Contacts of the helix formed by residues 334 - 351 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C PRO* 3.4 28.5 - - + -
20C THR* 5.2 0.9 - - - +
328C PHE* 4.5 13.8 + - + +
333C ASN* 1.3 90.0 + - - +
335C VAL* 1.3 65.0 + - - +
336C HIS* 3.5 13.9 + - + +
337C TYR* 3.2 27.7 + - - +
338C HIS* 3.3 20.3 - - - -
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C THR* 1.3 73.6 - - - +
336C HIS* 1.3 64.7 + - + +
338C HIS* 3.1 10.1 + - + +
339C GLU* 2.8 36.6 + - + +
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Residues in contact with HIS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C GLN 4.7 1.6 - - - -
321C CYS* 3.4 27.1 - - + +
322C GLU* 3.6 11.9 + - - -
323C ASN* 3.2 36.3 + - + +
324C ALA* 3.7 24.5 - - + -
328C PHE* 3.7 18.4 - - + -
334C THR* 3.2 11.1 + - - +
335C VAL* 1.3 80.1 - - + +
337C TYR* 1.3 66.8 + - - +
339C GLU* 3.0 26.7 + - - +
340C VAL* 2.9 29.5 + - - +
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Residues in contact with TYR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 2.9 35.2 + - - +
328C PHE* 3.8 15.1 - - - +
329C TYR* 3.6 19.3 - - - +
331C LEU 3.2 21.5 - - - +
332C PRO* 3.5 35.5 - - + +
334C THR* 3.2 23.6 + - - +
335C VAL 3.3 0.2 - - - -
336C HIS* 1.3 76.8 - - - +
338C HIS* 1.3 85.2 + + - +
340C VAL* 3.8 2.0 - - - +
341C MET* 3.1 60.6 + - + +
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Residues in contact with HIS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C PRO* 4.1 19.6 + - + -
333C ASN* 5.4 0.2 - - - -
334C THR 3.3 25.5 + - - -
335C VAL* 3.1 9.8 + - + +
337C TYR* 1.3 101.2 - + - +
339C GLU* 1.3 63.0 + - - +
341C MET* 3.4 4.5 + - - +
342C GLU* 3.1 24.6 + - - +
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C VAL* 3.9 20.9 - - + +
320C GLN 4.8 4.2 - - - +
321C CYS* 4.2 3.6 - - - -
335C VAL* 2.8 22.7 + - + +
336C HIS* 3.0 34.0 + - - +
338C HIS* 1.3 78.2 - - - +
340C VAL* 1.3 57.2 + - - +
342C GLU* 3.4 7.6 + - - +
343C GLU* 2.9 46.6 + - + +
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 4.3 9.0 - - + -
291C ILE* 3.6 35.9 - - + -
319C VAL* 4.6 7.0 - - + -
321C CYS* 3.5 18.4 - - - -
328C PHE* 3.5 26.5 - - + -
329C TYR* 5.3 3.6 - - + -
336C HIS 2.9 20.9 + - - +
337C TYR* 3.9 2.9 - - - +
339C GLU* 1.3 73.3 - - + +
341C MET* 1.3 63.7 + - + +
343C GLU* 3.3 6.4 + - - +
344C ILE* 2.9 37.8 + - + +
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Residues in contact with MET 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 4.0 17.9 - - + -
140C ARG* 4.2 8.3 - - + -
141C PHE* 4.2 12.8 - - + -
144C LEU* 3.8 29.4 - - + +
224C LEU* 6.3 0.7 - - + -
329C TYR* 3.7 20.0 - - + +
337C TYR* 3.1 65.4 + - + +
338C HIS* 3.8 5.2 - - - +
340C VAL* 1.3 76.7 - - + +
342C GLU* 1.3 59.0 + - - +
344C ILE* 3.5 8.2 + - + +
345C SER* 2.9 29.3 + - - -
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Residues in contact with GLU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C HIS 3.1 17.4 + - - +
339C GLU* 3.7 6.4 - - - +
341C MET* 1.3 74.5 - - - +
343C GLU* 1.3 56.5 + - + +
345C SER* 3.2 8.4 + - - -
346C ASP* 2.7 51.9 + - - +
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 3.8 9.4 - - + +
291C ILE* 5.8 0.4 - - + -
317C LYS* 3.6 31.3 + - - +
319C VAL* 3.8 38.2 - - + +
339C GLU* 2.9 32.0 + - + +
340C VAL* 3.5 9.9 - - + +
342C GLU* 1.3 74.8 - - + +
344C ILE* 1.3 56.9 + - - +
346C ASP* 3.4 12.1 + - - +
347C PHE* 2.8 30.5 + - - +
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 5.7 0.4 - - + -
141C PHE* 3.9 34.3 - - + -
144C LEU* 3.8 11.4 - - + -
222C ILE* 4.0 29.4 - - + -
224C LEU* 4.5 4.7 - - + -
289C LEU* 3.8 21.3 - - + -
291C ILE* 4.1 4.5 - - + -
340C VAL* 2.9 38.0 + - + +
341C MET* 3.7 9.6 - - - +
343C GLU* 1.3 69.3 - - - +
345C SER* 1.3 62.5 + - - +
347C PHE* 3.2 2.1 + - - +
348C LEU* 2.9 49.5 + - + +
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Residues in contact with SER 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 3.8 31.9 + - - +
341C MET 2.9 15.6 + - - -
342C GLU* 3.3 11.9 - - - -
344C ILE* 1.3 77.4 - - - +
346C ASP* 1.3 59.2 + - - +
348C LEU* 3.7 2.9 - - - +
349C ASN* 2.9 47.1 + - - +
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Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C GLU* 2.7 41.5 + - - +
343C GLU* 3.6 13.0 - - - +
345C SER* 1.3 74.8 + - - +
347C PHE* 1.3 53.6 + - - +
349C ASN* 3.3 8.8 + - - +
350C ALA* 2.7 38.9 + - + +
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Residues in contact with PHE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 3.8 19.9 - + - -
220C GLY* 3.9 8.3 - - - -
221C ASN 3.9 3.1 - - - -
222C ILE* 3.7 35.4 - - + -
287C LYS* 3.8 35.0 - - + -
288C SER 4.2 4.0 - - - -
289C LEU* 3.8 37.5 - - + -
315C HIS* 5.6 3.8 - + - -
317C LYS* 5.7 8.1 - - + -
343C GLU 2.8 21.0 + - - +
344C ILE 3.2 3.1 + - - +
346C ASP* 1.3 72.3 - - - +
348C LEU* 1.3 62.2 + - - +
350C ALA* 4.7 2.9 - - - -
351C ASN* 2.6 49.2 + - - +
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO* 4.3 12.7 - - + +
116C ILE* 3.9 20.2 - - + -
144C LEU* 3.7 18.4 - - + +
145C SER* 3.5 30.3 - - - -
193C PHE* 3.8 44.5 - - + -
222C ILE* 4.1 8.5 - - + -
344C ILE* 2.9 29.4 + - + +
345C SER* 3.7 2.7 - - - +
347C PHE* 1.3 74.1 - - - +
349C ASN* 1.3 66.4 + - - +
351C ASN 3.0 22.9 + - - -
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Residues in contact with ASN 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU 5.0 4.9 - - - +
145C SER* 5.3 5.2 - - - +
345C SER* 2.9 37.0 + - - +
346C ASP* 3.5 9.5 + - - +
348C LEU* 1.3 76.2 - - - +
350C ALA* 1.3 62.6 + - - +
351C ASN 3.1 4.0 + - - -
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Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C LYS* 5.4 2.7 + - - +
346C ASP* 2.7 21.9 + - + +
347C PHE* 4.2 5.2 - - - +
349C ASN* 1.3 73.4 - - - +
351C ASN* 1.3 66.9 + - - +
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Residues in contact with ASN 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ARG* 5.7 2.6 - - - +
193C PHE* 3.8 29.5 - - + -
219C CYS* 4.7 15.1 - - + +
287C LYS* 2.8 42.8 + - - +
347C PHE* 2.6 46.6 + - - +
348C LEU 3.0 14.7 + - - -
349C ASN 4.1 4.0 - - - -
350C ALA* 1.3 87.7 - - - +
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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
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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