 - - + -
140D ARG* 3.9 35.2 - - + +
141D PHE* 4.3 8.7 - - + -
144D LEU* 3.4 34.0 - - + +
224D LEU* 5.8 0.2 - - + -
329D TYR* 3.7 35.9 - - + +
337D TYR* 3.0 43.8 + - + +
338D HIS* 3.9 5.2 - - - +
340D VAL* 1.3 78.6 - - + +
342D GLU* 1.3 56.9 + - - +
344D ILE* 3.7 8.6 - - + +
345D SER 2.9 23.4 + - - -
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Residues in contact with GLU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASN* 4.8 14.4 + - - +
334A THR* 5.5 2.9 - - - +
335A VAL* 3.7 32.1 + - + +
144D LEU* 5.4 0.4 - - - -
338D HIS 3.1 13.6 + - - +
339D GLU* 3.6 8.6 - - - +
341D MET* 1.3 74.5 - - - +
343D GLU* 1.3 64.3 + - - +
345D SER* 3.2 6.5 + - - -
346D ASP* 2.8 46.2 + - - +
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Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU* 3.7 9.1 - - + +
291D ILE* 5.6 0.4 - - + -
317D LYS* 3.2 39.2 + - - +
319D VAL* 3.8 31.9 - - + +
339D GLU* 2.9 29.9 + - + +
340D VAL* 3.2 7.8 + - + +
342D GLU* 1.3 80.7 - - + +
344D ILE* 1.3 57.5 + - - +
346D ASP* 3.4 11.8 + - - +
347D PHE* 2.9 31.0 + - - +
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 5.6 0.7 - - + -
141D PHE* 3.9 33.9 - - + -
144D LEU* 4.1 11.9 - - + -
222D ILE* 3.9 22.9 - - + -
224D LEU* 4.4 4.7 - - + -
289D LEU* 3.7 19.5 - - + -
291D ILE* 4.1 8.1 - - + -
340D VAL* 2.9 38.2 + - + +
341D MET* 3.7 10.5 - - + +
343D GLU* 1.3 73.7 - - - +
345D SER* 1.3 65.8 + - - +
347D PHE* 3.2 2.6 + - - +
348D LEU* 3.0 42.2 + - + +
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Residues in contact with SER 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 3.9 30.5 + - - -
341D MET 2.9 18.2 + - - -
342D GLU* 3.2 7.6 + - - -
344D ILE* 1.3 77.6 - - - +
346D ASP* 1.3 64.5 + - - +
348D LEU* 3.4 10.8 + - - +
349D ASN* 3.0 37.1 + - - +
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Residues in contact with ASP 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D GLU* 2.8 41.8 + - - +
343D GLU* 3.7 13.3 - - - +
345D SER* 1.3 75.9 + - - +
347D PHE* 1.3 58.0 + - - +
349D ASN* 3.4 9.7 + - - +
350D ALA* 2.9 32.0 + - - +
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Residues in contact with PHE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D PHE* 4.0 9.6 - + - -
220D GLY* 4.0 16.4 - - - -
221D ASN 3.6 13.5 - - - -
222D ILE* 3.8 24.5 - - + -
287D LYS* 3.7 28.5 - - + -
288D SER 3.8 18.8 - - - -
289D LEU* 3.8 27.6 - - + -
315D HIS* 5.7 4.7 - + - -
317D LYS* 5.4 9.6 - - + -
343D GLU 2.9 18.2 + - - +
344D ILE 3.2 3.8 + - - +
346D ASP* 1.3 74.7 - - - +
348D LEU* 1.3 66.2 + - - +
350D ALA* 3.4 2.4 + - - -
351D ASN* 2.8 52.0 + - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D PRO* 4.2 11.7 - - + -
116D ILE* 4.0 16.6 - - + -
141D PHE 5.3 0.2 - - - +
144D LEU* 4.9 2.2 - - + -
145D SER* 3.5 33.9 - - - +
193D PHE* 3.7 44.5 - - + -
222D ILE* 4.0 14.4 - - + -
344D ILE* 3.0 36.8 + - + +
345D SER* 3.7 7.6 - - - +
347D PHE* 1.3 76.4 - - - +
349D ASN* 1.3 60.8 + - - +
351D ASN 3.7 0.5 - - - -
352D LEU* 2.9 34.6 + - - +
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Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU 5.6 2.0 - - - +
145D SER 5.6 2.4 - - - +
345D SER* 3.0 32.6 + - - +
346D ASP* 3.5 9.7 + - - +
348D LEU* 1.3 78.3 - - - +
350D ALA* 1.3 61.9 + - - +
351D ASN 3.4 0.5 + - - -
352D LEU* 3.8 15.3 + - - +
353D TYR* 5.0 5.5 + - - -
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ASP 2.9 18.0 + - - +
347D PHE* 3.8 5.6 - - - +
349D ASN* 1.3 76.0 - - - +
351D ASN* 1.3 68.7 + - - +
352D LEU 3.6 0.2 - - - -
353D TYR 4.9 5.6 + - - -
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Residues in contact with ASN 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D PHE* 3.9 10.3 - - + -
219D CYS* 3.6 34.7 - - - +
287D LYS* 3.2 28.7 - - - +
347D PHE* 2.8 52.5 + - - +
348D LEU 3.7 0.7 - - - -
349D ASN 3.2 0.2 - - - -
350D ALA* 1.3 88.1 - - - +
352D LEU* 1.3 66.8 + - - +
353D TYR* 3.3 9.1 + - - +
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO 3.9 20.4 - - - +
113D PHE 3.7 1.6 - - - -
114D PRO* 3.5 44.4 - - + -
191D ARG* 2.9 56.5 + - + +
193D PHE* 4.3 4.9 - - + -
219D CYS* 4.3 3.8 - - - -
348D LEU 2.9 15.5 + - - +
349D ASN* 3.8 11.0 + - - +
350D ALA 3.6 1.0 - - - -
351D ASN* 1.3 80.1 - - - +
353D TYR* 1.3 83.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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