Contacts of the helix formed by residues 605 - 618 (chain D) in PDB entry 6T8G
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 GLY 605 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601D MET* 4.5 11.0 - - - +
602D MET 5.4 1.1 - - - -
603D ILE 4.0 1.6 + - - -
604D VAL* 1.3 87.0 - - - +
606D LYS* 1.3 59.5 + - - -
607D LYS* 3.1 11.4 + - - +
608D VAL* 3.3 13.7 + - - +
609D GLU* 4.1 1.4 + - - +
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Residues in contact with LYS 606 (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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605D GLY* 1.3 70.2 - - - -
607D LYS* 1.3 60.5 + - + +
608D VAL 3.2 0.7 - - - -
609D GLU* 3.1 26.7 + - - +
610D GLU* 3.0 32.9 + - + +
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Residues in contact with LYS 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D ARG* 3.4 33.6 - - - +
604D VAL* 5.5 6.1 - - + -
605D GLY 3.1 2.5 + - - +
606D LYS* 1.3 76.5 - - + +
608D VAL* 1.3 61.0 + - + +
610D GLU* 3.3 14.7 + - - +
611D LEU* 2.9 33.2 + - + +
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Residues in contact with VAL 608 (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 ALA* 4.6 16.2 - - + -
528D LEU* 4.3 17.5 - - + -
597D PHE* 6.4 0.4 - - + -
600D MET* 4.2 35.2 - - + +
601D MET* 4.8 5.6 - - + +
604D VAL* 3.7 35.0 - - + -
605D GLY 3.3 8.2 + - - +
606D LYS 3.2 0.4 - - - -
607D LYS* 1.3 75.4 - - + +
609D GLU* 1.3 58.8 + - - +
611D LEU* 3.2 12.8 + - + +
612D ILE* 2.9 34.5 + - + +
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Residues in contact with GLU 609 (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 MET* 3.5 23.9 - - + +
605D GLY 4.1 1.2 + - - -
606D LYS* 3.1 35.0 + - - +
608D VAL* 1.3 79.6 - - - +
610D GLU* 1.3 56.0 + - - +
612D ILE* 3.3 5.1 + - - +
613D ALA* 2.9 25.6 + - - +
639D THR* 2.3 34.4 + - - +
641D LEU* 3.3 29.8 - - + +
642D ILE* 3.7 22.6 - - + +
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Residues in contact with GLU 610 (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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606D LYS* 3.0 18.9 + - + +
607D LYS* 3.3 17.3 + - - +
609D GLU* 1.3 73.9 - - - +
611D LEU* 1.3 60.8 + - - +
613D ALA* 3.3 8.9 - - + +
614D ARG* 2.9 44.5 + - + +
641D LEU* 4.1 15.5 - - + -
602E MET 5.0 6.3 - - - +
603E ILE* 4.5 20.0 - - + +
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Residues in contact with LEU 611 (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 ALA* 4.2 5.8 - - + +
528D LEU* 3.8 34.3 - - + +
529D ARG* 4.0 40.8 - - + +
532D VAL* 3.9 25.2 - - + +
607D LYS 2.9 20.0 + - - +
608D VAL* 3.2 19.2 + - + +
610D GLU* 1.3 73.4 - - - +
612D ILE* 1.3 60.5 + - - +
614D ARG* 3.9 5.6 - - + +
615D ILE* 3.0 37.2 + - + +
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Residues in contact with ILE 612 (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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528D LEU* 4.6 20.9 - - + -
594D VAL* 5.2 4.9 - - + -
597D PHE* 5.7 9.0 - - + -
601D MET* 6.1 0.9 - - + -
608D VAL* 2.9 26.5 + - + +
609D GLU* 3.5 7.6 - - - +
611D LEU* 1.3 74.9 - - - +
613D ALA* 1.3 58.0 + - - +
615D ILE* 3.9 4.9 - - + +
616D ALA* 2.9 31.0 + - + +
626D LEU* 4.0 34.8 - - + -
628D LEU* 4.4 19.1 - - + -
642D ILE* 3.7 30.1 - - + +
646D ILE* 5.0 4.9 - - + -
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Residues in contact with ALA 613 (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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609D GLU 2.9 15.2 + - - +
610D GLU* 3.3 13.2 - - - +
611D LEU 3.2 0.4 - - - -
612D ILE* 1.3 76.2 - - - +
614D ARG* 1.3 57.3 + - - +
617D GLN* 2.8 27.1 + - - +
641D LEU* 3.7 35.6 + - + +
645D ASN* 2.9 14.6 - - - +
599E ASP* 5.9 0.7 - - - +
603E ILE* 4.5 15.9 - - + +
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Residues in contact with ARG 614 (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 VAL* 5.2 14.4 - - + -
535D MET* 4.0 13.4 - - + +
610D GLU* 2.9 28.3 + - - +
611D LEU* 4.2 7.2 - - - +
613D ALA* 1.3 73.4 - - + +
615D ILE* 1.3 66.7 + - - +
617D GLN* 3.3 17.9 + - - +
618D LYS* 3.0 24.7 + - + +
520E ASP* 6.1 0.2 - - - -
521E MET* 4.4 15.3 - - + +
522E LYS* 5.6 7.5 - - - +
603E ILE* 3.4 40.1 + - + +
604E VAL* 5.8 0.6 - - - +
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Residues in contact with ILE 615 (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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461D HIS* 4.8 2.5 - - + -
528D LEU* 4.9 7.6 - - + +
531D SER* 3.9 19.5 - - - +
532D VAL* 3.7 39.5 - - + +
535D MET* 4.2 12.1 - - + +
611D LEU* 3.0 24.0 + - + +
612D ILE* 3.9 4.7 - - + +
614D ARG* 1.3 77.2 - - - +
616D ALA* 1.3 63.1 + - - +
617D GLN 3.3 0.2 + - - -
618D LYS 3.5 6.2 + - - +
619D ALA* 3.3 18.5 - - - +
624D ILE* 4.7 24.0 - - + +
626D LEU* 4.5 26.7 - - + -
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Residues in contact with ALA 616 (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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461D HIS* 3.4 35.0 + - + +
612D ILE* 2.9 19.9 + - + +
613D ALA* 4.9 0.2 - - - -
615D ILE* 1.3 73.8 - - - +
617D GLN* 1.3 63.7 + - - +
619D ALA* 4.6 0.5 - - - +
626D LEU* 4.9 4.7 - - + -
645D ASN* 3.2 34.0 - - + +
646D ILE* 4.3 13.5 - - + -
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Residues in contact with GLN 617 (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 ALA 2.8 13.6 + - - +
614D ARG* 3.4 17.6 - - - +
615D ILE 3.2 0.2 - - - -
616D ALA* 1.3 81.7 - - - +
618D LYS* 1.3 97.2 + - + +
619D ALA 3.4 4.5 + - - -
620D ARG 5.3 0.2 + - - -
645D ASN* 3.3 12.8 + - - +
499E PRO* 3.3 28.0 - - + +
500E LYS* 4.3 20.9 - - + +
519E THR 4.4 1.8 + - - -
521E MET* 3.4 23.5 - - - +
599E ASP* 4.3 10.1 - - - +
603E ILE* 3.7 19.6 - - + +
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Residues in contact with LYS 618 (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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535D MET* 3.2 39.0 - - + +
536D GLU* 5.1 7.0 - - - +
539D TYR* 3.4 39.4 + - + +
614D ARG* 3.0 9.5 + - + +
615D ILE 3.5 2.9 - - - +
617D GLN* 1.3 115.5 - - + +
619D ALA* 1.3 57.7 + - - +
622D ALA* 4.0 2.3 - - - +
624D ILE* 5.5 0.9 - - - +
499E PRO 3.0 27.2 + - - +
500E LYS* 6.2 0.9 - - - +
501E MET* 6.2 1.6 - - + +
519E THR* 3.2 27.1 + - + +
520E ASP* 5.3 5.8 - - - +
521E MET* 5.9 1.6 - - - +
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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