Contacts of the helix formed by residues 755 - 771 (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 SER 755 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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754A THR* 1.3 80.5 + - - +
756A THR* 1.3 60.2 - - - +
757A TYR* 4.1 6.3 + - - +
758A ASP* 3.0 31.0 + - - +
759A GLY* 2.8 25.3 + - - -
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Residues in contact with THR 756 (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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754A THR 3.5 3.9 + - - +
755A SER* 1.3 72.2 - - - +
757A TYR* 1.3 71.4 + - - +
759A GLY 4.5 0.4 - - - +
760A PHE* 3.3 21.5 + - - +
783A HIS* 5.3 6.7 - - + +
784A PHE* 3.6 25.8 - - + -
786A GLU* 5.4 2.8 - - - +
854A PHE* 6.4 1.6 - - - -
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Residues in contact with TYR 757 (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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755A SER* 3.1 7.2 + - - +
756A THR* 1.3 87.9 + - - +
758A ASP* 1.3 66.7 + - - +
760A PHE* 4.1 6.7 - + + +
761A GLY* 3.5 15.2 + - - -
854A PHE* 4.5 27.4 - + - -
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Residues in contact with ASP 758 (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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754A THR* 4.3 14.2 + - + +
755A SER* 3.0 22.2 + - - +
757A TYR* 1.3 81.8 - - - +
759A GLY* 1.3 65.0 + - - +
760A PHE 3.2 0.2 - - - -
761A GLY* 3.3 2.2 + - - +
762A LEU* 3.1 32.3 + - + +
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Residues in contact with GLY 759 (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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751A GLY* 3.9 21.7 - - - -
754A THR* 3.8 14.5 - - - +
755A SER 2.8 14.6 + - - -
756A THR 3.6 0.2 + - - -
757A TYR 3.5 0.2 - - - -
758A ASP* 1.3 78.2 - - - +
760A PHE* 1.3 59.8 + - - +
762A LEU* 3.5 4.1 + - - +
763A ALA* 3.0 24.4 + - - +
784A PHE* 3.8 11.6 - - - -
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Residues in contact with PHE 760 (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 3.3 17.3 + - - +
757A TYR* 4.1 8.1 - + + +
758A ASP 3.2 0.4 - - - -
759A GLY* 1.3 72.9 - - - +
761A GLY* 1.3 63.8 + - - +
763A ALA* 3.2 5.2 + - - +
764A TRP* 2.8 70.5 + + + +
784A PHE* 3.7 21.3 - + + -
786A GLU* 3.3 50.5 - - + +
787A LEU* 3.8 9.0 - - + -
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Residues in contact with GLY 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A TYR 3.5 8.8 + - - -
758A ASP* 3.3 6.7 + - - -
760A PHE* 1.3 87.0 - - - +
762A LEU* 1.3 58.1 + - - +
764A TRP* 3.6 4.2 - - - +
765A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 762 (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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725A PHE* 4.3 16.2 - - + -
729A MET* 3.9 29.6 - - + -
750A LEU* 5.0 4.7 - - + -
751A GLY* 5.7 2.0 - - - -
754A THR* 5.1 1.3 - - + -
758A ASP* 3.1 25.5 + - + +
759A GLY* 3.8 5.8 - - - +
761A GLY* 1.3 70.9 - - - +
763A ALA* 1.3 66.2 - - - +
764A TRP 3.0 1.9 + - - -
765A ALA* 3.1 4.9 + - + -
766A ILE* 2.9 44.4 + - + +
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Residues in contact with ALA 763 (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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750A LEU* 4.2 17.6 - - - +
759A GLY 3.0 16.4 + - - +
760A PHE* 3.7 6.5 - - - +
762A LEU* 1.3 77.4 - - - +
764A TRP* 1.3 56.3 + - - +
766A ILE* 4.8 1.3 - - - -
767A SER* 2.6 35.0 + - - -
780A PHE* 3.9 25.1 - - + -
784A PHE* 4.7 7.0 - - + -
787A LEU* 3.8 14.6 - - + +
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Residues in contact with TRP 764 (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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760A PHE* 2.8 47.7 + + + +
761A GLY* 3.6 6.5 - - - +
763A ALA* 1.3 74.2 - - - +
765A ALA* 1.3 63.6 + - + +
766A ILE 3.1 1.7 + - - -
767A SER* 3.3 1.9 + - - -
768A GLU* 2.9 49.3 + - - +
786A GLU 3.6 16.8 - - - -
787A LEU* 3.6 17.5 - - + +
789A ALA* 3.7 10.3 - - + -
790A LEU* 3.3 58.0 - - + +
793A GLN* 4.1 24.9 + - + +
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Residues in contact with ALA 765 (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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761A GLY 2.9 19.3 + - - +
762A LEU* 4.0 5.2 - - + +
764A TRP* 1.3 82.2 - - + +
766A ILE* 1.3 58.5 + - + +
768A GLU* 3.7 9.7 - - - +
769A TYR* 3.0 26.9 + - - +
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Residues in contact with ILE 766 (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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729A MET* 5.3 4.0 - - + -
732A THR* 3.7 34.1 - - + +
736A LEU* 4.4 19.7 - - + -
747A ILE* 5.1 2.2 - - + -
750A LEU* 4.1 26.0 - - + -
762A LEU* 2.9 33.7 + - + +
763A ALA* 4.3 2.5 - - - +
765A ALA* 1.3 76.5 - - + +
767A SER* 1.3 65.6 + - - +
768A GLU 3.0 0.9 - - - -
769A TYR* 2.8 17.1 + - - +
770A ILE* 2.8 37.5 + - + +
780A PHE* 5.9 0.2 - - + -
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Residues in contact with SER 767 (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* 3.5 26.7 - - - -
763A ALA 2.6 23.2 + - - -
766A ILE* 1.3 80.3 - - - +
768A GLU* 1.3 61.5 + - - +
770A ILE* 3.7 2.0 + - - -
771A ALA* 3.3 25.1 + - - +
780A PHE* 3.0 27.9 - - - -
787A LEU* 4.2 3.8 - - - +
790A LEU* 3.5 23.7 - - - +
797A VAL* 5.5 0.2 - - - +
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Residues in contact with GLU 768 (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* 2.9 37.6 + - - +
765A ALA* 3.7 9.6 - - - +
767A SER* 1.3 75.7 - - - +
769A TYR* 1.3 64.7 + - - +
771A ALA* 3.3 2.8 + - - +
772A THR* 2.7 39.2 + - + +
790A LEU* 4.0 8.4 - - + +
793A GLN* 3.9 12.7 - - - +
794A ILE* 4.1 18.2 - - + -
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Residues in contact with TYR 769 (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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736A LEU* 3.6 40.5 + - + -
737A ARG* 5.8 1.4 + - - -
765A ALA 3.0 19.0 + - - +
766A ILE* 2.8 12.9 + - - +
768A GLU* 1.3 72.1 - - - +
770A ILE* 1.3 66.3 + - - +
772A THR* 4.5 3.4 - - - -
773A LYS* 2.9 60.6 + - + +
774A ILE* 3.8 15.8 + - + -
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Residues in contact with ILE 770 (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* 4.1 20.9 - - + -
735A ILE* 5.9 2.7 - - + -
736A LEU* 3.9 21.3 - - + -
745A ILE* 4.3 29.4 - - + -
747A ILE* 4.0 23.1 - - + -
766A ILE* 2.8 38.4 + - + +
767A SER* 3.9 4.5 - - - +
769A TYR* 1.3 74.5 - - - +
771A ALA* 1.3 53.5 + - - +
772A THR 3.2 2.8 + - - -
774A ILE* 3.3 17.4 - - + +
775A GLY 2.7 32.4 + - - -
776A ALA 5.0 6.3 - - - +
778A CYS* 4.5 7.0 - - + -
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Residues in contact with ALA 771 (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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663A MET* 6.5 0.4 - - + -
664A PHE* 3.8 22.2 - - + -
767A SER 3.3 16.5 + - - +
768A GLU 3.3 1.5 + - - +
770A ILE* 1.3 77.7 - - - +
772A THR* 1.3 59.4 + - - +
775A GLY* 4.5 11.5 - - - +
776A ALA 6.0 0.9 - - - -
794A ILE* 4.2 15.1 - - + +
796A THR* 4.3 11.3 + - - +
797A VAL* 4.2 20.9 - - + -
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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