Contacts of the helix formed by residues 720 - 728 (chain U) in PDB entry 6FF7
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 720 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718U PHE* 3.3 6.7 - - - +
719U LEU* 1.3 81.6 - - - +
721U ILE* 1.3 64.8 + - - +
722U GLU* 3.1 12.1 - - - -
723U HIS* 3.2 10.0 + - - +
724U LEU* 3.1 21.1 + - - +
743U GLN 5.4 0.9 - - - -
744U ILE* 5.6 1.6 - - - +
745U PRO* 5.2 9.4 - - - -
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Residues in contact with ILE 721 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720U SER* 1.3 75.8 - - - +
722U GLU* 1.3 57.8 + - - +
724U LEU* 3.4 8.4 + - - +
725U LYS* 3.0 29.3 + - - +
743U GLN* 3.4 38.1 + - + +
744U ILE* 5.3 0.8 - - - +
745U PRO 5.6 0.2 - - - -
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Residues in contact with GLU 722 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720U SER* 3.1 8.4 - - - -
721U ILE* 1.3 76.3 - - - +
723U HIS* 1.3 64.6 + - - +
725U LYS* 3.4 6.1 + - - +
726U ALA* 3.1 25.3 + - - +
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Residues in contact with HIS 723 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718U PHE* 4.5 4.5 - - + -
719U LEU* 4.0 15.3 - - + +
720U SER* 3.2 24.6 + - - +
722U GLU* 1.3 78.1 - - - +
724U LEU* 1.3 62.3 + - - +
726U ALA* 3.4 6.7 + - - +
727U SER* 3.1 23.4 + - - -
801U GLN* 5.9 7.9 - - + -
802U PHE 5.6 1.4 - - - +
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Residues in contact with LEU 724 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718U PHE* 4.1 16.5 - - + +
720U SER 3.1 12.4 + - - +
721U ILE* 3.5 12.1 - - - +
722U GLU 3.2 0.2 - - - -
723U HIS* 1.3 77.8 - - - +
725U LYS* 1.3 58.1 + - - +
727U SER* 2.9 27.7 + - - -
728U PHE* 3.6 7.4 + - - +
747U PHE* 5.9 5.8 - - + -
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Residues in contact with LYS 725 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721U ILE 3.0 17.1 + - - +
722U GLU* 3.9 6.3 - - - +
724U LEU* 1.3 75.5 - - - +
726U ALA* 1.3 60.8 + - - +
727U SER 3.3 0.3 + - - -
728U PHE* 3.5 18.9 + - - +
729U PRO* 4.5 1.6 - - - +
733U VAL* 5.0 19.1 - - + -
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Residues in contact with ALA 726 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722U GLU 3.1 18.2 + - - +
723U HIS* 3.7 7.6 - - - +
725U LYS* 1.3 75.4 - - - +
727U SER* 1.3 60.9 + - - +
728U PHE 3.3 0.7 - - - -
729U PRO* 4.4 7.2 - - - +
804U HIS* 3.8 11.1 + - - +
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Residues in contact with SER 727 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723U HIS 3.1 11.9 + - - -
724U LEU* 2.9 16.5 + - - -
726U ALA* 1.3 78.8 - - - +
728U PHE* 1.3 57.6 + - - +
729U PRO 4.1 0.2 - - - -
802U PHE 5.3 5.2 - - - -
803U THR 5.2 0.9 - - - -
804U HIS* 3.2 33.5 - - - +
807U ILE* 4.2 20.8 - - - +
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Residues in contact with PHE 728 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724U LEU 3.6 6.6 + - - +
725U LYS* 3.5 11.8 + - - +
726U ALA 3.3 0.4 - - - -
727U SER* 1.3 80.6 - - - +
729U PRO* 1.3 64.2 - - - +
730U GLY 3.2 2.9 - - - -
731U HIS* 3.0 34.4 + - + +
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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