Contacts of the helix formed by residues 539 - 551 (chain C) in PDB entry 1EF1
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 539 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.9 27.5 - - + -
160A GLN* 4.3 2.9 - - - +
229B GLU* 4.1 22.9 - - - +
537C LYS 5.9 0.2 - - - -
538C LYS* 1.3 78.4 - - - +
540C ALA* 1.3 64.0 + - - +
541C ASN* 3.5 7.4 + - - +
542C ASP* 2.9 44.3 + - - +
543C MSE 3.1 16.1 + - - +
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Residues in contact with ALA 540 (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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229B GLU* 5.1 3.9 + - - +
231B ASN* 3.6 39.3 - - + +
232B ASP* 4.9 5.4 - - + +
539C THR* 1.3 73.3 - - - +
541C ASN* 1.4 57.9 + - - +
543C MSE 3.2 17.7 + - - +
544C ILE* 2.9 39.0 + - + +
540D ALA* 5.2 3.9 - - + +
543D MSE 5.3 0.2 - - - +
544D ILE* 4.1 16.6 - - + +
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Residues in contact with ASN 541 (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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113A ASP* 5.4 3.0 + - - -
116A TYR* 3.5 28.3 - - + +
200A MSE 3.9 19.0 - - - +
231A ASN 4.8 0.3 - - - +
233A ARG* 5.0 3.3 + - - +
234A LEU* 3.4 21.6 - - + +
231B ASN* 3.2 28.0 + - - +
539C THR* 3.3 6.1 + - - +
540C ALA* 1.4 75.2 - - - +
542C ASP* 1.3 56.3 + - - +
544C ILE* 3.6 14.7 - - - +
545C HIS* 2.8 37.1 + - - +
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Residues in contact with ASP 542 (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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116A TYR* 2.9 32.2 + - - -
119A PRO* 4.6 5.7 - - - +
156A ARG* 3.9 9.0 + - - -
160A GLN* 2.5 35.6 + - - +
533C ARG* 4.2 8.7 + - - +
538C LYS* 4.4 8.3 - - + -
539C THR* 2.9 33.0 + - - +
541C ASN* 1.3 75.4 - - - +
543C MSE 1.3 58.6 + - - +
545C HIS* 3.5 2.6 + - - +
546C ALA* 3.0 29.9 + - - +
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Residues in contact with MSE 543 (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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538C LYS* 3.9 31.9 - - + +
539C THR 3.1 20.3 + - - +
540C ALA* 3.6 9.6 - - - +
542C ASP* 1.3 74.8 - - - +
544C ILE* 1.3 64.6 + - - +
546C ALA* 3.4 5.2 + - - +
547C GLU* 3.0 25.8 + - - +
543D MSE 3.5 39.9 - - + +
544D ILE* 4.0 33.7 - - + +
547D GLU* 3.9 21.5 - - + +
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Residues in contact with ILE 544 (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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231A ASN 3.5 25.4 - - - +
232A ASP* 3.4 38.8 - - + +
234A LEU* 4.0 7.9 - - + -
540C ALA* 2.9 23.9 + - + +
541C ASN* 3.6 21.8 - - - +
543C MSE 1.3 75.2 - - - +
545C HIS* 1.3 59.6 + - - +
547C GLU* 3.2 1.9 + - - +
548C ASN* 2.9 45.4 + - - +
540D ALA* 4.1 12.3 - - + -
543D MSE 3.7 21.5 - - + +
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Residues in contact with HIS 545 (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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116A TYR* 3.6 24.0 - + + +
118A PRO* 3.6 37.2 - - + +
119A PRO* 5.8 0.2 - - + -
120A GLU* 5.6 1.5 + - - -
199A GLU* 4.5 18.5 + - - -
234A LEU* 3.8 9.1 - - + +
541C ASN 2.8 18.5 + - - +
542C ASP 3.8 4.3 - - - +
544C ILE* 1.3 78.6 - - - +
546C ALA* 1.4 60.6 + - + +
548C ASN* 3.2 10.0 + - - +
549C MSE 3.0 64.9 + - + +
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Residues in contact with ALA 546 (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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542C ASP 3.0 20.2 + - - +
543C MSE 3.4 5.6 + - - +
545C HIS* 1.4 77.5 - - + +
547C GLU* 1.3 57.9 + - - +
549C MSE 3.4 6.6 + - - +
550C ARG* 2.8 28.5 + - - +
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Residues in contact with GLU 547 (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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543C MSE 3.0 17.3 + - - +
544C ILE 3.6 3.8 - - - +
546C ALA* 1.3 73.4 - - - +
548C ASN* 1.3 66.0 + - - +
550C ARG* 2.9 47.7 + - - +
551C LEU* 3.0 45.0 + - + +
553C ARG* 5.4 2.9 - - - +
535D GLU 3.4 5.2 - - - +
536D SER* 4.3 0.9 - - - -
538D LYS* 3.2 34.2 + - + +
543D MSE 3.6 21.4 - - + +
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Residues in contact with ASN 548 (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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199A GLU* 4.8 10.9 + - - +
232A ASP* 5.5 0.2 - - - +
234A LEU* 4.2 9.9 + - - +
235A THR* 2.8 24.8 + - - -
544C ILE* 2.9 31.0 + - - +
545C HIS* 3.3 15.1 - - - +
547C GLU* 1.3 76.4 - - - +
549C MSE 1.3 63.2 + - + +
551C LEU 3.3 2.1 + - - -
552C GLY 3.1 5.0 + - - -
553C ARG* 2.9 71.5 + - + +
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Residues in contact with MSE 549 (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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199A GLU* 5.9 1.1 - - - +
545C HIS* 3.0 49.4 + - + +
546C ALA* 3.7 8.3 - - - +
548C ASN* 1.3 73.0 - - - +
550C ARG* 1.3 67.7 + - - +
552C GLY* 2.9 14.9 + - - +
553C ARG 4.3 15.7 - - - +
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Residues in contact with ARG 550 (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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546C ALA 2.8 17.1 + - - +
547C GLU* 2.9 44.7 + - - +
549C MSE 1.3 78.2 - - - +
551C LEU* 1.3 82.2 + - - +
552C GLY 3.3 0.9 + - - -
535D GLU* 3.2 23.7 + - - +
536D SER* 4.1 1.2 - - - +
538D LYS* 3.8 6.5 - - - +
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Residues in contact with LEU 551 (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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547C GLU* 3.0 34.6 + - + +
548C ASN 3.3 4.2 + - - +
549C MSE 3.2 0.2 - - - -
550C ARG* 1.3 105.2 - - - +
552C GLY* 1.3 61.2 + - - +
553C ARG* 3.5 35.4 - - + +
536D SER* 3.7 35.2 - - - +
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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