Contacts of the helix formed by residues 597 - 613 (chain J) in PDB entry 6XAV
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 597 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507J VAL* 5.0 1.8 - - - -
511J TYR* 4.9 5.8 - - - -
595J ALA* 3.6 3.6 - - - +
596J LEU* 1.3 81.0 - - - +
598J LYS* 1.3 66.7 + - - -
599J LYS 3.4 1.8 - - - -
600J ALA* 3.7 8.9 - - - +
601J ILE* 3.1 21.0 + - - +
727J ASP 5.5 1.1 - - - -
728J SER* 3.8 16.8 - - - -
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Residues in contact with LYS 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502J PRO 5.5 2.5 - - - +
503J SER* 5.7 6.7 - - - -
507J VAL* 4.1 20.5 - - + +
597J GLY* 1.3 72.4 - - - +
599J LYS* 1.3 95.2 + - + +
601J ILE* 3.5 2.8 + - - +
602J SER* 3.2 21.0 + - - -
728J SER 3.0 22.3 + - - +
729J GLY* 3.2 27.5 + - - +
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Residues in contact with LYS 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597J GLY 3.4 0.4 - - - -
598J LYS* 1.3 101.4 - - - +
600J ALA* 1.3 60.9 + - - +
602J SER* 2.4 27.5 + - - +
603J LYS* 2.9 30.9 + - - +
1247J LYS* 5.9 3.0 - - - +
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Residues in contact with ALA 600 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594J GLN* 4.3 12.6 + - + +
596J LEU* 3.6 39.5 - - + +
597J GLY* 3.5 5.9 + - - +
598J LYS 3.3 0.6 - - - -
599J LYS* 1.3 78.3 - - - +
601J ILE* 1.3 57.5 + - - +
603J LYS* 3.1 11.8 + - - +
604J MET* 2.8 31.5 + - - +
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Residues in contact with ILE 601 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501J VAL* 6.1 0.9 - - + -
502J PRO* 4.5 21.8 - - + -
506J VAL* 4.2 2.9 - - + +
507J VAL* 3.6 37.9 - - + +
510J LEU* 3.7 29.6 - - + -
596J LEU* 3.7 15.7 - - + +
597J GLY 3.1 15.6 + - - +
598J LYS 3.9 3.8 - - - +
599J LYS 3.3 0.2 - - - -
600J ALA* 1.3 75.5 - - - +
602J SER* 1.3 62.5 + - - +
604J MET* 3.2 19.9 - - + +
605J LEU* 3.2 25.1 + - + +
624J ILE* 5.0 13.7 - - + -
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Residues in contact with SER 602 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J PRO* 5.0 3.2 - - - +
501J VAL* 4.0 28.7 - - - +
598J LYS 3.2 11.2 + - - -
599J LYS* 2.4 38.6 + - - +
601J ILE* 1.3 75.8 - - - +
603J LYS* 1.3 56.4 + - - +
605J LEU* 3.5 4.1 + - - +
606J ASN* 2.6 35.2 + - - +
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Residues in contact with LYS 603 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599J LYS* 2.9 30.6 + - - +
600J ALA* 3.1 11.6 + - - +
602J SER* 1.3 75.9 - - - +
604J MET* 1.3 59.5 + - - +
605J LEU 3.1 5.1 + - - -
606J ASN* 2.8 28.7 - - - +
607J THR* 3.0 20.1 + - + +
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Residues in contact with MET 604 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510J LEU* 4.9 3.6 - - + -
579J LEU* 5.6 2.7 - - + -
583J VAL* 4.9 0.2 - - + -
587J LEU* 4.4 2.4 - - - +
591J ILE* 3.6 26.2 - - + -
592J VAL* 3.8 25.6 - - + -
594J GLN* 6.2 0.2 - - - +
596J LEU* 4.1 24.0 - - + -
600J ALA 2.8 15.6 + - - +
601J ILE* 3.2 31.6 - - + +
603J LYS* 1.3 72.7 - - - +
605J LEU* 1.3 60.1 + - + +
607J THR* 3.5 14.3 + - - -
608J CYS* 3.9 13.2 - - - +
620J PHE* 3.7 38.4 - - + -
624J ILE* 4.3 15.5 - - + -
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Residues in contact with LEU 605 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J PRO* 4.8 12.4 - - + +
500J ILE* 3.8 35.7 - - + +
501J VAL* 4.5 13.7 - - + +
502J PRO* 4.8 5.8 - - + -
601J ILE* 3.2 17.4 + - + +
602J SER 3.8 5.6 - - - +
603J LYS 3.1 0.8 - - - -
604J MET* 1.3 80.2 - - + +
606J ASN* 1.3 61.3 + - - +
608J CYS* 4.1 2.9 + - - +
609J TYR* 3.7 12.3 + - - +
617J THR* 3.9 28.5 - - + +
620J PHE* 5.1 8.1 - - + -
621J ALA* 4.3 25.1 - - + +
624J ILE* 5.1 10.3 - - + -
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Residues in contact with ASN 606 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J PRO* 3.7 32.2 - - + +
602J SER* 2.6 23.4 + - - -
603J LYS* 2.8 19.7 - - - +
605J LEU* 1.3 77.4 - - - +
607J THR* 1.3 85.3 + - - +
608J CYS 3.3 0.4 - - - -
609J TYR* 3.3 10.5 + - + +
610J ARG* 3.0 31.3 + - - +
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Residues in contact with THR 607 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587J LEU* 4.9 5.3 - - - +
591J ILE* 4.8 13.5 - - + +
603J LYS* 3.0 22.2 + - + +
604J MET* 3.5 12.6 + - - -
606J ASN* 1.3 84.2 + - - +
608J CYS* 1.3 65.2 + - - +
610J ARG* 3.2 28.0 + - - +
611J ILE* 3.1 35.9 + - - +
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Residues in contact with CYS 608 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584J PRO* 3.9 20.4 - - - -
587J LEU* 4.0 19.2 - - + +
604J MET 3.9 13.8 + - - +
605J LEU 4.2 5.2 - - - +
606J ASN 3.3 0.6 - - - -
607J THR* 1.3 82.4 + - - +
609J TYR* 1.3 57.1 + - - +
611J ILE 4.6 0.2 - - - +
612J LEU* 2.8 39.3 + - - +
613J GLY 3.6 0.5 + - - +
616J PRO* 4.5 11.9 - - - -
617J THR* 4.2 11.4 - - + +
620J PHE* 3.9 25.1 - - + -
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Residues in contact with TYR 609 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490J ILE* 3.7 29.1 - - + +
491J LEU* 3.8 36.8 - - + +
498J PRO* 6.3 0.9 - - + -
605J LEU 3.7 9.7 + - - +
606J ASN* 3.3 13.9 + - + +
607J THR 3.3 0.4 - - - -
608J CYS* 1.3 79.3 - - - +
610J ARG* 1.3 65.1 + - + +
613J GLY* 3.2 38.7 + - - -
614J LEU* 3.9 22.5 - - + +
617J THR* 3.2 20.0 + - + +
904J ALA 5.4 0.5 + - - -
905J ARG* 5.0 10.6 - - - -
906J GLY* 5.1 2.9 + - - -
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Residues in contact with ARG 610 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606J ASN* 3.0 18.0 + - - +
607J THR* 3.2 33.3 + - - +
609J TYR* 1.3 83.5 - - - +
611J ILE* 1.3 69.2 + - + +
613J GLY 4.6 0.5 + - - -
866J GLU* 5.1 25.1 - - + +
867J GLN* 6.2 2.5 - - - +
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Residues in contact with ILE 611 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J LYS* 5.6 11.4 - - + +
586J GLY* 4.0 20.0 - - - +
587J LEU* 5.1 5.8 - - + -
588J PRO* 5.7 4.7 - - + -
607J THR* 3.1 21.9 + - - +
608J CYS* 5.1 0.2 - - - -
610J ARG* 1.3 92.2 - - + +
612J LEU* 1.3 79.5 + - + +
613J GLY 3.4 0.6 + - - -
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Residues in contact with LEU 612 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J LYS* 6.3 4.3 - - + -
584J PRO* 3.7 30.3 - - + -
585J LYS* 4.8 1.8 - - + +
586J GLY* 3.7 26.0 - - - +
587J LEU* 3.8 15.5 - - + -
608J CYS* 2.8 16.0 + - - +
611J ILE* 1.3 92.4 - - + +
613J GLY* 1.3 59.1 + - - +
616J PRO* 3.2 44.8 - - + +
7W GLN* 4.6 2.4 + - - +
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Residues in contact with GLY 613 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609J TYR* 3.2 28.7 + - - -
610J ARG 4.5 0.6 + - - -
611J ILE 3.4 2.6 + - - -
612J LEU* 1.3 79.9 - - - +
614J LEU* 1.3 54.5 + - - -
616J PRO* 4.3 0.2 - - - -
617J THR* 2.6 29.1 + - - -
7W GLN* 3.5 9.0 - - - -
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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
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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