Contacts of the helix formed by residues 606 - 627 (chain K) in PDB entry 6D6Q
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 ILE 606 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474K CYS* 5.3 2.2 - - + -
475K ILE 5.0 4.9 - - - +
476K CYS* 4.0 19.1 - - + -
585K LYS* 4.8 6.5 - - + +
586K ALA* 3.9 26.5 - - + -
588K LEU* 4.6 1.1 - - + -
596K ARG* 3.3 33.9 - - - +
603K ASN* 3.2 2.0 + - - -
604K ASP 4.0 0.2 - - - -
605K ASP* 1.3 103.9 - - - +
607K THR* 1.3 69.0 + - - +
608K THR 3.2 2.2 - - - -
609K SER* 2.9 10.7 + - - -
610K LEU* 2.9 46.5 + - + -
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Residues in contact with THR 607 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596K ARG* 3.0 36.1 + - - +
597K ILE* 3.7 0.9 - - - +
601K ASN* 3.2 33.4 + - - +
602K MET* 4.5 1.6 - - - -
603K ASN* 2.7 33.6 + - - -
606K ILE* 1.3 74.6 - - - +
608K THR* 1.3 56.5 + - + +
610K LEU* 3.3 8.3 + - - +
611K ARG* 2.9 46.5 + - + +
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Residues in contact with THR 608 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602K MET* 5.3 5.8 - - + -
603K ASN 3.2 29.7 + - - +
604K ASP* 4.5 13.8 + - - +
605K ASP 5.1 0.5 + - - -
606K ILE 4.5 1.0 + - - -
607K THR* 1.3 74.5 - - + +
609K SER* 1.3 72.8 + - - +
611K ARG* 3.3 9.4 + - - +
612K GLY* 2.9 22.7 + - - -
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Residues in contact with SER 609 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474K CYS* 4.4 18.7 + - - -
476K CYS* 5.1 7.9 - - - -
491K HIS* 4.2 5.7 - - - -
492K CYS* 3.3 42.4 + - - +
605K ASP 4.8 0.2 - - - -
606K ILE* 2.9 12.7 + - - -
608K THR* 1.3 83.1 + - - +
610K LEU* 1.3 62.9 + - - +
612K GLY* 3.7 0.7 - - - -
613K LEU* 2.9 30.2 + - - +
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Residues in contact with LEU 610 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476K CYS* 3.4 25.6 - - - +
478K VAL* 5.2 11.0 - - + -
588K LEU* 4.4 12.1 - - + -
593K ALA* 4.3 4.5 - - + +
596K ARG* 4.1 18.6 - - + -
597K ILE* 3.6 29.4 - - + -
606K ILE* 2.9 36.9 + - + +
607K THR* 3.6 9.9 - - - +
609K SER* 1.3 76.5 + - - +
611K ARG* 1.3 55.8 + - - +
613K LEU* 3.7 8.3 - - + +
614K ASN* 2.5 39.4 + - - +
662K MET* 5.5 7.4 - - + -
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Residues in contact with ARG 611 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597K ILE* 2.4 46.5 + - + +
598K ASP* 4.4 2.9 - - - +
600K ALA* 3.6 25.9 - - - +
601K ASN* 2.6 29.9 + - - +
602K MET* 4.6 13.3 - - - +
607K THR* 2.9 25.5 + - - +
608K THR* 3.8 8.3 - - - +
610K LEU* 1.3 71.7 - - - +
612K GLY* 1.3 58.4 + - - +
613K LEU 3.0 4.9 + - - -
614K ASN* 3.2 6.8 + - - +
615K LYS* 3.0 38.0 + - + +
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Residues in contact with GLY 612 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492K CYS* 4.1 10.8 - - - -
500K LEU* 4.9 2.4 - - - +
568K HIS* 6.5 0.7 - - - -
608K THR 2.9 16.3 + - - -
609K SER 3.7 1.3 - - - -
611K ARG* 1.3 75.3 - - - +
613K LEU* 1.3 56.5 + - - +
615K LYS* 3.9 15.5 - - - +
616K LEU* 3.5 28.2 + - - +
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Residues in contact with LEU 613 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476K CYS* 6.6 0.4 - - - -
490K LEU* 3.9 23.3 - - + -
491K HIS* 4.2 15.3 - - - +
492K CYS* 3.9 24.0 - - + +
502K VAL* 4.9 2.5 - - + -
609K SER* 2.9 20.4 + - - +
610K LEU* 3.7 8.7 - - + +
612K GLY* 1.3 76.5 - - - +
614K ASN* 1.3 60.0 + - - +
615K LYS 3.1 1.3 - - - -
616K LEU* 3.4 3.4 + - - +
617K ALA* 2.9 27.7 + - - +
662K MET* 3.2 30.1 - - + -
666K PHE* 3.2 47.5 - - + -
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Residues in contact with ASN 614 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597K ILE* 2.9 37.8 - - + +
610K LEU* 2.5 27.8 + - - +
611K ARG* 3.8 4.3 - - - +
613K LEU* 1.3 72.8 - - - +
615K LYS* 1.3 66.0 + - - +
617K ALA* 3.2 6.7 + - - +
618K LYS* 2.9 33.7 + - - +
658K GLU* 4.9 14.4 - - + +
659K THR* 4.3 7.9 - - - +
662K MET* 3.4 37.7 - - - +
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Residues in contact with LYS 615 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568K HIS* 4.9 18.6 + - + +
611K ARG* 3.0 24.4 + - + +
612K GLY* 3.9 14.8 - - - +
613K LEU 3.1 0.2 - - - -
614K ASN* 1.3 75.6 - - - +
616K LEU* 1.3 65.2 + - + +
618K LYS* 2.9 18.2 + - - +
619K ILE* 2.8 31.9 + - + +
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Residues in contact with LEU 616 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492K CYS* 4.4 1.1 - - - -
500K LEU* 3.7 35.4 - - + -
502K VAL* 4.1 13.2 - - + -
566K MET* 5.0 7.6 - - - -
567K ASN 3.4 24.9 - - - +
568K HIS* 4.2 17.0 - - - +
570K ALA* 3.9 17.9 - - + +
612K GLY 3.5 16.8 + - - +
613K LEU* 3.4 7.9 + - - +
615K LYS* 1.3 79.9 - - + +
617K ALA* 1.3 56.7 + - - +
619K ILE* 3.7 6.8 - - + +
620K LEU* 2.9 37.1 + - + +
666K PHE* 4.2 10.1 - - + -
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Residues in contact with ALA 617 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613K LEU 2.9 14.9 + - - +
614K ASN 3.2 10.3 - - - +
615K LYS 3.0 0.4 - - - -
616K LEU* 1.3 77.0 - - - +
618K LYS* 1.3 58.5 + - + +
620K LEU* 3.7 5.5 - - - +
621K LYS* 2.8 30.0 + - - +
661K SER* 5.8 0.2 - - - +
662K MET* 3.4 40.8 - - + -
665K GLU* 4.3 6.0 - - + +
666K PHE* 3.6 10.5 - - + -
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Residues in contact with LYS 618 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614K ASN* 2.9 21.2 + - - +
615K LYS* 2.9 11.0 + - - +
617K ALA* 1.3 76.4 - - + +
619K ILE* 1.3 66.2 + - + +
621K LYS* 3.5 6.7 - - - +
622K LYS* 3.0 29.1 + - + +
658K GLU* 2.9 45.4 + - + -
661K SER* 6.1 0.4 - - - +
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Residues in contact with ILE 619 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568K HIS 4.7 12.6 - - - +
569K ASN* 3.5 35.9 - - - +
570K ALA* 3.9 7.9 - - + -
615K LYS* 2.8 49.9 + - + +
616K LEU* 3.7 10.1 - - + +
618K LYS* 1.3 78.8 - - + +
620K LEU* 1.3 66.3 + - - +
622K LYS* 3.3 25.2 - - - +
623K ARG* 2.9 31.9 + - + +
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Residues in contact with LEU 620 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566K MET* 5.1 6.3 - - + -
570K ALA* 3.6 35.7 - - + +
616K LEU* 2.9 27.1 + - + +
617K ALA* 3.8 4.3 - - - +
619K ILE* 1.3 73.1 - - - +
621K LYS* 1.3 58.1 + - - +
623K ARG* 3.6 11.3 - - - +
624K ARG* 2.9 34.0 + - - +
665K GLU* 4.2 17.9 - - + +
666K PHE* 4.7 18.4 - - + -
669K LEU* 4.5 28.9 - - + -
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Residues in contact with LYS 621 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617K ALA 2.8 18.4 + - - +
618K LYS* 3.5 9.2 - - - +
619K ILE 3.2 0.4 - - - -
620K LEU* 1.3 77.5 - - - +
622K LYS* 1.3 57.6 + - - +
624K ARG* 3.3 3.3 + - - +
625K ILE* 2.9 54.1 + - + +
631K THR* 5.6 11.2 + - - -
661K SER* 3.8 25.3 - - - +
665K GLU* 2.9 40.8 + - + +
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Residues in contact with LYS 622 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618K LYS* 3.0 15.5 + - + +
619K ILE* 3.3 33.0 - - - +
621K LYS* 1.3 76.6 - - - +
623K ARG* 1.3 61.6 + - - +
625K ILE* 3.3 14.9 + - + +
626K GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 623 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569K ASN* 3.0 25.6 + - - +
570K ALA 2.3 33.8 + - - -
571K GLU* 3.6 19.0 + - - +
619K ILE* 2.9 22.3 + - + +
620K LEU* 3.6 12.6 - - - +
622K LYS* 1.3 79.7 - - + +
624K ARG* 1.3 56.8 + - - +
626K GLU* 3.2 16.8 + - - +
627K LYS* 2.9 23.3 + - - +
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Residues in contact with ARG 624 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620K LEU 2.9 17.4 + - - +
621K LYS* 4.0 4.9 + - - +
623K ARG* 1.3 73.2 - - - +
625K ILE* 1.3 63.4 + - - +
627K LYS* 2.9 43.0 + - + +
628K GLY 3.2 5.5 + - - -
629K ALA* 3.3 27.9 + - + +
664K GLU* 5.4 2.2 + - - +
665K GLU* 2.2 43.1 + - - +
668K LEU* 3.1 44.8 - - - +
669K LEU 5.3 0.4 - - - +
672K ILE* 5.2 8.1 - - - +
767K LEU* 4.2 18.7 - - - +
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Residues in contact with ILE 625 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621K LYS* 2.9 51.3 + - + +
622K LYS* 3.5 11.4 - - + +
623K ARG 3.3 0.2 - - - -
624K ARG* 1.3 76.6 - - - +
626K GLU* 1.3 62.3 + - - +
628K GLY* 3.0 16.1 + - - -
629K ALA* 4.1 15.4 - - + +
631K THR* 5.9 9.4 - - + -
723K GLU* 3.7 9.0 - - - +
726K ASP* 5.2 9.2 - - - +
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Residues in contact with GLU 626 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622K LYS 2.9 13.7 + - - +
623K ARG* 3.3 17.4 - - - +
625K ILE* 1.3 76.0 - - - +
627K LYS* 1.3 58.2 + - - +
628K GLY* 3.1 1.8 + - - -
719K LYS* 4.7 8.5 + - - -
723K GLU* 4.4 7.8 - - - +
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Residues in contact with LYS 627 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623K ARG 2.9 8.6 + - - +
624K ARG* 2.9 35.1 + - + +
626K GLU* 1.3 76.3 - - - +
628K GLY* 1.3 56.5 + - - +
629K ALA 3.6 1.5 + - - +
672K ILE* 6.1 2.8 - - - +
676K LYS* 6.1 1.2 - - - +
719K LYS* 4.5 10.1 + - - +
767K LEU 5.5 2.5 - - - +
768K ALA* 4.3 23.5 - - + +
769K SER* 5.3 10.1 - - - +
770K PRO* 5.4 5.0 - - - +
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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
------------------------------------------------------------
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