Contacts of the helix formed by residues 825 - 836 (chain A) in PDB entry 1OFD
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 ASP 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808A ALA* 4.0 17.5 - - - +
811A ALA* 5.4 4.6 - - - +
826A HIS* 1.3 72.7 + - - +
827A TYR* 3.1 18.8 + - + +
828A GLU* 3.6 33.6 + - + +
829A LEU* 3.6 14.2 + - - +
1176A PHE* 5.8 2.1 - - - -
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Residues in contact with HIS 826 (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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804A SER* 3.2 31.0 + - - +
807A LYS* 3.7 52.4 + - + +
808A ALA* 3.3 12.8 - - - +
811A ALA* 5.0 7.6 - - + -
825A ASP* 1.3 79.1 + - - +
827A TYR* 1.3 57.4 + - - +
829A LEU* 3.5 8.4 + - - +
830A TYR* 3.1 26.0 + - - +
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Residues in contact with TYR 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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805A LEU* 3.8 16.2 - - + -
808A ALA* 3.4 14.5 - - + +
825A ASP* 3.1 12.1 + - + +
826A HIS* 1.3 78.3 - - - +
828A GLU* 1.3 61.7 + - + +
829A LEU 3.4 0.2 - - - -
830A TYR* 3.5 32.1 + + - +
831A ARG* 2.8 59.0 + - + +
1173A PHE* 5.2 0.4 - + - -
1176A PHE* 3.7 46.1 + + + +
1177A ILE* 3.4 27.9 - - + +
1180A GLU* 4.1 2.7 + - - -
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Residues in contact with GLU 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 ASP* 3.6 26.0 + - + +
826A HIS 3.3 0.6 - - - -
827A TYR* 1.3 79.6 - - + +
829A LEU* 1.3 66.1 + - - +
831A ARG* 3.7 9.1 - - + +
832A GLN* 3.3 38.1 + - - +
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Residues in contact with LEU 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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804A SER* 4.6 10.5 - - - -
825A ASP 3.6 9.8 + - - +
826A HIS* 3.5 13.1 + - - +
827A TYR 3.4 0.2 - - - -
828A GLU* 1.3 77.7 - - - +
830A TYR* 1.3 60.1 + - - +
832A GLN* 3.6 12.9 + - + +
833A TYR* 3.0 40.6 + - + +
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Residues in contact with TYR 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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801A MET* 3.6 44.4 - - + -
804A SER* 4.0 8.9 - - - +
805A LEU* 3.7 37.3 - - + +
826A HIS 3.1 18.1 + - - +
827A TYR* 3.6 45.3 - + - +
828A GLU 3.3 0.2 - - - -
829A LEU* 1.3 75.7 - - - +
831A ARG* 1.3 70.3 + - - +
833A TYR* 3.4 17.9 + - - +
834A LEU* 3.6 33.1 + - + +
1109A LYS* 4.1 23.5 + - - +
1110A THR* 4.7 0.4 + - - -
1130A ILE* 4.4 8.8 - - + +
1173A PHE* 4.7 1.7 - + - -
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Residues in contact with ARG 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 TYR* 2.8 45.5 + - + +
828A GLU* 3.7 11.7 - - + +
829A LEU 3.2 0.4 - - - -
830A TYR* 1.3 85.0 - - - +
832A GLN* 1.3 61.1 + - + +
834A LEU* 3.5 19.1 + - - +
835A LYS* 3.4 56.4 + - - +
1110A THR* 2.9 29.0 + - - +
1112A TRP* 4.8 3.2 - - - +
1180A GLU* 2.8 42.7 + - - -
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Residues in contact with GLN 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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828A GLU* 3.3 25.8 + - - +
829A LEU* 4.2 13.5 - - + +
831A ARG* 1.3 78.3 - - + +
833A TYR* 1.3 66.6 + - - +
834A LEU 3.1 1.1 - - - -
835A LYS* 3.8 8.7 - - + +
836A ASP* 3.2 37.4 + - - +
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Residues in contact with TYR 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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794A TYR* 4.1 11.7 + - - -
798A SER* 5.3 1.6 - - - -
800A GLU* 3.7 34.3 - - + +
801A MET* 4.3 27.4 - - + -
804A SER* 4.0 15.5 - - - -
829A LEU* 3.0 44.5 + - + +
830A TYR* 3.4 13.2 + - - +
832A GLN* 1.3 78.2 - - - +
834A LEU* 1.3 61.9 + - + +
836A ASP* 3.8 8.5 + - - +
837A ARG* 4.0 5.5 + - - -
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Residues in contact with LEU 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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794A TYR* 4.4 4.7 - - - +
796A MET* 3.5 22.6 - - + +
801A MET* 4.5 11.2 - - + -
830A TYR* 3.6 30.7 + - + +
831A ARG* 3.5 19.4 + - - +
832A GLN 3.1 0.6 - - - -
833A TYR* 1.3 82.8 - - - +
835A LYS* 1.3 57.8 + - + +
837A ARG* 3.0 37.2 + - - +
1109A LYS* 2.9 35.0 - - + +
1110A THR* 3.4 27.4 - - + +
1113A ASP* 5.8 0.2 - - - +
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Residues in contact with LYS 835 (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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831A ARG* 3.4 53.0 + - - +
832A GLN* 3.5 8.7 + - + -
833A TYR 3.5 0.4 - - - -
834A LEU* 1.3 76.1 - - + +
836A ASP* 1.3 63.4 + - - +
837A ARG* 3.1 15.8 + - - +
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Residues in contact with ASP 836 (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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794A TYR* 5.6 0.2 - - - -
832A GLN* 3.2 27.0 + - - +
833A TYR* 4.2 5.8 - - - +
834A LEU 3.3 0.4 - - - -
835A LYS* 1.3 79.3 - - - +
837A ARG* 1.3 65.9 + - - +
838A PRO* 3.7 3.5 - - - +
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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