Contacts of the helix formed by residues 826 - 834 (chain A) in PDB entry 2O8C
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 PHE 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A PRO* 3.8 35.0 - - + -
803A THR* 4.5 7.6 - - + -
804A ALA* 3.3 52.5 - - + -
806A THR* 4.1 14.4 - - + -
811A LEU* 4.3 12.1 - - + +
822A CYS* 3.9 17.5 - - + -
824A GLN* 3.3 55.0 - - + +
825A SER* 1.3 78.0 + - - +
827A GLY* 1.3 61.3 + - - -
828A ILE 3.3 2.7 - - - -
829A HIS* 3.1 21.0 + - - +
830A VAL* 3.4 15.8 + - + +
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Residues in contact with GLY 827 (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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670A PRO* 5.7 0.4 - - - +
825A SER 2.7 14.3 + - - -
826A PHE* 1.3 71.5 - - - +
828A ILE* 1.3 60.6 + - - +
830A VAL* 3.5 11.4 + - - +
831A ALA 3.8 1.9 + - - -
1190B PHE* 3.6 28.8 - - - -
1219B THR* 4.6 2.9 - - - -
1223B ASP* 3.3 20.8 + - - -
1227B ILE* 3.8 10.6 - - - +
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Residues in contact with ILE 828 (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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825A SER* 3.8 15.9 - - - +
826A PHE 3.3 0.8 - - - -
827A GLY* 1.3 76.1 - - - +
829A HIS* 1.3 63.8 + - - +
831A ALA* 3.2 18.5 + - + +
832A GLU 3.5 0.3 + - - -
841A ILE* 3.4 27.2 - - + +
844A ALA* 4.2 22.0 - - + +
845A LYS* 4.7 11.2 - - + -
848A ALA* 3.7 31.0 - - + -
1222B PHE* 4.7 2.2 - - + -
1223B ASP* 3.5 16.6 - - + +
1226B ALA* 5.2 7.9 - - + -
1227B ILE* 4.7 9.4 - - + -
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Residues in contact with HIS 829 (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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806A THR* 4.7 20.8 - - + +
807A THR 4.2 10.3 + - - -
808A GLU* 3.5 37.7 + - - -
810A THR 4.3 17.7 - - - -
811A LEU* 4.6 17.6 - - + +
826A PHE* 3.1 15.7 + - - +
828A ILE* 1.3 78.6 - - - +
830A VAL* 1.3 59.8 + - + +
832A GLU* 3.4 24.7 + - - +
833A LEU* 3.0 28.6 + - + +
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Residues in contact with VAL 830 (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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811A LEU* 3.8 22.0 - - + -
826A PHE* 3.4 17.9 - - + +
827A GLY* 3.8 11.2 - - - +
828A ILE 3.2 0.8 - - - -
829A HIS* 1.3 76.7 - - - +
831A ALA* 1.3 58.9 + - - +
833A LEU* 3.2 11.8 + - + +
834A ALA* 2.9 27.0 + - - +
1190B PHE* 4.3 11.0 - - + -
1191B PHE* 3.8 34.5 - - + -
1194B LEU* 3.7 15.7 - - + -
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Residues in contact with ALA 831 (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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827A GLY 3.8 2.6 + - - +
828A ILE* 3.2 14.5 + - - +
830A VAL* 1.3 75.9 - - - +
832A GLU* 1.3 62.8 + - - +
834A ALA 3.2 8.7 + - - +
835A ASN 3.4 4.5 + - - -
836A PHE* 3.1 48.4 + - + -
841A ILE* 3.8 11.4 - - + -
1194B LEU* 3.5 17.3 - - + +
1227B ILE* 4.7 10.5 - - + -
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Residues in contact with GLU 832 (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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808A GLU* 4.0 19.4 - - - +
828A ILE 3.5 2.7 + - - +
829A HIS* 3.4 29.9 + - - +
830A VAL 3.3 0.2 - - - -
831A ALA* 1.3 78.4 - - - +
833A LEU* 1.3 61.9 + - - +
835A ASN* 3.5 11.3 + - - +
836A PHE* 4.6 3.9 + - - +
841A ILE* 3.8 28.8 - - + +
845A LYS* 4.9 12.7 + - - -
577B ARG* 5.7 1.2 + - - -
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Residues in contact with LEU 833 (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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808A GLU 5.1 3.1 + - - +
809A GLU* 3.4 38.6 - - + +
810A THR* 4.8 0.4 - - - -
811A LEU* 4.1 30.7 - - + +
829A HIS* 3.0 18.4 + - + +
830A VAL* 3.4 16.4 - - + +
831A ALA 3.1 0.2 - - - -
832A GLU* 1.3 78.0 - - - +
834A ALA* 1.3 56.4 + - - +
835A ASN 3.2 4.9 + - - -
577B ARG* 4.4 14.8 + - - +
578B HIS* 5.4 0.9 - - - -
1191B PHE* 4.0 23.8 - - + -
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Residues in contact with ALA 834 (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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830A VAL 2.9 15.3 + - - +
831A ALA 3.2 6.4 + - - +
833A LEU* 1.3 74.5 - - - +
835A ASN* 1.3 66.3 + - - +
836A PHE* 4.8 1.3 - - + -
577B ARG* 5.7 0.2 - - - -
578B HIS* 3.0 23.3 + - - -
1191B PHE* 3.7 17.9 - - + -
1194B LEU* 4.1 12.8 - - + +
1195B SER* 3.9 25.1 - - - +
1198B ALA* 3.5 9.3 - - - +
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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