Contacts of the helix formed by residues 772 - 779 (chain E) in PDB entry 1XFV
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 GLU 772 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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761E GLN* 3.6 20.2 - - - +
764E LEU* 4.7 2.5 - - - -
770E ASN 3.3 7.0 + - - +
771E ILE* 1.3 75.3 - - - +
773E PHE* 1.3 67.6 + - - +
774E LYS* 4.7 17.7 - - + +
775E LEU* 3.6 31.3 + - + +
776E LEU* 3.1 21.1 + - - +
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Residues in contact with PHE 773 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726E ILE* 4.0 27.6 - - + -
729E TYR* 3.2 54.3 - + + -
756E ILE* 5.3 0.7 - - + -
757E THR* 3.6 29.8 - - + +
760E VAL* 3.8 30.5 - - + -
761E GLN* 3.2 25.5 + - - +
764E LEU* 5.0 2.9 - - - -
772E GLU* 1.3 68.2 - - + +
774E LYS* 1.3 70.6 + - + +
775E LEU 2.5 17.3 + - - -
776E LEU* 2.8 18.3 + - + -
777E TYR* 3.0 28.2 + + + +
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Residues in contact with LYS 774 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E GLU* 4.7 16.1 - - - +
773E PHE* 1.3 87.9 - - + +
775E LEU* 1.3 68.0 - - + +
777E TYR* 3.8 5.4 - - - +
778E LYS* 3.2 32.3 + - + +
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Residues in contact with LEU 775 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770E ASN 5.4 2.0 - - - +
771E ILE* 5.8 0.7 - - - -
772E GLU* 3.7 36.1 - - + +
773E PHE 2.5 4.9 + - - -
774E LYS* 1.3 77.7 - - + +
776E LEU* 1.3 57.6 - - - +
777E TYR 2.9 1.8 - - - -
778E LYS* 2.6 34.7 + - + +
779E GLN* 3.0 26.4 + - - +
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Residues in contact with LEU 776 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E ILE* 4.5 8.1 - - + -
726E ILE* 3.9 19.7 - - + -
760E VAL* 5.3 1.6 - - + -
764E LEU* 4.6 20.0 - - + -
771E ILE* 4.5 14.6 - - + +
772E GLU 3.1 14.3 + - - +
773E PHE* 2.8 7.8 + - - +
775E LEU* 1.3 75.0 - - - +
777E TYR* 1.3 52.2 + - - +
779E GLN* 3.5 18.9 + - - +
780E LEU* 2.6 41.0 - - + +
793E PHE* 3.7 37.0 - - + -
796E ILE* 4.0 20.5 - - + +
797E ILE* 5.1 2.7 - - + -
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Residues in contact with TYR 777 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726E ILE* 4.6 14.8 - - + +
729E TYR* 3.6 36.2 - + - -
730E ASN* 3.7 29.0 + - + -
733E GLU* 4.1 17.7 - - + +
773E PHE* 3.0 31.7 + + + +
774E LYS* 3.8 6.3 - - - +
775E LEU 2.7 4.6 + - - -
776E LEU* 1.3 73.6 - - - +
778E LYS* 1.3 70.7 + - + +
780E LEU* 2.8 24.4 + - + +
782E PHE* 3.1 37.4 - + - -
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Residues in contact with LYS 778 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774E LYS* 3.2 22.6 + - + +
775E LEU* 2.6 20.0 + - + +
777E TYR* 1.3 79.7 - - + +
779E GLN* 1.3 59.7 + - + +
780E LEU 2.9 15.1 + - - +
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Residues in contact with GLN 779 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775E LEU* 3.0 30.5 + - - +
776E LEU* 3.6 11.7 - - - +
777E TYR 3.0 0.6 + - - -
778E LYS* 1.3 74.4 - - + +
780E LEU* 1.3 64.2 + - - +
792E VAL* 4.5 10.9 - - - +
796E ILE* 3.8 33.1 - - + +
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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
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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