Contacts of the helix formed by residues 865 - 869 (chain A) in PDB entry 1SO2
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 ARG 865 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861A LEU* 6.4 0.2 - - - +
862A TYR 3.7 5.9 - - - +
863A LEU 3.4 2.1 - - - -
864A SER* 1.3 94.0 + - - +
866A PRO* 1.3 71.1 - - - +
867A GLU* 3.6 29.3 + - - +
868A TYR* 3.2 50.0 + - + +
869A ASN* 4.0 2.3 + - - +
869C ASN* 4.9 5.9 + - - +
871C LEU 3.9 6.9 + - - -
872C LEU* 3.8 22.5 + - - +
874C LEU 2.4 33.7 + - - -
875C ASP 3.9 2.6 - - - -
876C HIS* 4.0 20.6 + - - +
879C PHE* 3.9 33.3 - - - +
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Residues in contact with PRO 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A GLN* 4.5 3.1 - - - +
865A ARG* 1.3 85.4 - - + +
867A GLU* 1.3 67.7 + - + +
868A TYR 2.9 6.5 + - - -
869A ASN* 3.0 23.5 + - + +
876C HIS* 3.5 35.7 - - + +
835D ALA 5.0 8.7 - - - +
969D LEU 4.6 7.8 - - - +
970D GLY 5.9 0.7 - - - +
971D LEU* 3.4 33.2 - - + -
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Residues in contact with GLU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A GLN* 3.0 33.5 - - + +
722A ASN* 3.2 21.1 + - + +
865A ARG* 3.6 28.4 + - - +
866A PRO* 1.3 88.3 - - - +
868A TYR* 1.3 76.9 + - + +
869A ASN 3.5 0.4 - - - -
876C HIS* 5.2 2.3 - - - -
837D ASN* 4.7 15.6 + - - -
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Residues in contact with TYR 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A GLN* 3.6 6.7 - - - +
722A ASN* 3.7 23.8 - - + -
723A TYR* 3.7 28.6 - + + +
726A ALA* 3.7 16.7 - - + +
861A LEU* 3.2 43.7 - - + +
862A TYR* 3.6 14.6 - - - +
864A SER* 4.0 0.2 - - - -
865A ARG* 3.2 42.6 + - + +
866A PRO 2.9 1.4 + - - -
867A GLU* 1.3 94.7 + - + +
869A ASN* 1.3 54.0 + - - +
870A PHE* 2.6 34.5 + - - -
869C ASN* 3.8 15.4 + - - -
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Residues in contact with ASN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A GLN* 4.1 10.1 + - - +
862A TYR* 2.8 35.8 + - + +
865A ARG 4.0 2.1 + - - +
866A PRO* 3.0 21.4 + - + +
867A GLU 3.5 0.4 - - - -
868A TYR* 1.3 72.2 - - - +
870A PHE* 1.3 61.6 + - - +
871A LEU 3.2 0.9 + - - -
872A LEU* 3.2 45.6 + - - +
879A PHE* 5.6 1.0 - - - -
969D LEU 5.1 3.1 - - - +
970D GLY* 3.6 22.4 + - - +
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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