Contacts of the helix formed by residues 718 - 726 (chain B) in PDB entry 1FO4
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 718 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717B GLY* 1.3 71.9 - - - -
719B LEU* 1.3 60.4 + - - +
720B LYS* 3.3 9.7 + - - +
721B LYS* 3.0 42.2 + - + +
722B GLY 2.8 21.0 + - - -
893B ASN* 2.7 20.9 + - - +
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Residues in contact with LEU 719 (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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715B GLU* 3.7 13.9 + - + +
716B LYS 5.5 0.7 - - - +
717B GLY 4.0 2.0 + - - -
718B ASP* 1.3 69.3 + - - +
720B LYS* 1.3 68.1 + - - +
722B GLY* 3.0 1.6 + - - -
723B PHE* 2.9 41.2 + - + -
858B ALA* 4.4 1.1 - - + +
859B LEU 3.4 24.2 - - - +
860B GLU* 2.9 28.7 - - + +
893B ASN* 3.7 24.2 - - + +
894B ILE* 3.9 4.7 - - - +
895B ARG* 3.1 42.6 - - + -
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Residues in contact with LYS 720 (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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718B ASP* 3.3 7.5 + - - +
719B LEU* 1.3 76.9 - - - +
721B LYS* 1.3 61.0 + - - +
723B PHE* 3.5 7.9 + - - +
724B SER* 2.9 30.5 + - - +
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Residues in contact with LYS 721 (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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718B ASP* 3.0 35.9 + - + +
720B LYS* 1.3 75.2 - - - +
722B GLY* 1.3 66.1 + - - +
724B SER* 3.2 7.4 + - - -
725B GLU* 2.9 54.5 + - + +
893B ASN* 6.1 0.4 - - - +
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Residues in contact with GLY 722 (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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718B ASP 2.8 11.9 + - - -
719B LEU 3.0 3.5 + - - -
721B LYS* 1.3 76.5 - - - +
723B PHE* 1.3 61.2 + - - +
725B GLU* 3.2 10.4 + - - +
726B ALA 3.2 16.1 + - - -
857B VAL* 3.4 16.1 - - - +
858B ALA* 3.8 7.6 - - - -
893B ASN* 3.5 26.7 - - - +
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Residues in contact with PHE 723 (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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719B LEU* 2.9 38.5 + - + +
720B LYS* 3.9 7.0 - - - +
722B GLY* 1.3 75.3 - - - +
724B SER* 1.3 64.1 + - - +
726B ALA* 3.0 23.4 + - - +
729B VAL* 4.3 20.4 - - + +
847B LYS* 3.3 64.6 - - + +
848B VAL 4.4 0.4 - - - -
849B GLY* 4.0 8.3 - - - -
858B ALA* 3.7 18.8 - - + +
859B LEU 4.5 2.2 - - - -
860B GLU* 3.2 33.2 - - + -
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Residues in contact with SER 724 (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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720B LYS* 2.9 18.8 + - - +
721B LYS* 3.2 12.8 + - - -
723B PHE* 1.3 77.8 - - - +
725B GLU* 1.3 62.3 + - - +
726B ALA 4.4 3.1 - - - +
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Residues in contact with GLU 725 (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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721B LYS* 2.9 47.4 - - + +
722B GLY* 3.2 12.3 + - - +
723B PHE 3.1 1.0 - - - -
724B SER* 1.3 78.9 - - - +
726B ALA* 1.3 64.3 + - - +
727B ASP* 4.4 1.4 - - - +
851B MET* 3.3 24.5 - - + +
857B VAL* 4.8 9.2 - - + +
893B ASN* 4.9 4.7 + - - -
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Residues in contact with ALA 726 (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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722B GLY 3.2 4.3 + - - +
723B PHE 3.0 18.9 + - - +
724B SER 4.4 3.1 - - - +
725B GLU* 1.3 79.6 - - - +
727B ASP* 1.3 64.8 + - - +
728B ASN* 3.5 8.4 - - - +
729B VAL* 4.2 5.7 - - + +
849B GLY* 3.7 6.7 - - - -
850B PHE 3.5 15.5 - - - +
851B MET* 3.8 2.9 - - - -
857B VAL* 3.5 26.5 - - + -
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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