Contacts of the helix formed by residues 800 - 812 (chain A) in PDB entry 1T65
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 800 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751A TRP* 4.1 1.1 - - - -
798A GLN 4.0 8.1 - - - +
799A ILE* 1.3 78.0 - - - +
801A PRO* 1.3 74.2 - - - +
802A GLN* 3.5 12.7 + - - +
803A GLU* 3.0 41.7 + - - +
804A PHE* 3.0 20.8 + - - +
841A ILE* 4.5 1.0 - - - +
855A ARG* 5.3 0.4 - - - +
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Residues in contact with PRO 801 (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 TRP* 3.9 25.3 - - + -
799A ILE 4.5 1.8 - - - +
800A THR* 1.3 87.0 - - - +
802A GLN* 1.3 75.7 + - - +
804A PHE* 3.5 4.1 + - + +
805A LEU* 3.1 34.4 + - + +
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Residues in contact with GLN 802 (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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674A LEU* 4.0 31.6 - - + +
678A GLU* 5.2 8.3 + - - -
800A THR* 3.1 9.2 + - - +
801A PRO* 1.3 101.0 - - - +
803A GLU* 1.3 64.7 + - - +
805A LEU* 3.4 10.5 + - + +
806A CYS* 3.2 19.2 + - - +
841A ILE* 3.3 23.7 - - + +
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Residues in contact with GLU 803 (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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799A ILE* 3.4 3.3 - - + +
800A THR* 3.0 41.1 + - - +
802A GLN* 1.3 72.4 - - - +
804A PHE* 1.3 65.7 + - - +
806A CYS* 3.3 3.9 + - - +
807A MET* 2.9 42.6 + - + +
838A LEU* 5.1 1.6 - - - -
841A ILE* 3.5 21.5 - - + +
842A ILE* 4.8 3.9 - - + +
846A ARG* 4.5 9.0 + - - -
855A ARG* 2.8 48.8 + - - +
859A LEU* 4.0 18.0 - - + +
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Residues in contact with PHE 804 (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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681A GLU* 3.8 13.0 - - - -
747A PHE* 3.6 34.3 - + - -
748A ALA* 4.0 8.5 - - + -
751A TRP* 3.4 72.7 - + + -
794A PHE* 4.1 2.9 - + - -
799A ILE* 4.3 1.6 - - + -
800A THR 3.0 12.0 + - - +
801A PRO* 3.5 11.2 - - + +
803A GLU* 1.3 76.9 - - - +
805A LEU* 1.3 71.1 + - + +
807A MET* 3.7 11.1 - - - +
808A LYS* 2.9 54.3 + - + +
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Residues in contact with LEU 805 (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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674A LEU* 4.9 6.3 - - + -
677A LEU* 3.9 26.0 - - + +
678A GLU* 4.0 33.7 - - + +
681A GLU* 3.7 36.6 - - + +
718A TRP* 5.5 0.5 - - - -
801A PRO* 3.1 18.7 + - + +
802A GLN* 3.8 14.8 - - + +
803A GLU 3.3 0.4 - - - -
804A PHE* 1.3 92.5 - - + +
806A CYS* 1.3 61.0 + - - +
808A LYS* 3.5 7.1 + - - +
809A ALA* 3.2 21.8 + - - +
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Residues in contact with CYS 806 (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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673A PHE* 3.9 22.4 - - + -
674A LEU* 5.4 2.0 - - + -
677A LEU* 4.0 11.4 - - + +
802A GLN 3.2 15.1 + - - +
803A GLU* 3.9 3.1 - - - +
805A LEU* 1.3 78.1 - - - +
807A MET* 1.3 63.8 + - - +
809A ALA* 3.4 4.1 + - - +
810A LEU* 3.1 22.9 + - - +
834A TYR* 3.9 13.0 - - - -
837A GLU 4.2 2.0 - - - -
838A LEU* 3.8 44.0 - - + -
841A ILE* 4.9 4.5 - - + -
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Residues in contact with MET 807 (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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747A PHE* 3.8 25.8 - - + -
799A ILE* 3.4 38.4 - - + -
803A GLU* 2.9 32.3 + - + +
804A PHE* 3.7 4.5 - - - +
806A CYS* 1.3 75.9 - - - +
808A LYS* 1.3 63.5 + - - +
810A LEU* 3.2 12.2 + - - +
811A LEU* 3.1 23.7 + - - +
838A LEU* 4.4 15.5 - - + -
859A LEU* 4.0 30.5 - - + +
862A LEU* 4.6 8.7 - - + -
863A LEU* 3.7 19.2 - - + +
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Residues in contact with LYS 808 (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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681A GLU* 2.9 39.2 + - - -
682A PRO* 4.8 2.6 - - - +
718A TRP* 3.7 26.6 - - + +
744A LEU* 3.1 46.1 - - + +
747A PHE* 3.8 17.2 - - + -
748A ALA* 4.0 19.7 - - + -
804A PHE* 2.9 41.7 + - + +
805A LEU* 3.8 6.6 + - - +
807A MET* 1.3 78.2 - - - +
809A ALA* 1.3 62.3 + - - +
811A LEU* 3.2 7.7 + - - +
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Residues in contact with ALA 809 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A LEU* 4.6 5.6 - - + -
718A TRP* 3.9 14.0 - - + -
722A LEU* 4.2 16.4 - - + -
805A LEU 3.2 11.6 + - - +
806A CYS* 3.7 9.4 - - - +
807A MET 3.3 0.4 - - - -
808A LYS* 1.3 78.6 - - - +
810A LEU* 1.3 62.1 - - - +
812A LEU* 3.1 20.6 + - - +
813A PHE* 3.5 11.3 - - - -
834A TYR* 3.6 27.4 - - + -
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Residues in contact with LEU 810 (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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806A CYS 3.1 16.8 + - - +
807A MET* 3.2 11.2 + - - +
809A ALA* 1.3 77.6 - - - +
811A LEU* 1.3 59.7 + - - +
813A PHE* 3.0 18.3 + - + +
814A SER* 2.9 18.1 + - - +
831A ARG* 4.2 12.7 + - + +
834A TYR* 3.3 38.1 - - + +
835A ILE* 3.7 36.1 - - + +
838A LEU* 3.8 26.7 - - + -
863A LEU* 4.3 18.6 - - + -
916A PHE* 5.3 0.9 - - + -
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Residues in contact with LEU 811 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A SER* 3.4 18.4 + - - -
743A GLY* 3.9 13.2 - - - +
744A LEU* 3.8 13.5 - - + +
747A PHE* 3.5 49.4 - - + -
807A MET 3.1 13.0 + - - +
808A LYS* 3.4 9.9 - - - +
809A ALA 3.1 0.6 - - - -
810A LEU* 1.3 76.8 - - - +
812A LEU* 1.3 61.8 + - - +
813A PHE 3.1 0.6 + - - -
814A SER* 3.5 15.3 + - - +
863A LEU* 3.8 26.7 - - + +
866A VAL* 4.5 10.5 - - + -
867A GLN* 4.0 24.6 + - - +
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Residues in contact with LEU 812 (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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715A VAL* 5.8 0.4 - - + -
718A TRP* 4.3 4.7 - - + -
719A ALA* 4.0 9.0 - - + -
722A LEU* 3.5 29.8 - - + -
725A PHE* 3.8 21.5 - - + -
736A VAL* 3.6 44.2 - - + +
737A ILE* 4.2 13.2 - - + -
740A SER* 3.8 12.0 + - - -
744A LEU* 3.8 26.2 - - + +
808A LYS 3.7 2.0 + - - -
809A ALA 3.1 13.0 + - - +
811A LEU* 1.3 78.9 - - - +
813A PHE* 1.3 70.0 + - + +
814A SER 3.5 0.4 + - - -
815A ILE 5.1 1.4 + - - +
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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