Contacts of the helix formed by residues 692 - 696 (chain C) in PDB entry 5IFE
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 HIS 692 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652C CYS* 2.4 37.9 + - + +
653C LYS* 3.5 27.8 - - + +
661C ARG* 4.8 5.6 - - - -
665C ILE* 5.4 3.1 - - + +
688C GLU 4.8 2.4 + - - -
689C ILE 3.0 29.0 + - - -
690C ILE* 4.5 3.4 - - - -
691C GLU* 1.3 83.9 - - + +
693C GLY* 1.3 68.2 + - - +
694C LEU 3.1 3.5 + - - -
695C VAL* 3.3 25.0 + - + +
696C ASP* 4.0 7.0 + - + +
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Residues in contact with GLY 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C ILE* 4.3 9.4 - - - -
690C ILE 3.2 10.3 + - - -
691C GLU 3.1 2.6 - - - -
692C HIS* 1.3 86.4 - - - +
694C LEU* 1.3 60.7 + - - +
695C VAL 3.2 1.2 + - - -
696C ASP* 3.6 13.3 + - - +
701C VAL* 3.8 3.8 - - - +
702C ARG* 3.3 26.5 + - - +
705C SER* 3.5 14.4 - - - -
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Residues in contact with LEU 694 (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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691C GLU* 3.6 17.7 - - + +
692C HIS 3.1 1.2 + - - -
693C GLY* 1.3 77.2 - - - +
695C VAL* 1.3 66.7 + - + +
696C ASP 3.6 0.4 - - - -
702C ARG* 3.3 17.7 - - - -
705C SER* 3.2 24.0 - - - +
706C ALA* 3.8 19.7 - - + +
709C ILE* 5.0 4.5 - - + -
727C VAL* 3.6 31.4 - - + -
730C PRO* 4.3 19.1 - - + -
731C LEU* 4.0 16.4 - - + +
738C HIS* 4.8 3.8 + - - -
746C PHE* 3.9 30.4 - - + -
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Residues in contact with VAL 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C GLU 5.6 0.2 - - - +
692C HIS* 3.3 20.2 - - + +
693C GLY 3.2 0.2 - - - -
694C LEU* 1.3 85.1 - - + +
696C ASP* 1.3 64.9 + - - +
697C GLU* 3.8 2.9 + - - +
702C ARG* 4.5 1.3 - - - +
730C PRO* 5.3 9.9 - - + -
737C GLN* 6.3 0.4 - - - +
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Residues in contact with ASP 696 (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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661C ARG* 2.4 43.2 + - - -
692C HIS* 4.0 5.1 + - + +
693C GLY* 3.6 12.0 + - - +
694C LEU 3.6 1.6 - - - -
695C VAL* 1.3 81.8 - - - +
697C GLU* 1.3 85.2 + - - +
698C GLN* 3.1 7.6 + - - +
701C VAL* 3.4 24.5 - - + +
702C ARG* 3.2 23.9 + - - -
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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