Contacts of the helix formed by residues 862 - 868 (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 SER 862 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860B VAL 3.7 0.8 + - - -
861B GLU* 1.3 77.5 - - - +
863B VAL* 1.3 64.6 + - - +
864B GLU* 3.2 21.2 + - - +
865B SER* 3.1 33.8 + - - -
866B ILE* 3.1 13.3 + - - +
1182B ARG* 4.1 6.1 - - - +
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Residues in contact with VAL 863 (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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862B SER* 1.3 71.3 - - - +
864B GLU* 1.3 64.2 + - - +
866B ILE* 3.2 2.6 + - - +
867B VAL* 2.9 35.0 + - - +
1175B TYR* 2.9 44.9 - - + +
1178B ALA* 3.7 14.4 - - + -
1179B GLU* 3.6 48.9 - - + +
1182B ARG* 3.8 10.8 - - - +
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Residues in contact with GLU 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B SER* 3.2 21.4 - - - +
863B VAL* 1.3 88.9 + - - +
865B SER* 1.3 56.1 + - - +
867B VAL* 3.7 14.4 - - - +
868B LYS* 3.3 32.5 - - - +
895B LEU 4.7 0.7 - - - +
1175B TYR* 4.6 17.7 + - + +
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Residues in contact with SER 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B GLU* 3.1 23.4 + - - +
862B SER* 3.1 26.0 + - - -
864B GLU* 1.3 76.8 - - - +
866B ILE* 1.3 64.3 + - - +
868B LYS* 3.6 21.8 + - - +
869B ARG* 4.4 7.6 + - - +
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Residues in contact with ILE 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B GLU* 3.5 30.7 - - + +
862B SER 3.1 12.6 + - - +
863B VAL* 3.8 5.6 - - - +
865B SER* 1.3 74.3 - - - +
867B VAL* 1.3 61.8 + - - +
869B ARG* 3.0 30.5 + - - +
870B PHE* 3.6 27.1 - - + -
1178B ALA* 3.7 18.8 - - + +
1181B VAL* 3.9 18.8 - - + -
1182B ARG* 3.5 32.3 - - + -
1185B LEU* 4.6 2.0 - - + -
1193B LEU* 4.1 15.9 - - + -
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Residues in contact with VAL 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B VAL 2.9 14.3 + - - +
864B GLU* 3.7 11.9 - - - +
866B ILE* 1.3 77.0 - - - +
868B LYS* 1.3 58.0 + - - +
870B PHE* 3.0 42.6 + - + +
895B LEU* 3.4 44.2 - - + +
897B ALA* 3.3 15.2 - - - +
1174B PHE* 3.9 26.9 - - + +
1175B TYR* 4.0 20.0 - - + +
1178B ALA* 4.2 1.8 - - + -
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Residues in contact with LYS 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B GLU* 3.3 26.1 + - - +
865B SER* 3.8 13.2 - - - +
866B ILE 3.2 1.2 - - - -
867B VAL* 1.3 75.8 - - - +
869B ARG* 1.3 60.1 + - + +
870B PHE 3.3 3.3 + - - +
895B LEU 4.3 10.3 - - - +
896B GLY* 3.9 31.0 - - - +
897B ALA* 4.4 3.7 - - - +
898B LYS* 4.3 14.9 + - - -
1124B GLU* 4.4 3.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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