Contacts of the helix formed by residues 334 - 353 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.5 27.8 - - + -
20A THR* 5.4 0.7 - - - +
328A PHE* 4.5 13.0 + - + +
332A PRO 3.8 0.4 - - - -
333A ASN* 1.3 92.2 + - - +
335A VAL* 1.3 64.8 + - - +
336A HIS* 3.5 12.9 + - + +
337A TYR* 3.1 27.9 + - - +
338A HIS* 3.2 21.5 - - - -
338D HIS* 5.8 0.2 - - - -
342D GLU* 5.5 3.4 - - - +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A THR* 1.3 73.9 - - - +
336A HIS* 1.3 62.7 + - + +
338A HIS* 3.1 9.2 + - - +
339A GLU* 2.9 34.3 + - + +
335D VAL* 4.9 9.6 - - + -
338D HIS* 3.3 33.2 - - + +
339D GLU* 3.8 25.1 - - + +
342D GLU* 3.7 38.9 + - + +
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Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN 4.5 0.9 - - - -
321A CYS* 3.5 32.3 - - + +
322A GLU* 3.4 16.4 + - - -
323A ASN* 3.3 35.6 + - + +
324A ALA* 3.7 19.7 - - + -
328A PHE* 3.8 18.4 - - + -
334A THR* 3.2 11.2 + - - +
335A VAL* 1.3 81.1 - - + +
337A TYR* 1.3 62.8 + - - +
339A GLU* 2.9 28.3 + - - +
340A VAL* 2.9 29.6 + - - +
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Residues in contact with TYR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.3 31.5 + - - +
328A PHE* 3.8 15.8 - - - +
329A TYR* 3.7 25.8 - - - +
330A LEU 5.0 0.7 - - - -
331A LEU 3.2 24.5 - - - +
332A PRO* 3.5 35.4 - - + +
334A THR* 3.1 25.2 + - - +
335A VAL 3.2 0.2 - - - -
336A HIS* 1.3 76.3 - - - +
338A HIS* 1.3 80.5 + + - +
340A VAL* 3.9 1.8 - - - +
341A MET* 3.0 53.5 + - + +
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Residues in contact with HIS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PRO* 4.1 18.7 + - + -
334A THR 3.2 25.7 + - - -
335A VAL* 3.1 7.0 + - - +
337A TYR* 1.3 94.5 - + - +
339A GLU* 1.3 65.9 + - - +
341A MET* 3.4 4.4 + - - +
342A GLU* 3.1 17.0 + - - +
335D VAL* 3.5 20.9 - - + +
338D HIS* 3.7 50.9 + + + -
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.8 20.7 - - + +
320A GLN 4.7 4.7 - - - +
321A CYS* 4.7 2.2 - - - -
335A VAL* 2.9 21.2 + - + +
336A HIS* 2.9 35.4 + - - +
338A HIS* 1.3 77.1 - - - +
340A VAL* 1.3 59.5 + - + +
342A GLU* 3.2 5.4 + - - +
343A GLU* 2.9 44.2 + - + +
335D VAL* 4.0 21.9 - - + +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 4.2 12.1 - - + -
291A ILE* 3.9 30.7 - - + -
319A VAL* 4.2 10.1 - - + -
321A CYS* 3.6 27.8 - - - -
328A PHE* 3.7 15.3 - - + -
329A TYR* 5.1 0.7 - - + -
336A HIS 2.9 19.2 + - - +
337A TYR 3.9 2.9 - - - +
339A GLU* 1.3 77.1 - - + +
341A MET* 1.3 66.5 + - + +
343A GLU* 3.2 6.2 + - - +
344A ILE* 2.8 44.8 + - + +
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Residues in contact with MET 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.9 15.7 - - + -
140A ARG* 4.1 28.5 - - + +
141A PHE* 4.1 9.9 - - + -
144A LEU* 3.6 31.9 - - + +
224A LEU* 5.8 0.4 - - + -
329A TYR* 3.8 23.1 - - + +
337A TYR* 3.0 62.2 + - + +
338A HIS* 4.0 6.1 - - - +
340A VAL* 1.3 77.7 - - + +
342A GLU* 1.3 56.7 + - - +
344A ILE* 3.4 8.0 + - + -
345A SER* 3.0 28.2 + - - -
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 5.5 0.2 - - - -
338A HIS 3.1 14.1 + - - +
339A GLU* 3.4 8.7 - - - +
341A MET* 1.3 75.4 - - - +
343A GLU* 1.3 63.2 + - + +
345A SER* 3.2 7.5 + - - -
346A ASP* 2.9 45.4 + - - +
323D ASN* 4.9 11.1 + - - -
334D THR* 6.0 0.2 - - - -
335D VAL* 3.6 30.9 + - + +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.7 9.4 - - + +
291A ILE* 5.8 0.9 - - + -
317A LYS* 2.9 37.5 + - - -
319A VAL* 3.9 31.2 - - + +
339A GLU* 2.9 31.3 + - + +
340A VAL* 3.7 6.5 - - + +
342A GLU* 1.3 76.7 - - + +
344A ILE* 1.3 57.4 + - - +
346A ASP* 3.3 14.0 + - - +
347A PHE* 2.9 31.2 + - - +
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 5.7 1.6 - - + -
141A PHE* 3.8 34.3 - - + -
144A LEU* 4.1 12.1 - - + -
222A ILE* 4.1 25.4 - - + -
224A LEU* 4.5 5.2 - - + -
289A LEU* 3.8 20.0 - - + -
291A ILE* 4.1 7.4 - - + -
340A VAL* 2.8 34.6 + - + +
341A MET* 3.7 11.0 - - + +
343A GLU* 1.3 75.0 - - - +
345A SER* 1.3 64.2 + - - +
347A PHE* 3.3 2.3 + - - +
348A LEU* 2.9 46.0 + - + +
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.8 32.9 + - - +
341A MET 3.0 13.6 + - - -
342A GLU* 3.6 10.8 - - - -
344A ILE* 1.3 78.2 - - - +
346A ASP* 1.3 64.0 + - - +
348A LEU* 3.7 8.2 - - - +
349A ASN* 3.0 37.2 + - - -
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LYS* 6.4 0.2 - - - -
342A GLU* 2.9 40.2 + - - +
343A GLU* 3.7 15.2 - - - +
345A SER* 1.3 74.9 + - - +
347A PHE* 1.3 56.9 + - - +
349A ASN* 3.3 9.1 + - - +
350A ALA* 2.8 33.1 + - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 3.8 20.9 - + - -
220A GLY* 3.9 6.1 - - - -
221A ASN 3.7 4.3 - - - -
222A ILE* 3.7 33.4 - - + -
287A LYS* 3.7 28.7 - - + -
288A SER 3.9 9.9 - - - -
289A LEU* 3.7 39.0 - - + -
315A HIS* 5.8 3.1 - + - -
317A LYS* 5.4 8.7 - - + -
343A GLU 2.9 17.4 + - - +
344A ILE 3.6 2.9 - - - +
346A ASP* 1.3 74.8 - - - +
348A LEU* 1.3 66.3 + - - +
350A ALA* 3.4 2.6 + - - -
351A ASN* 2.9 51.9 + - - +
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Residues in contact with LEU 348 (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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114A PRO* 4.2 13.9 - - + -
116A ILE* 4.0 11.0 - - + -
141A PHE 5.4 0.4 - - - +
144A LEU* 5.2 1.1 - - + -
145A SER* 3.5 34.5 - - - +
193A PHE* 3.5 48.7 - - + -
222A ILE* 3.9 13.7 - - + -
344A ILE* 2.9 36.0 + - + +
345A SER* 3.7 6.7 - - - +
347A PHE* 1.3 76.7 - - - +
349A ASN* 1.3 64.8 + - - +
351A ASN 3.2 2.3 + - - -
352A LEU* 3.2 27.5 + - - +
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Residues in contact with ASN 349 (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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145A SER 5.7 1.2 - - - +
345A SER* 3.0 32.0 + - - +
346A ASP* 3.6 10.1 + - - +
348A LEU* 1.3 77.8 - - - +
350A ALA* 1.3 62.7 + - - +
351A ASN 3.2 0.9 + - - -
352A LEU* 3.7 19.2 + - - +
353A TYR* 4.7 2.9 + - - +
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Residues in contact with ALA 350 (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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346A ASP 2.8 22.7 + - - +
347A PHE* 3.8 5.2 - - - +
348A LEU 3.3 0.2 - - - -
349A ASN* 1.3 73.4 - - - +
351A ASN* 1.3 68.2 + - - +
352A LEU 3.6 0.4 + - - -
353A TYR 4.9 3.7 + - - -
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Residues in contact with ASN 351 (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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193A PHE* 3.7 17.9 - - + -
219A CYS* 3.6 31.8 - - - +
287A LYS* 3.3 33.0 + - - +
347A PHE* 2.9 50.6 + - - +
348A LEU 3.2 1.5 + - - -
349A ASN 3.2 0.2 - - - -
350A ALA* 1.3 87.6 - - - +
352A LEU* 1.3 61.8 + - - +
353A TYR 3.6 4.5 - - - +
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Residues in contact with LEU 352 (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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112A PRO* 3.8 27.1 - - + +
113A PHE 3.5 8.1 - - - +
114A PRO* 3.5 46.0 - - + -
191A ARG* 2.9 48.4 + - + +
193A PHE* 4.5 5.2 - - + -
219A CYS* 5.1 1.7 - - - -
348A LEU 3.2 13.5 + - - +
349A ASN* 3.7 15.7 + - - +
350A ALA 3.6 0.8 - - - -
351A ASN* 1.3 78.8 - - - +
353A TYR* 1.3 62.8 + - + +
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Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO* 5.5 8.5 - - + -
191A ARG* 4.4 8.8 + - - +
349A ASN 4.7 3.2 + - - +
350A ALA 4.9 3.7 + - - -
351A ASN 3.6 3.3 - - - +
352A LEU* 1.3 83.0 - - + +
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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