Contacts of the helix formed by residues 796 - 816 (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 ASN 796 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794D GLN 4.1 0.6 + - - -
795D VAL* 1.3 92.9 - - - +
797D GLN* 1.3 66.3 + - - +
798D THR* 3.5 9.9 + - - +
799D GLU* 2.9 47.3 + - - +
800D ARG 3.1 14.7 + - - -
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Residues in contact with GLN 797 (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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512D VAL* 5.2 13.6 - - + +
513D SER* 5.2 2.4 + - - +
596D LEU 5.2 1.6 + - - -
599D ILE* 5.1 2.8 - - - +
600D GLU* 2.8 33.5 + - - +
603D ASN* 4.6 0.4 - - - +
722D VAL* 3.6 34.7 + - + +
795D VAL 3.4 1.4 + - - -
796D ASN* 1.3 69.5 - - - +
798D THR* 1.3 67.6 + - - +
799D GLU 3.0 0.2 + - - -
800D ARG* 3.1 25.7 + - - +
801D TYR* 2.8 54.1 + - + -
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Residues in contact with THR 798 (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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722D VAL* 3.8 30.6 - - + +
796D ASN* 3.3 9.2 - - - +
797D GLN* 1.3 77.6 - - - +
799D GLU* 1.3 57.7 + - - +
801D TYR* 3.6 2.6 + - - +
802D GLU* 3.1 27.5 + - + +
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Residues in contact with GLU 799 (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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795D VAL* 3.7 19.1 - - + +
796D ASN* 2.9 31.2 + - - +
798D THR* 1.3 74.2 - - - +
800D ARG* 1.3 60.4 + - - +
801D TYR 3.0 1.8 - - - -
802D GLU* 3.1 4.9 + - + +
803D LYS* 2.8 35.4 + - + +
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Residues in contact with ARG 800 (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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512D VAL* 6.0 1.6 - - - +
600D GLU* 3.0 37.8 + - - -
784D MET* 3.8 12.6 - - - +
788D TRP* 2.9 83.4 + - + +
792D GLY 3.4 24.5 - - - +
793D ALA 4.0 10.4 + - - -
795D VAL* 2.7 32.8 + - + +
796D ASN 3.1 2.1 + - - +
797D GLN* 3.1 24.7 + - - +
799D GLU* 1.3 79.3 - - - +
801D TYR* 1.3 64.8 + - - +
803D LYS* 3.8 4.3 + - - +
804D PHE* 3.4 12.1 + - - +
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Residues in contact with TYR 801 (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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600D GLU* 2.8 22.1 + - - -
603D ASN* 3.0 44.1 + - + +
604D THR* 5.1 0.2 - - - -
607D ILE* 4.1 6.5 - - + -
722D VAL* 3.5 21.3 - - + -
723D THR 3.7 5.2 - - - +
724D PHE* 3.2 40.0 - - + -
725D GLU 5.4 0.9 - - - +
788D TRP* 4.1 12.8 - + - -
797D GLN* 2.8 38.2 + - + +
798D THR* 3.9 4.0 - - - +
800D ARG* 1.3 102.3 - - - +
802D GLU* 1.3 66.3 + - - +
804D PHE 3.1 2.1 + - - -
805D ASN* 3.0 18.3 + - - +
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Residues in contact with GLU 802 (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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798D THR* 3.1 18.9 + - + +
799D GLU* 3.1 5.6 + - + +
801D TYR* 1.3 75.4 - - - +
803D LYS* 1.3 65.4 + - - +
805D ASN* 2.8 37.5 + - - +
806D GLN* 3.0 49.4 + - - +
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Residues in contact with LYS 803 (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* 5.2 14.6 - - - +
788D TRP* 4.6 22.2 + - + +
792D GLY* 6.0 3.8 - - - -
799D GLU* 2.8 18.2 + - + +
800D ARG* 3.9 6.7 - - - +
802D GLU* 1.3 77.9 - - - +
804D PHE* 1.3 56.4 + - + +
806D GLN* 3.7 11.9 + - - +
807D ILE* 3.0 49.5 + - + +
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Residues in contact with PHE 804 (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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532D LEU* 4.0 16.8 - - + -
607D ILE* 3.6 21.3 - - + -
611D VAL* 3.6 26.5 - - + -
724D PHE* 4.0 12.1 - - + -
787D LEU* 3.4 41.3 - - + -
788D TRP* 3.2 40.2 - + - -
800D ARG 3.4 4.5 + - - +
801D TYR 3.1 7.2 + - - +
802D GLU 3.1 0.8 - - - -
803D LYS* 1.3 77.4 - - + +
805D ASN* 1.3 58.7 + - - +
806D GLN 3.2 1.6 - - - -
807D ILE* 3.9 25.6 - - + -
808D LEU* 2.7 41.6 + - + +
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Residues in contact with ASN 805 (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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657D PRO* 5.6 0.2 - - - +
658D GLN* 2.8 35.2 - - - +
724D PHE* 3.6 13.2 - - + -
725D GLU* 3.1 18.6 - - + +
801D TYR 3.0 13.0 + - - +
802D GLU* 2.8 34.7 + - - +
804D PHE* 1.3 76.7 - - - +
806D GLN* 1.3 58.1 + - - +
809D THR* 3.1 28.1 + - - -
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Residues in contact with GLN 806 (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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802D GLU* 3.0 44.3 + - - +
803D LYS* 4.0 9.9 - - - +
805D ASN* 1.3 75.1 - - - +
807D ILE* 1.3 66.6 + - - +
808D LEU 3.1 1.6 - - - -
809D THR* 3.2 5.7 + - - -
810D ALA* 2.8 26.6 + - - +
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Residues in contact with ILE 807 (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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532D LEU* 4.5 23.1 - - + -
803D LYS* 3.0 50.8 + - + +
804D PHE* 3.9 30.7 - - + +
806D GLN* 1.3 75.5 - - + +
808D LEU* 1.3 57.9 + - - +
810D ALA* 3.5 6.3 + - - +
811D LEU* 3.1 44.2 + - + +
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Residues in contact with LEU 808 (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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607D ILE* 4.7 10.1 - - + -
610D ALA* 3.8 27.8 - - + -
611D VAL* 4.2 17.5 - - + +
614D LEU* 3.4 33.6 - - + +
656D MET* 4.3 4.5 - - - -
658D GLN* 3.5 17.3 - - + +
724D PHE* 3.8 26.9 - - + -
804D PHE* 2.7 32.7 + - + +
805D ASN 4.0 1.1 - - - +
807D ILE* 1.3 70.7 - - - +
809D THR* 1.3 66.2 + - - +
810D ALA 3.1 1.3 - - - -
811D LEU* 3.3 8.3 + - + +
812D SER* 3.0 23.2 + - - -
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Residues in contact with THR 809 (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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658D GLN* 3.1 28.4 + - - +
661D ARG* 6.0 2.2 - - - +
805D ASN* 3.1 18.2 + - - -
806D GLN* 3.2 6.3 + - - -
808D LEU* 1.3 76.2 - - - +
810D ALA* 1.3 61.9 + - - +
812D SER* 3.2 4.7 + - - -
813D ARG* 3.0 47.6 + - + +
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Residues in contact with ALA 810 (chain D).
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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806D GLN 2.8 17.3 + - - +
807D ILE* 3.5 7.6 - - - +
809D THR* 1.3 75.9 - - - +
811D LEU* 1.3 66.2 + - + +
813D ARG* 3.0 11.0 + - - +
814D LYS* 2.9 23.5 + - - +
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Residues in contact with LEU 811 (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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532D LEU* 6.2 1.3 - - + -
611D VAL* 5.7 6.1 - - + -
614D LEU* 3.5 41.7 - - + +
615D GLY* 4.8 7.4 - - - +
807D ILE* 3.1 36.1 + - + +
808D LEU* 3.3 11.9 + - + +
810D ALA* 1.3 75.4 - - + +
812D SER* 1.3 62.2 + - - +
814D LYS* 3.3 28.9 + - - +
815D LEU* 3.0 30.0 + - + +
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Residues in contact with SER 812 (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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614D LEU* 3.6 11.6 - - - +
658D GLN* 2.7 32.5 + - - -
661D ARG* 3.3 19.1 + - - +
662D LEU* 3.3 14.2 - - - +
808D LEU 3.0 13.4 + - - -
809D THR* 3.5 10.1 - - - -
810D ALA 3.1 0.2 - - - -
811D LEU* 1.3 77.3 - - - +
813D ARG* 1.3 57.3 + - - +
815D LEU* 4.1 1.3 - - - +
816D GLU* 3.1 30.5 + - - +
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Residues in contact with ARG 813 (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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661D ARG* 3.4 30.9 - - - +
809D THR* 3.0 35.5 + - + +
810D ALA* 3.5 10.1 - - - +
812D SER* 1.3 75.0 - - - +
814D LYS* 1.3 65.1 + - - +
816D GLU 4.5 0.2 - - - -
817D PRO* 3.2 30.8 - - + +
818D PRO* 4.0 19.8 - - + +
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Residues in contact with LYS 814 (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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810D ALA 2.9 12.3 + - - +
811D LEU* 3.3 32.2 + - - +
813D ARG* 1.3 76.9 - - - +
815D LEU* 1.3 70.6 + - + +
817D PRO* 4.0 7.8 - - - +
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Residues in contact with LEU 815 (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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613D ILE 4.3 0.2 - - - +
614D LEU* 3.7 44.2 - - + +
617D THR* 5.0 5.6 - - - +
618D GLY 5.8 2.0 - - - +
623D ARG* 3.9 43.0 + - - +
662D LEU* 5.0 4.3 - - + -
664D LYS* 5.6 0.9 + - - -
811D LEU* 3.0 19.9 + - + +
812D SER* 4.1 3.4 - - - +
814D LYS* 1.3 90.0 - - + +
816D GLU* 1.3 71.4 + - + +
817D PRO* 3.9 2.7 - - - +
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Residues in contact with GLU 816 (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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623D ARG* 2.9 26.3 + - - +
661D ARG* 2.8 32.2 + - - +
662D LEU* 3.6 16.4 - - + -
663D GLU* 3.4 10.0 + - - +
664D LYS* 3.2 48.8 + - + +
665D THR* 3.1 22.2 + - - -
812D SER 3.1 8.4 + - - +
813D ARG 3.4 2.7 - - - -
815D LEU* 1.3 87.6 - - + +
817D PRO* 1.3 68.3 - - - +
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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