Contacts of the helix formed by residues 547 - 552 (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 ASN 547 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLU* 5.3 2.6 + - - +
121C ARG* 5.3 6.7 - - - +
224C ASP* 4.5 4.6 - - - +
540C MET* 4.5 0.9 - - - -
545C THR* 3.2 5.9 - - + +
546C ASP* 1.3 79.6 - - + +
548C ILE* 1.3 55.9 + - - +
549C ARG* 2.3 58.8 + - - +
550C ASP* 2.7 64.0 + - - +
551C VAL 4.0 0.5 + - - -
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Residues in contact with ILE 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ARG* 5.5 5.4 - - - +
223C ALA 3.9 8.3 - - - +
224C ASP* 3.6 44.9 + - - +
225C ARG* 4.7 0.4 - - - +
226C GLN* 4.4 17.0 - - + +
229C PHE* 5.9 1.3 - - + -
536C ASP* 3.9 22.9 - - + +
540C MET* 3.3 37.7 - - + -
546C ASP 3.8 3.6 + - - -
547C ASN* 1.3 72.2 + - - +
549C ARG* 1.3 65.2 + - + +
550C ASP 3.0 0.7 - - - -
551C VAL* 3.0 20.8 + - + +
552C ILE* 3.6 21.7 + - + +
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Residues in contact with ARG 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 3.5 29.4 + - - -
122C LEU* 4.4 18.6 - - + +
125C ARG* 2.8 26.2 + - - +
223C ALA* 3.0 32.5 + - - +
224C ASP* 4.9 1.4 + - - -
226C GLN* 4.1 15.4 + - - +
547C ASN* 2.3 51.1 + - - +
548C ILE* 1.3 80.0 - - + +
550C ASP* 1.3 56.9 + - - +
551C VAL 3.2 0.2 - - - -
552C ILE* 2.9 13.2 - - - +
555C PRO* 3.7 23.2 - - + +
556C LYS 4.7 9.0 + - - -
557C THR* 5.1 1.4 - - - +
558C THR* 3.4 25.3 + - - +
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Residues in contact with ASP 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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121C ARG* 4.2 13.4 + - - -
125C ARG* 4.4 6.4 + - - +
134C MET* 3.9 17.2 - - - +
137C ARG* 2.8 57.1 + - - +
138C LEU* 4.1 5.4 - - - +
545C THR* 3.2 18.5 - - + +
547C ASN* 2.7 39.3 + - - +
549C ARG* 1.3 81.1 - - - +
551C VAL* 1.3 55.6 + - - -
552C ILE 3.4 0.9 - - - -
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Residues in contact with VAL 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 4.4 4.0 - - + -
138C LEU* 3.3 17.3 - - - +
141C ARG* 2.7 43.0 + - - +
536C ASP* 4.1 6.3 - - + +
539C THR* 3.8 26.2 - - + -
540C MET* 3.9 28.9 - - + +
543C THR* 4.0 15.3 - - - +
545C THR* 4.1 10.1 - - + +
548C ILE* 3.0 26.9 - - + +
550C ASP* 1.3 79.7 - - - +
552C ILE* 1.3 56.4 + - + +
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Residues in contact with ILE 552 (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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125C ARG* 2.9 11.6 + - - -
138C LEU* 4.4 2.6 - - - +
141C ARG* 3.8 17.5 - - - +
226C GLN* 4.0 27.6 - - + +
228C GLU 5.1 4.3 - - - +
229C PHE* 6.1 1.1 - - + -
536C ASP* 3.8 12.6 - - - +
548C ILE* 3.6 29.8 - - + +
549C ARG 2.9 18.6 + - - +
550C ASP 4.5 0.2 - - - -
551C VAL* 1.3 82.3 - - - +
553C ALA* 1.3 63.5 + - - +
554C PHE 3.8 23.1 - - - +
555C PRO* 3.5 7.0 - - + +
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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
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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