Contacts of the helix formed by residues 771 - 783 (chain B) in PDB entry 5TDF
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 THR 771 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719B ILE* 3.9 11.7 - - + -
749B ALA* 6.2 0.7 - - + -
750B THR* 4.3 16.7 + - + +
765B ALA* 4.1 14.8 - - + -
767B GLN 4.3 1.3 - - - +
768B ALA* 3.2 26.3 + - + +
770B GLU* 1.3 80.2 - - - +
772B ALA* 1.3 64.8 + - - +
773B VAL* 3.7 5.8 + - - +
774B ALA* 3.2 16.1 + - - +
775B LYS* 3.1 24.2 + - - +
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Residues in contact with ALA 772 (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 ILE* 3.9 12.3 - - + +
744B CYS* 3.5 24.7 - - + +
745B ILE 3.4 25.6 - - - +
746B GLY* 3.5 20.7 + - - -
747B THR* 3.6 3.6 - - + +
750B THR* 5.5 0.2 + - - -
770B GLU 3.8 1.0 + - - -
771B THR* 1.3 74.3 - - - +
773B VAL* 1.3 57.9 + - - +
775B LYS* 4.0 1.9 - - - +
776B ASN* 2.9 37.1 + - - -
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Residues in contact with VAL 773 (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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747B THR* 3.9 27.8 - - + +
750B THR* 3.5 31.9 - - + +
771B THR* 3.2 3.6 + - - +
772B ALA* 1.3 78.2 - - - +
774B ALA* 1.3 63.2 + - - +
776B ASN* 3.9 6.1 - - - +
777B GLN* 3.1 25.2 + - + +
904B GOL 5.1 1.5 + - - +
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Residues in contact with ALA 774 (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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725B TYR* 3.8 14.2 + - - +
768B ALA 3.5 15.7 - - - +
769B SER* 4.0 3.8 - - - +
771B THR* 3.2 21.0 + - - +
773B VAL* 1.3 79.1 - - - +
775B LYS* 1.3 62.3 + - - +
777B GLN* 3.3 6.8 + - - +
778B ALA* 3.0 24.1 + - - +
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Residues in contact with LYS 775 (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 GLU 2.7 32.1 + - - -
719B ILE* 4.4 0.2 - - - +
720B GLY 2.9 21.4 + - - +
721B GLY 3.0 14.4 + - - +
722B THR* 4.7 0.2 - - - -
724B GLU* 2.7 36.2 + - + +
725B TYR* 3.7 22.2 - - + +
744B CYS* 4.0 13.7 - - - -
769B SER 3.5 12.6 - - - +
770B GLU 3.6 14.1 - - - -
771B THR 3.1 13.2 + - - +
772B ALA* 4.0 2.7 - - - +
774B ALA* 1.3 73.7 - - - +
776B ASN* 1.3 65.4 + - - +
778B ALA* 3.3 2.6 + - - +
779B LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 776 (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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743B TRP* 3.4 30.7 - - - -
744B CYS* 2.8 51.6 + - - +
747B THR* 3.8 7.3 - - - +
772B ALA 2.9 20.7 + - - +
773B VAL* 3.9 4.9 - - - +
775B LYS* 1.3 76.2 - - - +
777B GLN* 1.3 63.3 + - - +
779B LEU* 3.3 7.1 + - - +
780B LYS* 3.0 24.8 + - - +
786B VAL* 4.0 8.1 - - + +
904B GOL 3.9 20.7 - - - +
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Residues in contact with GLN 777 (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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773B VAL* 3.1 20.1 + - + +
774B ALA* 3.6 5.8 - - - +
776B ASN* 1.3 78.3 - - - +
778B ALA* 1.3 62.5 + - - +
780B LYS* 3.1 34.3 + - - +
781B GLU* 2.5 66.7 + - - +
904B GOL 3.5 7.1 + - - +
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Residues in contact with ALA 778 (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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725B TYR* 3.5 35.9 - - + -
728B CYS* 3.6 7.6 - - - -
774B ALA 3.0 12.7 + - - +
775B LYS 3.8 2.9 - - - +
777B GLN* 1.3 76.0 - - - +
779B LEU* 1.3 62.3 + - - +
781B GLU* 3.3 12.4 + - - +
782B ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 779 (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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724B GLU* 3.6 32.5 - - + +
727B ILE* 4.2 13.2 - - + -
728B CYS* 3.7 14.4 - - - -
742B CYS* 3.6 27.8 - - + -
744B CYS* 3.9 17.3 - - - -
775B LYS* 2.9 23.4 + - - +
776B ASN* 3.8 7.6 - - - +
778B ALA* 1.3 74.8 - - - +
780B LYS* 1.3 63.7 + - - +
782B ALA* 3.1 7.4 + - - -
783B GLY 3.3 0.3 + - - -
784B VAL* 3.0 45.4 + - + +
786B VAL* 3.9 11.0 - - + -
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Residues in contact with LYS 780 (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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776B ASN 3.0 15.5 + - - +
777B GLN* 3.1 32.8 + - - +
779B LEU* 1.3 76.3 - - - +
781B GLU* 1.3 62.9 + - + +
783B GLY* 3.3 12.6 + - - -
784B VAL 3.8 12.7 - - - +
786B VAL* 3.6 16.5 - - + +
904B GOL 2.8 41.5 + - - +
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Residues in contact with GLU 781 (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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777B GLN* 2.5 50.5 + - - +
778B ALA* 3.8 9.8 - - - +
779B LEU 3.3 0.4 - - - -
780B LYS* 1.3 78.0 - - + +
782B ALA* 1.3 59.0 + - - +
783B GLY 3.5 0.5 + - - -
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Residues in contact with ALA 782 (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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728B CYS* 3.7 37.5 - - + +
731B ILE* 3.4 23.0 - - + +
732B LYS* 5.4 1.0 + - + -
778B ALA 3.0 16.0 + - - +
779B LEU 3.1 6.0 + - - +
781B GLU* 1.3 76.1 - - - +
783B GLY* 1.3 58.3 + - - +
784B VAL* 3.5 3.8 - - + +
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Residues in contact with GLY 783 (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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731B ILE* 4.4 8.3 - - - +
740B ILE 5.8 0.5 + - - -
780B LYS 3.3 11.0 + - - -
781B GLU 3.3 2.0 + - - -
782B ALA* 1.3 80.1 - - - +
784B VAL* 1.3 64.5 + - - +
785B PHE* 3.8 15.6 + - - -
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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