Contacts of the helix formed by residues 871 - 878 (chain C) in PDB entry 1S0V
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 871 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837C GLU* 5.0 1.6 - - - +
869C ASN 3.6 2.3 + - - +
870C LEU* 1.3 79.5 - - - +
872C LEU* 1.3 55.5 + - - +
873C ARG* 2.6 58.2 + - - +
874C ASP* 2.7 49.5 + - - +
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Residues in contact with LEU 872 (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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548C ALA* 4.4 11.9 - - + +
551C ARG* 2.7 44.6 - - + +
833C VAL* 2.9 42.1 - - + +
836C TYR* 3.0 38.6 - - + +
837C GLU* 3.2 24.7 - - + +
870C LEU* 3.8 16.2 - - + +
871C ASN* 1.3 71.8 + - - +
873C ARG* 1.3 58.7 + - - +
874C ASP 3.2 0.4 - - - -
875C ILE* 3.3 14.6 + - + +
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Residues in contact with ARG 873 (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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833C VAL* 3.4 22.7 - - - +
834C ASP* 5.0 6.9 - - - +
837C GLU* 3.3 31.8 + - - +
871C ASN* 2.6 35.2 + - - +
872C LEU* 1.3 70.9 - - - +
874C ASP* 1.3 54.5 + - - -
875C ILE 2.9 5.8 - - - -
876C LEU* 2.7 48.5 + - + +
877C GLU* 4.1 1.4 + - - +
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Residues in contact with ASP 874 (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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561C LEU 4.1 0.2 - - - -
562C LEU* 3.3 21.9 - - + +
563C PRO* 3.1 41.4 - - + +
870C LEU* 5.0 1.1 - - + -
871C ASN* 2.7 50.8 + - - +
873C ARG* 1.3 77.4 - - - +
875C ILE* 1.3 55.5 + - - +
876C LEU 3.0 0.4 - - - -
877C GLU* 2.9 19.5 + - - +
878C SER 3.3 1.6 + - - -
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Residues in contact with ILE 875 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544C GLN* 6.1 0.4 - - - +
548C ALA* 5.5 4.9 - - + -
561C LEU* 3.2 48.2 - - + +
829C ARG* 3.2 42.2 + - + +
832C MET* 4.0 28.3 - - + -
833C VAL* 3.6 9.4 - - + -
870C LEU* 5.4 4.7 - - + -
872C LEU* 3.3 23.2 + - + +
873C ARG 2.8 1.6 + - - -
874C ASP* 1.3 73.4 - - - +
876C LEU* 1.3 57.5 + - - +
877C GLU 3.0 6.1 + - - -
878C SER* 3.6 7.0 + - - -
881C ALA* 5.4 4.7 - - + -
883C ALA* 4.8 8.3 - - - +
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Residues in contact with LEU 876 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826C LYS* 4.4 20.1 + - + +
829C ARG* 3.8 17.3 + - + -
830C GLU* 3.1 57.9 - - + +
833C VAL* 3.8 10.5 - - + -
873C ARG* 2.7 38.7 + - + +
875C ILE* 1.3 78.9 - - - +
877C GLU* 1.3 68.5 + - + +
878C SER 3.8 0.2 - - - -
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Residues in contact with GLU 877 (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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563C PRO* 2.7 29.4 - - + +
826C LYS* 6.3 0.2 - - - +
829C ARG* 5.5 0.2 - - - +
873C ARG 5.4 1.3 - - - +
874C ASP* 2.9 12.1 + - - +
876C LEU* 1.3 88.8 - - + +
878C SER* 1.3 53.3 + - - +
879C ASP* 3.7 10.6 + - - +
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Residues in contact with SER 878 (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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560C ASN* 2.4 30.2 + - - +
561C LEU 3.1 25.1 - - - -
562C LEU 3.3 12.8 + - - -
563C PRO* 3.8 7.6 - - - -
564C SER 5.3 0.2 + - - -
829C ARG* 2.5 32.5 + - - +
874C ASP 3.3 2.3 + - - -
875C ILE* 3.6 7.7 + - - -
876C LEU 3.8 0.4 - - - -
877C GLU* 1.3 75.2 - - - +
879C ASP* 1.3 53.2 + - - +
880C PHE* 3.4 3.5 + - - -
881C ALA* 3.4 7.8 + - - +
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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