Contacts of the helix formed by residues 796 - 816 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B GLN 3.8 0.6 + - - -
795B VAL* 1.3 84.3 - - - +
797B GLN* 1.3 68.2 + - - +
798B THR* 3.8 11.2 + - - +
799B GLU* 3.2 49.7 + - - +
800B ARG* 3.0 18.2 + - - +
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Residues in contact with GLN 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B VAL* 6.3 1.7 - - + +
513B SER* 5.2 3.1 + - - -
596B LEU 5.4 0.7 - - - +
599B ILE* 4.5 4.5 - - - +
600B GLU* 3.5 16.9 + - - +
603B ASN* 3.9 2.8 + - - -
720B GLN 5.7 0.2 + - - -
722B VAL* 3.4 46.8 - - + +
795B VAL 3.6 1.8 + - - -
796B ASN* 1.3 72.3 - - - +
798B THR* 1.3 59.9 + - - +
800B ARG* 2.9 28.6 + - - +
801B TYR* 2.8 54.5 + - + +
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Residues in contact with THR 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B VAL* 3.7 28.0 - - - +
796B ASN* 3.2 10.1 + - - +
797B GLN* 1.3 79.9 - - - +
799B GLU* 1.3 61.4 + - + +
801B TYR* 3.6 2.9 + - - +
802B GLU* 3.0 28.6 + - + +
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Residues in contact with GLU 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B VAL* 3.8 18.5 - - + +
796B ASN* 3.2 32.5 + - - +
798B THR* 1.3 80.5 - - + +
800B ARG* 1.3 64.7 + - - +
802B GLU* 3.3 5.9 + - + +
803B LYS* 3.0 24.0 + - + +
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Residues in contact with ARG 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B GLU* 2.9 40.2 + - - -
784B MET* 3.9 14.4 - - - +
788B TRP* 3.1 73.5 + - + +
792B GLY 3.5 22.7 - - - +
793B ALA 3.7 8.3 + - - -
795B VAL* 2.8 27.8 + - + +
796B ASN 3.0 9.7 + - - +
797B GLN* 2.9 27.6 + - - +
799B GLU* 1.3 74.8 - - - +
801B TYR* 1.3 68.3 + - + +
803B LYS* 3.3 15.6 + - - +
804B PHE* 3.4 5.0 + - - -
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Residues in contact with TYR 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B GLU* 2.8 28.0 + - - -
603B ASN* 3.0 38.6 + - + +
607B ILE* 3.8 17.3 - - + -
722B VAL* 3.6 32.3 - - + -
723B THR 3.8 1.3 - - - +
724B PHE* 3.4 40.3 - - + -
725B GLU 5.1 1.8 - - - +
788B TRP* 3.9 11.2 - + - -
797B GLN* 2.8 30.1 + - + +
798B THR* 4.1 3.6 - - - +
800B ARG* 1.3 94.0 - - - +
802B GLU* 1.3 65.0 + - - +
804B PHE 3.3 1.7 + - - -
805B ASN* 3.0 19.1 + - - +
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Residues in contact with GLU 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B THR* 3.0 20.3 + - + +
799B GLU* 3.3 7.4 + - + +
801B TYR* 1.3 78.0 - - - +
803B LYS* 1.3 63.9 + - - +
805B ASN* 3.2 29.6 + - - +
806B GLN* 3.1 47.8 + - - +
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Residues in contact with LYS 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B PRO* 5.2 18.2 - - - +
787B LEU 5.4 0.7 - - - -
788B TRP* 4.1 23.3 - - + +
799B GLU* 3.0 13.5 + - + +
800B ARG* 3.3 10.8 - - + +
802B GLU* 1.3 78.7 - - - +
804B PHE* 1.3 60.8 + - + +
806B GLN* 3.5 10.1 + - - +
807B ILE* 3.0 49.7 + - + +
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Residues in contact with PHE 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B LEU* 4.1 14.8 - - + -
607B ILE* 4.0 13.2 - - + -
611B VAL* 3.5 31.0 - - + -
724B PHE* 3.9 19.7 - - + -
787B LEU* 3.4 42.4 - - + -
788B TRP* 3.4 43.1 - + - -
800B ARG 3.4 2.5 + - - +
801B TYR 3.3 2.9 + - - +
802B GLU 3.3 0.2 - - - -
803B LYS* 1.3 80.8 - - + +
805B ASN* 1.3 67.8 + - - +
807B ILE* 3.9 26.2 - - + -
808B LEU* 2.8 31.8 + - + +
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Residues in contact with ASN 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B GLN* 3.3 18.6 - - - +
724B PHE* 3.7 11.3 - - + -
725B GLU* 3.4 19.9 - - + +
801B TYR 3.0 13.5 + - - +
802B GLU* 3.3 34.4 + - - +
804B PHE* 1.3 80.3 - - - +
806B GLN* 1.3 62.1 + - - +
809B THR* 3.0 26.5 + - - -
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Residues in contact with GLN 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B GLU* 3.1 41.9 + - - +
803B LYS* 3.7 9.6 - - - +
805B ASN* 1.3 80.5 - - + +
807B ILE* 1.3 63.7 + - + +
809B THR* 3.3 7.0 + - - +
810B ALA* 2.9 24.5 + - - +
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Residues in contact with ILE 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B LEU* 4.4 17.7 - - + -
611B VAL* 5.7 0.7 - - + -
803B LYS* 3.0 45.8 + - + +
804B PHE* 3.3 36.3 + - + +
806B GLN* 1.3 74.6 - - + +
808B LEU* 1.3 62.1 + - + +
810B ALA* 2.8 23.9 + - - +
811B LEU* 2.9 31.9 + - + +
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Residues in contact with LEU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ILE* 4.9 4.3 - - - +
610B ALA* 3.7 20.6 - - + -
611B VAL* 3.9 37.5 - - + +
614B LEU* 4.0 18.1 - - + +
656B MET* 4.1 7.4 - - - -
658B GLN* 3.7 16.5 - - + +
724B PHE* 3.7 29.2 - - + -
725B GLU* 4.8 1.3 - - - +
804B PHE* 2.8 28.3 + - + +
805B ASN 4.1 0.7 - - - +
807B ILE* 1.3 76.5 - - + +
809B THR* 1.3 55.9 + - - +
811B LEU* 3.3 13.7 + - + +
812B SER* 3.0 30.0 + - - -
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Residues in contact with THR 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B GLN* 3.2 26.8 + - - +
805B ASN* 3.0 20.5 + - - -
806B GLN* 3.7 6.5 - - - +
808B LEU* 1.3 76.0 - - - +
810B ALA* 1.3 65.2 + - - +
812B SER* 3.5 3.5 + - - -
813B ARG* 3.2 40.5 + - - +
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Residues in contact with ALA 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B GLN 2.9 12.8 + - - +
807B ILE* 2.8 12.4 + - - +
809B THR* 1.3 76.0 - - - +
811B LEU* 1.3 67.9 + - + +
813B ARG* 3.6 4.5 + - - +
814B LYS* 3.2 25.8 + - - +
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Residues in contact with LEU 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B LEU* 6.5 0.4 - - + -
611B VAL* 5.8 3.4 - - + -
614B LEU* 3.7 42.0 - - + +
615B GLY* 4.1 9.9 - - - +
807B ILE* 2.9 34.0 + - + +
808B LEU* 3.7 14.1 - - + +
809B THR 3.2 0.2 - - - -
810B ALA* 1.3 77.2 - - + +
812B SER* 1.3 67.5 + - - +
813B ARG 3.0 0.5 + - - -
814B LYS* 3.1 9.4 + - + +
815B LEU* 2.9 28.4 + - + +
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Residues in contact with SER 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B LEU* 3.6 13.6 - - - +
658B GLN* 2.8 35.2 + - - -
661B ARG* 2.7 38.0 + - - -
662B LEU* 3.4 11.8 - - - +
808B LEU 3.0 16.6 + - - -
809B THR 4.0 3.4 - - - -
810B ALA 3.5 0.2 - - - -
811B LEU* 1.3 76.8 - - - +
813B ARG* 1.3 52.1 + - - +
815B LEU* 4.0 0.7 - - - -
816B GLU* 3.1 18.0 + - - +
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Residues in contact with ARG 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B ARG* 3.1 22.9 - - - +
809B THR* 3.2 32.6 + - - +
810B ALA* 4.2 4.5 - - - +
811B LEU 3.1 0.8 - - - -
812B SER* 1.3 75.9 - - - +
814B LYS* 1.3 67.3 + - - +
817B PRO* 3.3 25.5 - - - +
818B PRO* 3.9 29.7 - - + +
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Residues in contact with LYS 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B ALA 3.2 14.6 + - - +
811B LEU* 3.1 14.3 + - + +
813B ARG* 1.3 79.7 - - - +
815B LEU* 1.3 67.7 + - + +
816B GLU 3.4 0.2 + - - -
817B PRO* 3.9 9.5 - - - +
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Residues in contact with LEU 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B ILE 4.6 0.2 - - - +
614B LEU* 3.6 44.4 - - + +
617B THR* 4.7 4.0 - - - +
618B GLY 5.6 4.3 - - - +
623B ARG* 3.8 48.5 + - - +
662B LEU* 4.5 2.9 - - + -
664B LYS* 5.2 2.1 + - - -
811B LEU* 2.9 17.7 + - + +
812B SER 4.1 3.1 - - - +
814B LYS* 1.3 81.1 - - + +
816B GLU* 1.3 68.6 + - + +
817B PRO* 4.0 3.2 - - - +
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Residues in contact with GLU 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B ARG* 2.6 28.1 + - - +
661B ARG* 2.5 35.4 + - - +
662B LEU* 2.9 45.6 - - + -
663B GLU* 3.0 6.4 + - - +
664B LYS* 3.1 32.6 + - + +
665B THR* 2.7 22.7 + - - -
812B SER 3.1 3.6 + - - -
813B ARG 3.6 2.7 - - - -
815B LEU* 1.3 85.2 - - - +
817B PRO* 1.3 62.8 - - - +
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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
------------------------------------------------------------
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