Contacts of the helix formed by residues 779 - 793 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520D PHE* 3.9 19.7 - - + -
559D MET* 3.1 24.0 - - + -
562D ARG* 4.3 19.6 - - - +
775D ASN* 3.7 16.4 - - - +
776D GLU* 2.9 46.5 + - - +
778D CYS* 1.3 78.9 - - - +
780D THR* 1.3 65.9 + - - +
781D GLU* 3.3 9.1 - - + +
782D PHE* 3.1 12.5 + - + +
783D GLN* 3.1 22.8 + - - +
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Residues in contact with THR 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D PHE* 3.7 33.7 - - + -
559D MET* 4.7 2.6 - - - +
600D GLU* 4.6 1.6 - - + -
601D ARG* 2.9 52.3 + - - +
604D THR* 4.5 8.5 - - + +
778D CYS 3.7 1.8 + - - -
779D LYS* 1.3 69.5 - - - +
781D GLU* 1.3 62.5 + - - +
783D GLN* 3.3 10.7 + - - +
784D MET* 2.9 50.0 + - + +
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Residues in contact with GLU 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D PHE* 3.0 35.0 - - + +
516D ARG 2.9 32.3 + - - +
517D PRO* 4.4 5.1 - - + +
520D PHE* 3.5 42.6 - - + -
559D MET* 6.3 0.4 - - + -
779D LYS* 4.6 6.1 - - + +
780D THR* 1.3 79.9 - - - +
782D PHE* 1.3 61.9 + - - +
784D MET* 3.4 10.5 + - - +
785D ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D PHE* 3.9 22.9 - + + -
522D SER* 4.0 17.7 - - - -
524D PHE* 4.1 20.2 - - + -
525D LEU* 3.6 25.1 - - + -
536D LEU* 6.4 0.2 - - + -
539D ARG* 6.2 0.7 - - - -
540D ALA* 5.7 1.3 - - + -
773D GLU* 5.8 0.7 - - + -
776D GLU* 3.1 38.8 - - + +
777D ILE* 3.9 21.3 - - + -
779D LYS* 3.1 5.4 + - + +
781D GLU* 1.3 79.4 - - - +
783D GLN* 1.3 65.4 + - - +
785D ARG* 3.1 7.5 + - - +
786D LEU* 3.0 52.3 + - + -
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Residues in contact with GLN 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D ARG* 4.6 6.3 + - - +
604D THR* 3.5 26.8 - - + +
605D MET* 3.7 25.2 + - - +
608D GLY* 6.3 1.1 - - - -
777D ILE* 2.9 28.9 + - + +
778D CYS* 3.6 21.6 + - - +
779D LYS 3.1 8.3 + - - +
780D THR* 3.3 7.0 + - - +
782D PHE* 1.3 79.3 - - - +
784D MET* 1.3 55.6 + - - +
786D LEU* 3.3 6.8 + - - +
787D LEU* 2.9 39.9 + - + +
839D UNX 3.9 14.1 - - - -
840D UNX 4.1 13.0 - - - -
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Residues in contact with MET 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D SER* 5.0 4.3 - - - +
515D PHE* 4.3 16.6 - - + -
517D PRO* 4.1 13.9 - - + -
600D GLU* 4.2 12.1 - - - +
604D THR* 3.9 17.3 - - - +
780D THR* 2.9 38.7 + - + +
781D GLU* 3.8 5.4 - - - +
783D GLN* 1.3 74.8 - - - +
785D ARG* 1.3 57.8 - - - +
788D TRP* 2.8 46.9 + - + +
793D ALA* 3.6 32.6 - - + +
800D ARG* 3.8 27.8 - - - +
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Residues in contact with ARG 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D PRO* 3.3 33.4 + - + +
518D ASN* 4.4 7.2 + - - -
520D PHE* 3.1 27.8 + - + -
525D LEU* 3.7 30.1 - - + +
526D PRO 2.7 30.9 + - - -
527D PRO* 3.4 14.5 + - - +
529D ASN* 3.3 20.8 - - - +
781D GLU 3.1 15.4 + - - +
782D PHE 3.1 9.7 + - - +
784D MET* 1.3 74.9 - - - +
786D LEU* 1.3 60.8 + - - +
789D GLY* 2.9 30.9 + - - -
790D SER* 3.3 37.7 - - - +
793D ALA* 4.6 0.2 - - - -
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Residues in contact with LEU 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D LEU* 4.5 1.5 - - + +
529D ASN* 4.6 2.2 - - - +
530D LYS 4.2 0.7 - - - +
532D LEU* 2.7 35.8 + - - -
533D GLU 4.5 1.5 + - - +
536D LEU* 3.4 48.2 - - + +
537D LEU* 4.5 13.0 - - + -
540D ALA* 4.5 14.6 - - + -
777D ILE* 4.5 4.9 - - + -
782D PHE* 3.0 46.1 + - + +
783D GLN* 3.6 12.1 - - + +
785D ARG* 1.3 79.0 - - - +
787D LEU* 1.3 59.9 + - + +
841D UNX 4.4 16.6 - - - -
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Residues in contact with LEU 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D PRO* 3.7 6.2 - - - +
532D LEU* 3.7 19.2 - - + +
537D LEU* 5.8 2.2 - - + -
604D THR* 3.9 26.2 - - + +
607D ILE* 4.1 9.0 - - + -
608D GLY* 4.0 14.8 - - - +
611D VAL* 3.8 32.1 - - + -
783D GLN* 2.9 26.6 + - + +
786D LEU* 1.3 79.9 - - + +
788D TRP* 1.3 86.9 + - + +
804D PHE* 3.4 29.7 - - + -
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Residues in contact with TRP 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D PRO* 3.7 13.2 - - - +
604D THR* 3.8 15.3 - - - -
607D ILE* 3.9 24.9 - - + -
784D MET* 2.8 30.8 + - + +
787D LEU* 1.3 104.0 - - + +
789D GLY* 1.3 66.2 + - - +
792D GLY* 3.3 21.4 + - - +
793D ALA* 3.6 16.6 - - - -
800D ARG* 2.9 81.4 + - + +
801D TYR* 4.1 5.4 - + - -
803D LYS* 4.6 20.1 + - + +
804D PHE* 3.2 26.7 - + - -
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Residues in contact with GLY 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D ASN* 3.7 1.3 - - - -
530D LYS 3.6 4.9 - - - -
531D PRO* 3.4 28.5 - - - +
785D ARG* 2.9 22.7 + - - +
788D TRP* 1.3 84.9 - - - +
790D SER* 1.3 59.7 + - - -
791D LYS 3.2 3.4 - - - -
793D ALA* 3.2 20.1 + - - +
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Residues in contact with SER 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ASN* 2.6 30.8 + - - +
527D PRO 4.3 3.8 - - - -
528D GLU* 3.7 8.0 + - - +
529D ASN* 2.8 40.1 + - - +
785D ARG* 3.3 38.6 - - - +
789D GLY* 1.3 70.6 - - - -
791D LYS* 1.3 57.8 + - - +
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Residues in contact with LYS 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ASN* 3.9 12.0 + - - +
528D GLU* 6.0 1.6 - - - +
529D ASN 4.5 1.9 + - - +
531D PRO* 6.3 0.2 - - - +
789D GLY 3.2 0.2 - - - -
790D SER* 1.3 82.8 + - - +
792D GLY* 1.3 62.4 + - - +
793D ALA 3.3 3.2 + - - -
794D GLN* 3.8 9.4 + - - +
795D VAL* 4.9 3.3 + - - +
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Residues in contact with GLY 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788D TRP* 3.3 23.8 + - - +
791D LYS* 1.3 76.9 - - - +
793D ALA* 1.3 58.1 + - - +
794D GLN 3.2 7.0 + - - -
795D VAL* 3.5 20.3 + - - +
800D ARG* 3.4 18.0 - - - +
803D LYS* 6.0 4.0 - - - -
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Residues in contact with ALA 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D PRO* 3.4 36.9 - - + +
518D ASN* 4.3 4.5 - - - +
784D MET* 3.6 36.3 - - + +
785D ARG* 4.5 1.1 - - + +
788D TRP* 3.6 7.4 - - + -
789D GLY 3.2 18.5 + - - +
791D LYS 3.3 1.0 - - - -
792D GLY* 1.3 76.7 - - - +
794D GLN* 1.3 57.1 + - - +
795D VAL 3.4 2.4 + - - -
800D ARG* 4.0 8.6 + - - +
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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