Contacts of the helix formed by residues 535 - 543 (chain C) in PDB entry 1EQR
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 535 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C ARG* 3.2 27.4 - - + +
144C ILE* 4.4 12.8 - - + -
145C THR* 3.8 31.9 - - + -
212C ILE* 4.3 9.9 - - + -
230C THR* 3.1 40.3 + - + +
232C ILE* 4.0 28.3 - - + -
533C PHE 3.3 4.2 + - - -
534C GLY* 1.3 71.7 - - - +
536C ASP* 1.3 57.6 + - - +
538C LEU* 3.4 6.6 - - + +
539C THR* 2.7 40.9 + - - +
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Residues in contact with ASP 536 (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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141C ARG* 2.5 35.8 + - - +
229C PHE* 3.3 30.3 - - - +
230C THR* 3.4 14.5 + - - +
534C GLY* 3.2 1.7 - - - -
535C LEU* 1.3 76.3 + - - +
537C ARG* 1.3 57.8 + - - +
539C THR* 2.9 6.8 + - - -
540C MET* 2.8 33.6 + - + +
548C ILE* 3.9 29.8 - - + +
551C VAL* 4.1 1.6 - - + +
552C ILE* 3.8 12.4 - - - +
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Residues in contact with ARG 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASP* 3.8 23.2 + - - +
481C TYR* 3.2 68.4 + - + -
482C GLU 4.9 6.7 - - - +
483C VAL* 4.7 12.8 - - + -
534C GLY* 3.6 10.7 + - - +
535C LEU 3.5 0.2 - - - -
536C ASP* 1.3 78.6 - - - +
538C LEU* 1.3 54.2 + - - +
540C MET* 3.0 32.4 + - + +
541C LEU* 2.8 46.8 + - - +
546C ASP* 4.7 4.8 + - - +
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Residues in contact with LEU 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 5.0 2.9 - - + -
232C ILE* 4.0 27.1 - - + -
251C LEU* 5.7 0.9 - - + -
252C VAL* 5.2 5.4 - - + -
255C LEU* 4.3 19.7 - - + -
256C TRP* 4.4 23.8 - - + -
478C ILE* 5.1 0.4 - - + -
483C VAL* 3.8 34.3 - - + +
533C PHE* 4.4 15.7 - - + -
534C GLY 3.3 11.8 + - - +
535C LEU* 3.4 13.7 - - + +
537C ARG* 1.3 77.9 - - - +
539C THR* 1.3 60.8 + - - +
541C LEU* 3.7 4.4 + - + +
542C LEU* 3.0 39.7 + - + +
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Residues in contact with THR 539 (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 ARG 4.4 7.9 - - - +
141C ARG* 3.7 45.0 + - + +
144C ILE* 4.0 15.7 - - + +
535C LEU* 2.7 24.9 + - - +
536C ASP* 2.9 10.0 + - - -
538C LEU* 1.3 75.8 - - - +
540C MET* 1.3 55.0 - - - +
543C THR* 2.5 39.5 + - + +
551C VAL* 3.8 21.8 - - + -
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Residues in contact with MET 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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224C ASP* 4.3 6.5 - - + +
536C ASP* 2.8 13.1 + - + +
537C ARG* 3.0 60.5 + - + +
539C THR* 1.3 73.1 - - - +
541C LEU* 1.3 67.2 + - + +
543C THR* 3.0 13.9 + - - -
544C GLY* 3.1 10.9 + - - -
545C THR* 3.1 26.2 + - - +
546C ASP* 4.4 5.6 - - - +
547C ASN 4.5 0.2 - - - -
548C ILE* 3.3 57.2 - - + +
551C VAL* 3.9 18.2 - - + -
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Residues in contact with LEU 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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256C TRP* 4.2 17.7 - - + -
260C LYS* 4.2 1.4 + - - -
425C TRP* 3.4 23.6 - - + -
478C ILE* 4.1 21.8 - - + +
479C ASN* 4.5 15.9 - - + +
481C TYR* 3.5 29.6 - - + -
483C VAL* 3.6 30.7 - - + -
537C ARG* 2.8 30.9 + - - +
538C LEU* 4.0 4.0 - - - +
540C MET* 1.3 73.4 - - + +
542C LEU* 1.3 61.3 + - - +
543C THR 3.2 1.4 + - - -
544C GLY* 3.5 8.5 + - - -
545C THR 5.2 0.4 - - - -
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Residues in contact with LEU 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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140C THR* 4.6 0.3 - - - +
144C ILE* 3.4 42.0 - - + -
255C LEU* 4.5 14.4 - - + +
256C TRP* 3.5 49.1 - - + -
259C VAL* 4.3 16.8 - - + +
260C LYS* 3.7 41.8 + - + +
425C TRP* 5.2 0.4 - - + -
538C LEU* 3.0 29.1 + - + +
539C THR 4.1 1.1 - - - +
540C MET 3.2 0.4 - - - -
541C LEU* 1.3 76.0 - - - +
543C THR* 1.3 64.0 + - + +
544C GLY 3.6 0.4 - - - -
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Residues in contact with THR 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.9 28.7 + - - +
140C THR* 3.6 35.2 - - + +
260C LYS* 5.3 1.1 - - - +
539C THR* 2.5 26.0 + - + +
540C MET 3.0 2.0 + - - -
542C LEU* 1.3 84.1 - - + +
544C GLY* 1.3 57.8 + - - +
545C THR* 3.0 25.9 + - - -
551C VAL* 4.0 3.1 - - - +
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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