Contacts of the helix formed by residues 784 - 793 (chain A) in PDB entry 3THW
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 PHE 784 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A THR* 4.2 3.2 - - - +
750A LEU 4.0 14.8 - - - -
751A GLY 3.4 26.7 - - - -
756A THR* 3.6 35.4 - - + -
759A GLY* 3.8 7.0 - - - -
760A PHE* 3.7 26.2 - - + -
763A ALA* 4.7 9.0 - - + -
780A PHE* 6.1 0.2 - + - -
782A THR* 2.9 24.4 + - - +
783A HIS* 1.3 101.8 - + - +
785A HIS* 1.3 64.5 + - - +
786A GLU* 3.2 20.4 - - - +
787A LEU* 3.5 26.1 + - + +
788A THR 4.4 0.7 + - - -
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Residues in contact with HIS 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A THR* 4.7 5.4 - - + -
783A HIS 3.0 9.1 + - - +
784A PHE* 1.3 68.5 - - - +
786A GLU* 1.3 65.4 + - - +
787A LEU 2.9 10.9 + - - -
788A THR* 3.0 38.3 + - - +
821A VAL* 3.9 26.0 - - + +
822A CYS 5.0 4.9 + - - -
854A PHE* 3.5 25.4 + - + -
855A GLN* 5.2 8.8 - - + +
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Residues in contact with GLU 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A THR* 5.4 2.3 - - - +
760A PHE* 3.3 33.2 - - + +
764A TRP* 3.6 9.9 - - - -
783A HIS 4.8 0.2 - - - +
784A PHE* 3.2 21.9 - - - -
785A HIS* 1.3 90.3 + - - +
787A LEU* 1.3 60.2 + - - +
788A THR 3.3 0.2 - - - -
789A ALA* 3.6 12.9 + - - +
854A PHE* 3.6 53.8 - - + +
855A GLN 5.2 9.0 - - - +
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Residues in contact with LEU 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A ILE* 3.2 21.0 - - + +
760A PHE* 3.8 8.1 - - + -
763A ALA* 3.8 9.4 - - + +
764A TRP* 3.6 48.0 - - + +
767A SER* 4.2 5.2 - - - +
780A PHE* 4.0 34.5 - - + -
782A THR* 4.2 19.3 - - + +
784A PHE* 3.5 19.9 + - + +
785A HIS 2.9 0.6 + - - -
786A GLU* 1.3 76.9 - - - +
788A THR* 1.3 56.6 + - - +
789A ALA 3.0 5.4 - - - -
790A LEU* 3.0 33.0 + - + +
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Residues in contact with THR 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A ILE* 4.1 8.3 - - + -
668A THR* 4.1 18.8 - - + -
784A PHE 4.5 0.7 - - - +
785A HIS* 3.0 43.1 + - - +
787A LEU* 1.3 77.2 - - - +
789A ALA* 1.3 63.1 + - - +
790A LEU 3.0 0.9 - - - -
791A ALA* 3.1 22.2 + - - +
792A ASN* 5.1 1.0 + - - -
799A ASN* 3.2 35.5 - - - +
821A VAL* 4.1 10.6 - - + +
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Residues in contact with ALA 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764A TRP* 3.7 12.1 - - + -
785A HIS 5.6 0.2 - - - +
786A GLU* 3.6 15.8 + - - +
787A LEU 3.0 0.8 - - - -
788A THR* 1.3 78.4 + - - +
790A LEU* 1.3 63.5 + - - +
791A ALA 3.0 2.0 - - - -
792A ASN* 3.2 33.3 + - - +
793A GLN* 4.4 2.8 + - - +
855A GLN 4.8 14.4 - - - +
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Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A PHE* 5.3 0.7 - - + -
666A ILE* 4.3 11.4 - - + -
764A TRP* 3.3 48.6 - - + +
767A SER* 3.5 33.9 - - - +
768A GLU* 4.0 13.9 - - + +
787A LEU* 3.0 21.7 + - + +
789A ALA* 1.3 72.2 - - - +
791A ALA* 1.3 56.4 + - - +
792A ASN 2.9 11.8 + - - -
793A GLN* 3.4 17.8 + - - +
794A ILE* 3.7 29.9 + - + +
797A VAL* 4.3 8.5 - - + +
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Residues in contact with ALA 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A ILE* 4.8 1.1 - - + +
788A THR 3.1 15.3 + - - +
789A ALA 3.0 1.2 - - - -
790A LEU* 1.3 76.6 - - - +
792A ASN* 1.3 63.1 + - - +
794A ILE 4.1 6.7 - - - +
795A PRO* 5.8 0.5 - - - +
797A VAL* 3.5 42.1 - - + +
798A ASN* 4.3 4.9 - - - +
799A ASN* 3.9 14.6 - - + +
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Residues in contact with ASN 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A THR 5.1 0.8 + - - -
789A ALA* 3.2 26.4 + - - +
790A LEU 2.9 0.8 + - - -
791A ALA* 1.3 84.4 - - - +
793A GLN* 1.3 68.9 + - + +
794A ILE* 3.4 2.2 - - - -
795A PRO* 5.7 0.5 - - - +
866A MET 5.3 6.2 + - - -
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Residues in contact with GLN 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764A TRP* 4.1 29.8 + - + +
768A GLU* 3.9 17.3 - - - +
789A ALA 5.2 2.7 - - - +
790A LEU* 3.4 10.7 + - - +
792A ASN* 1.3 82.1 - - + +
794A ILE* 1.3 67.3 - - + +
795A PRO* 3.6 9.2 - - - +
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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