Contacts of the helix formed by residues 779 - 789 (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 LYS 779 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B PHE* 4.0 26.0 - - + -
559B MET* 3.9 23.8 - - + -
562B ARG* 5.1 6.7 - - - +
775B ASN* 3.8 18.8 - - - +
776B GLU* 2.7 47.5 + - - +
778B CYS* 1.3 76.7 - - - +
780B THR* 1.3 65.5 + - - +
781B GLU* 4.3 7.0 - - + +
782B PHE* 3.1 20.4 + - + +
783B GLN* 3.2 15.2 + - - +
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Residues in contact with THR 780 (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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515B PHE* 3.6 34.0 - - + -
559B MET* 5.1 2.4 - - - +
600B GLU* 4.4 3.4 - - + -
601B ARG* 2.9 56.9 + - - +
604B THR* 4.6 5.8 - - - -
778B CYS 3.6 2.0 + - - -
779B LYS* 1.3 72.2 - - - +
781B GLU* 1.3 58.5 + - - +
783B GLN* 3.4 11.2 + - - +
784B MET* 3.0 53.6 + - + +
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Residues in contact with GLU 781 (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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515B PHE* 3.9 22.3 - - + -
516B ARG* 3.0 38.8 + - - +
517B PRO* 4.1 7.1 - - + +
520B PHE* 3.7 38.5 - - + +
779B LYS* 4.9 5.6 - - + +
780B THR* 1.3 75.0 - - - +
782B PHE* 1.3 65.3 + - - +
784B MET* 3.3 10.7 + - - +
785B ARG* 3.1 26.3 + - - +
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Residues in contact with PHE 782 (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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520B PHE* 3.5 26.6 - + + -
522B SER* 3.3 28.0 - - - -
524B PHE* 3.5 26.9 - - + -
525B LEU* 3.7 19.2 - - + +
536B LEU* 6.2 0.9 - - + -
540B ALA* 6.0 0.9 - - + -
773B GLU* 5.9 0.4 - - + -
776B GLU* 3.3 36.1 - - + +
777B ILE* 3.9 29.6 - - + -
779B LYS* 3.1 7.8 + - + +
781B GLU* 1.3 77.2 - - - +
783B GLN* 1.3 57.7 + - - +
785B ARG* 3.0 7.7 + - - +
786B LEU* 3.0 41.9 + - + +
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Residues in contact with GLN 783 (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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544B PHE* 6.4 0.4 - - - -
601B ARG* 4.7 6.6 + - - +
604B THR* 3.4 28.4 - - + +
605B MET* 3.6 29.0 + - - +
608B GLY* 5.9 1.9 - - - -
777B ILE* 3.3 23.6 + - + +
778B CYS* 3.7 18.6 + - - +
779B LYS 3.2 10.4 + - - +
780B THR* 3.8 7.6 + - - +
781B GLU 3.4 0.2 - - - -
782B PHE* 1.3 75.0 - - - +
784B MET* 1.3 57.2 + - - +
786B LEU* 3.5 11.0 + - + +
787B LEU* 3.0 37.0 + - + +
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Residues in contact with MET 784 (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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513B SER* 5.9 0.9 - - - +
515B PHE* 4.2 14.6 - - + -
517B PRO* 3.9 23.8 - - + -
600B GLU* 4.0 14.6 - - + -
604B THR* 3.9 15.7 - - - +
780B THR* 3.0 42.2 + - + +
781B GLU 3.7 4.7 - - - +
782B PHE 3.3 0.2 - - - -
783B GLN* 1.3 75.7 - - - +
785B ARG* 1.3 57.5 + - - +
788B TRP* 3.0 36.2 + - + -
793B ALA* 3.5 37.6 - - + +
800B ARG* 3.9 25.6 - - - +
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Residues in contact with ARG 785 (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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517B PRO* 3.0 31.8 + - + +
518B ASN 5.3 2.2 + - - -
520B PHE* 2.7 38.3 + - - -
521B GLU* 4.4 4.4 - - - +
525B LEU* 3.3 32.2 + - + +
526B PRO 2.7 25.5 + - - -
527B PRO* 4.0 11.9 + - - +
529B ASN* 2.5 47.5 - - - +
781B GLU 3.1 10.5 + - - +
782B PHE 3.0 9.8 + - - +
784B MET* 1.3 75.3 - - - +
786B LEU* 1.3 63.1 + - - +
789B GLY* 2.9 26.8 + - - +
790B SER* 3.8 20.6 - - - -
793B ALA* 4.6 0.2 - - - -
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Residues in contact with LEU 786 (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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525B LEU* 5.0 3.1 - - + -
529B ASN* 4.8 1.6 - - - -
530B LYS 4.7 0.2 - - - +
532B LEU* 2.8 33.7 + - - +
533B GLU 4.6 1.0 + - - +
536B LEU* 3.6 44.6 - - + -
537B LEU* 4.0 18.3 - - + +
540B ALA* 4.3 23.6 - - + -
777B ILE* 4.6 5.8 - - + -
782B PHE* 3.0 39.6 + - + +
783B GLN* 3.6 11.7 - - + +
784B MET 3.3 0.2 - - - -
785B ARG* 1.3 77.5 - - - +
787B LEU* 1.3 60.0 + - + +
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Residues in contact with LEU 787 (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* 3.5 14.4 - - - +
532B LEU* 3.8 12.0 - - + +
537B LEU* 5.5 2.2 - - + -
604B THR* 3.9 19.1 - - + +
607B ILE* 3.6 23.1 - - + -
608B GLY* 4.2 8.7 - - - +
611B VAL* 3.9 21.1 - - + -
783B GLN* 3.0 23.2 + - + +
786B LEU* 1.3 83.1 - - + +
788B TRP* 1.3 85.7 + - + +
803B LYS* 5.4 1.0 - - - -
804B PHE* 3.4 42.3 - - + -
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Residues in contact with TRP 788 (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* 3.5 17.9 - - - +
604B THR* 3.7 21.8 - - - -
607B ILE* 3.9 30.3 - - + -
784B MET* 3.0 33.8 + - + +
787B LEU* 1.3 100.4 - - + +
789B GLY* 1.3 61.6 + - - +
792B GLY* 3.4 33.5 + - - +
793B ALA* 3.8 2.2 - - - -
800B ARG* 3.1 69.3 + - + +
801B TYR* 3.9 12.3 - + - -
803B LYS* 4.1 18.6 - - + +
804B PHE* 3.4 23.9 - + - -
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Residues in contact with GLY 789 (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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529B ASN 3.8 0.7 - - - -
530B LYS 3.8 4.0 - - - -
531B PRO* 3.6 24.0 - - - +
785B ARG* 2.9 22.2 + - - +
788B TRP* 1.3 76.9 - - - +
790B SER* 1.3 58.0 - - - -
791B LYS 3.1 11.5 + - - -
793B ALA* 3.1 25.5 + - - +
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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