Contacts of the helix formed by residues 825 - 836 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808B ALA* 4.3 10.9 - - - +
811B ALA* 5.8 4.7 - - - +
826B HIS* 1.3 64.7 + - - +
827B TYR* 3.1 26.6 + - + +
828B GLU* 2.9 47.3 + - + +
829B LEU* 3.6 7.6 + - - +
1176B PHE* 5.0 5.7 - - - -
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Residues in contact with HIS 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804B SER* 3.5 20.3 - - - +
807B LYS* 3.3 48.6 - - + +
808B ALA* 3.4 23.1 - - - +
811B ALA* 5.3 6.1 - - + -
825B ASP* 1.3 74.9 - - - +
827B TYR* 1.3 63.4 + - - +
829B LEU* 3.5 9.3 + - - +
830B TYR* 3.2 15.6 + - - +
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Residues in contact with TYR 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805B LEU* 3.9 10.1 - - + -
808B ALA* 3.4 17.2 - - + +
825B ASP* 3.1 16.5 + - + +
826B HIS* 1.3 80.4 - - - +
828B GLU* 1.3 53.2 + - + +
830B TYR* 3.1 33.4 + + - +
831B ARG* 2.8 62.3 + - + +
1173B PHE* 5.5 0.4 - + - -
1176B PHE* 3.7 48.4 + + + +
1177B ILE* 3.6 25.6 - - + +
1180B GLU* 4.8 3.9 + - - +
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Residues in contact with GLU 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825B ASP* 2.9 35.6 + - + +
826B HIS 3.2 0.2 - - - -
827B TYR* 1.3 79.4 - - - +
829B LEU* 1.3 64.6 + - + +
830B TYR 3.3 0.9 + - - -
831B ARG* 3.4 6.8 + - - +
832B GLN* 3.3 29.2 + - - +
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Residues in contact with LEU 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804B SER* 4.1 12.3 - - - -
825B ASP 3.6 6.9 + - - +
826B HIS* 3.5 12.2 + - - +
827B TYR 3.4 0.4 - - - -
828B GLU* 1.3 78.7 - - + +
830B TYR* 1.3 60.6 + - - +
832B GLN* 3.7 21.7 + - + +
833B TYR* 3.3 40.9 + - + +
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Residues in contact with TYR 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B MET* 3.7 36.1 - - + -
804B SER* 3.4 15.7 + - - +
805B LEU* 3.6 42.7 - - + +
826B HIS 3.2 10.7 + - - +
827B TYR* 3.1 50.8 + + - +
829B LEU* 1.3 74.9 - - - +
831B ARG* 1.3 67.8 + - - +
832B GLN 3.0 5.9 + - - -
833B TYR* 3.1 16.7 + - - +
834B LEU* 3.5 37.2 + - + +
1109B LYS* 4.2 22.5 + - - +
1110B THR* 4.9 0.8 + - - -
1130B ILE* 4.4 4.6 - - + +
1173B PHE* 4.6 2.3 - + - -
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Residues in contact with ARG 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827B TYR* 2.8 48.2 + - + +
828B GLU* 3.8 7.2 - - - +
830B TYR* 1.3 80.2 - - - +
832B GLN* 1.3 56.4 + - - +
834B LEU* 3.6 15.2 + - - +
835B LYS* 3.2 58.8 + - + +
1110B THR* 2.8 36.9 + - - +
1111B GLY 4.6 0.2 - - - +
1112B TRP* 4.4 4.8 - - - +
1180B GLU* 2.5 45.6 + - - -
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Residues in contact with GLN 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828B GLU* 3.3 19.1 + - - +
829B LEU* 3.9 21.6 - - + +
830B TYR 3.0 0.6 - - - -
831B ARG* 1.3 77.5 - - + +
833B TYR* 1.3 63.4 + - - +
834B LEU 3.2 0.7 - - - -
835B LYS* 4.1 7.2 - - + +
836B ASP* 3.3 37.6 + - - +
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Residues in contact with TYR 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B TYR* 3.7 17.1 + - - +
798B SER* 5.6 0.9 - - - -
800B GLU* 3.5 36.6 + - + +
801B MET* 3.6 41.7 - - + -
804B SER* 3.9 11.7 - - - -
829B LEU* 3.3 33.9 + - + +
830B TYR* 3.1 8.6 + - - +
832B GLN* 1.3 78.9 - - - +
834B LEU* 1.3 62.3 + - - +
836B ASP* 4.0 4.4 + - - +
837B ARG* 3.9 8.5 + - - +
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Residues in contact with LEU 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B TYR* 4.2 4.3 - - - +
796B MET* 3.4 35.0 - - + +
801B MET* 4.5 11.4 - - + -
830B TYR* 3.5 41.2 + - + +
831B ARG* 3.6 15.7 + - - +
832B GLN 3.2 0.2 - - - -
833B TYR* 1.3 78.0 - - - +
835B LYS* 1.3 60.7 + - - +
837B ARG* 2.9 38.5 + - - +
1109B LYS* 3.6 20.2 - - + +
1110B THR* 3.7 22.4 - - - +
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Residues in contact with LYS 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B ARG* 3.2 51.2 + - + +
832B GLN* 4.9 5.6 - - + -
833B TYR 3.7 0.2 - - - -
834B LEU* 1.3 74.1 - - - +
836B ASP* 1.3 58.8 - - - +
837B ARG* 3.0 25.0 + - - +
1180B GLU* 6.2 0.4 - - - -
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Residues in contact with ASP 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B GLN* 3.3 29.9 + - - +
833B TYR* 4.0 6.1 - - - +
834B LEU 3.3 0.2 - - - -
835B LYS* 1.3 77.0 - - - +
837B ARG* 1.3 62.8 + - - +
838B PRO* 3.7 1.7 - - - +
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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