Contacts of the helix formed by residues 779 - 793 (chain A) in PDB entry 3T6A
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 LYS 779 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A PHE* 3.9 24.6 - - + -
559A MET* 3.5 22.0 - - + -
562A ARG* 5.0 5.2 - - - +
775A ASN* 4.0 18.7 + - - +
776A GLU* 2.9 46.2 + - - +
778A CYS* 1.3 77.7 - - - +
780A THR* 1.3 65.5 + - - +
781A GLU* 4.4 5.2 - - + +
782A PHE* 3.3 12.1 + - + +
783A GLN* 3.0 24.0 + - - +
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Residues in contact with THR 780 (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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515A PHE* 3.9 27.5 - - + -
559A MET* 4.2 3.2 - - - +
600A GLU* 4.4 0.9 - - + +
601A ARG* 3.1 58.9 + - - +
604A THR* 4.2 10.8 - - + +
778A CYS 3.5 2.4 + - - -
779A LYS* 1.3 68.1 - - - +
781A GLU* 1.3 57.7 + - - +
783A GLN* 3.1 11.4 + - - +
784A MET* 2.7 57.0 + - + +
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Residues in contact with GLU 781 (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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514A SER 5.5 0.2 - - - +
515A PHE* 3.7 25.5 - - + -
516A ARG 2.8 44.4 + - - +
517A PRO* 3.5 5.4 - - + +
520A PHE* 3.9 34.0 - - + -
779A LYS* 5.0 4.3 - - + -
780A THR* 1.3 77.2 - - - +
782A PHE* 1.3 62.5 + - - +
784A MET* 3.1 14.7 + - - +
785A ARG* 3.0 24.8 + - - +
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Residues in contact with PHE 782 (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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520A PHE* 3.8 30.8 - + + -
522A SER* 4.3 6.1 - - - -
524A PHE* 3.9 25.4 - - + -
525A LEU* 3.3 31.8 - - + +
536A LEU* 5.6 2.2 - - + -
776A GLU* 3.4 31.4 - - + +
777A ILE* 3.8 26.5 - - + -
779A LYS* 3.3 6.0 + - + +
780A THR 3.3 0.4 - - - -
781A GLU* 1.3 77.4 - - - +
783A GLN* 1.3 65.7 + - - +
785A ARG* 3.1 8.3 + - - +
786A LEU* 3.0 48.6 + - + -
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Residues in contact with GLN 783 (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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601A ARG* 4.6 3.6 - - - +
604A THR* 3.7 23.9 - - + +
605A MET* 3.8 28.2 + - - +
608A GLY* 6.1 0.2 - - - -
777A ILE* 3.0 28.7 + - + +
778A CYS* 3.2 24.0 + - - +
779A LYS 3.0 13.8 + - - +
780A THR* 3.5 10.2 + - - +
782A PHE* 1.3 79.7 - - + +
784A MET* 1.3 63.5 + - - +
786A LEU* 3.2 10.6 + - + +
787A LEU* 3.0 29.0 + - + +
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Residues in contact with MET 784 (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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513A SER* 6.3 0.7 - - - -
515A PHE* 4.2 15.9 - - + +
517A PRO* 4.1 22.2 - - + -
600A GLU* 3.7 30.3 - - + +
604A THR* 4.0 14.8 - - - +
780A THR* 2.7 37.3 + - + +
781A GLU* 3.1 6.9 + - - +
783A GLN* 1.3 71.4 - - - +
785A ARG* 1.3 63.6 + - - +
787A LEU 3.4 0.2 + - - -
788A TRP* 3.0 39.0 + - + -
793A ALA* 3.8 20.2 - - + +
800A ARG* 3.7 24.5 - - - +
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Residues in contact with ARG 785 (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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517A PRO* 3.4 30.0 + - + +
518A ASN* 4.7 4.6 + - - +
520A PHE* 2.9 30.6 + - + -
525A LEU* 3.6 30.1 + - + +
526A PRO 2.8 29.3 + - - -
527A PRO* 3.5 16.0 + - - +
529A ASN* 2.7 40.6 - - - +
781A GLU 3.0 17.0 + - - +
782A PHE 3.4 8.5 - - - +
784A MET* 1.3 73.4 - - - +
786A LEU* 1.3 61.2 + - - +
789A GLY* 2.9 28.1 + - - -
790A SER* 3.8 22.4 - - - +
793A ALA* 4.5 0.2 - - - -
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Residues in contact with LEU 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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525A LEU* 5.1 4.0 - - + +
529A ASN* 4.5 3.4 - - - -
530A LYS 4.4 1.0 - - - +
531A PRO 3.9 0.2 - - - -
532A LEU* 2.9 31.8 + - - +
533A GLU* 4.5 2.4 + - + +
536A LEU* 3.7 37.7 - - + +
537A LEU* 3.8 24.2 - - + -
540A ALA* 4.5 8.5 - - + -
777A ILE* 4.4 15.9 - - + -
782A PHE* 3.0 41.8 + - + +
783A GLN* 3.4 14.1 - - + +
785A ARG* 1.3 79.4 - - - +
787A LEU* 1.3 61.8 + - + +
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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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531A PRO* 3.6 12.6 - - - +
532A LEU* 3.7 15.6 - - + +
537A LEU* 5.7 1.6 - - + -
604A THR* 3.9 21.1 - - + +
607A ILE* 3.9 21.8 - - + -
608A GLY* 4.3 8.5 - - - +
611A VAL* 4.1 18.6 - - + -
783A GLN* 3.0 18.3 + - + +
785A ARG 3.3 0.2 - - - -
786A LEU* 1.3 83.2 - - + +
788A TRP* 1.3 88.0 + - + +
789A GLY 3.6 0.2 - - - -
803A LYS* 5.6 1.0 + - - -
804A PHE* 3.4 41.5 - - + -
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Residues in contact with TRP 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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531A PRO* 3.7 17.5 - - - +
604A THR* 3.9 20.4 - - - -
607A ILE* 4.0 23.3 - - + -
784A MET* 3.0 35.0 + - + -
787A LEU* 1.3 95.7 - - + +
789A GLY* 1.3 61.7 + - - +
792A GLY* 3.4 22.2 + - - -
793A ALA* 3.6 20.4 - - - +
800A ARG* 3.0 78.2 + - + +
801A TYR* 4.0 3.6 - + - -
803A LYS* 4.1 21.8 + - + +
804A PHE* 3.5 25.9 - + - -
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Residues in contact with GLY 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASN* 3.6 14.1 - - - -
531A PRO* 3.7 15.0 - - - +
785A ARG* 2.9 24.3 + - - +
787A LEU 3.6 1.2 - - - -
788A TRP* 1.3 77.4 - - - +
790A SER* 1.3 61.4 + - - -
791A LYS 3.2 3.6 - - - -
793A ALA* 2.9 28.1 + - - +
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Residues in contact with SER 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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518A ASN* 2.7 31.2 - - - +
527A PRO 4.3 7.0 - - - -
528A GLU* 3.9 10.2 - - - +
529A ASN* 2.8 32.7 + - - +
785A ARG* 3.8 28.0 - - - +
789A GLY* 1.3 72.6 - - - -
791A LYS* 1.3 67.6 + - - +
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Residues in contact with LYS 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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518A ASN* 4.0 9.3 + - - +
528A GLU* 4.0 22.8 + - + +
789A GLY* 4.3 0.4 - - - -
790A SER* 1.3 92.0 + - - +
792A GLY* 1.3 65.2 + - - +
793A ALA 3.2 2.6 + - - -
794A GLN* 3.6 8.8 + - - +
795A VAL* 4.6 3.5 + - - +
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Residues in contact with GLY 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 TRP* 3.4 22.8 + - - +
791A LYS* 1.3 74.4 - - - +
793A ALA* 1.3 58.3 + - - +
794A GLN 2.9 12.2 + - - -
795A VAL* 3.0 27.9 + - - +
800A ARG* 3.4 12.6 - - - +
803A LYS* 6.2 1.6 - - - -
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Residues in contact with ALA 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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517A PRO* 3.6 36.3 - - + +
518A ASN* 3.8 6.5 - - - +
784A MET* 3.8 24.5 - - + +
785A ARG* 4.5 1.6 - - - +
788A TRP* 3.6 12.2 - - - +
789A GLY 2.9 22.9 + - - +
791A LYS 3.2 1.4 - - - -
792A GLY* 1.3 74.8 - - - +
794A GLN* 1.3 59.4 + - - +
795A VAL 3.6 0.4 - - - -
800A ARG* 3.6 15.2 + - - +
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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