Contacts of the helix formed by residues 597 - 613 (chain D) in PDB entry 6RIN
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507D VAL* 5.2 6.7 - - - +
511D TYR* 4.8 7.6 - - - -
595D ALA* 3.6 4.2 - - - +
596D LEU* 1.3 82.7 - - - +
598D LYS* 1.3 61.7 + - - -
599D LYS 3.8 0.4 - - - -
600D ALA* 3.8 10.2 - - - +
601D ILE* 3.8 15.1 + - - +
727D ASP 5.2 1.8 - - - -
728D SER* 3.6 17.3 - - - -
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Residues in contact with LYS 598 (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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501D VAL* 3.3 33.2 - - + +
502D PRO 4.2 1.8 - - - -
503D SER* 4.2 20.2 - - - +
507D VAL* 4.7 13.2 - - + -
597D GLY* 1.3 72.0 - - - -
599D LYS* 1.3 70.9 + - + +
600D ALA 3.1 0.9 - - - -
601D ILE* 3.1 9.5 - - + +
602D SER* 3.0 22.2 + - - -
728D SER 3.3 14.4 + - - +
729D GLY* 3.7 16.4 - - - +
35F TRP* 3.4 33.4 - - + +
38F SER* 4.4 18.0 + - - -
39F LEU* 5.0 12.0 - - - +
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Residues in contact with LYS 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D GLU* 5.9 1.6 + - - -
598D LYS* 1.3 78.4 - - + +
600D ALA* 1.3 62.6 + - - +
602D SER* 3.2 9.2 + - - -
603D LYS* 3.0 28.2 + - + +
31F LYS* 5.4 13.6 + - - +
34F THR* 5.6 4.6 - - - +
35F TRP* 4.2 39.2 - - + +
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Residues in contact with ALA 600 (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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591D ILE* 5.1 3.7 - - - +
594D GLN* 4.0 21.3 - - - +
596D LEU* 3.8 18.4 - - + +
597D GLY* 3.8 21.5 - - - +
598D LYS 3.1 1.2 - - - +
599D LYS* 1.3 80.6 - - - +
601D ILE* 1.3 57.4 + - - +
603D LYS* 3.2 14.7 + - - +
604D MET* 2.9 27.3 + - - +
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Residues in contact with ILE 601 (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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501D VAL* 5.6 0.9 - - + -
502D PRO* 4.0 35.0 - - + -
506D VAL* 5.7 0.2 - - + -
507D VAL* 5.0 11.9 - - + -
510D LEU* 3.6 32.1 - - + -
596D LEU* 4.6 5.1 - - + +
597D GLY 3.8 13.6 + - - +
598D LYS* 3.1 22.3 + - + +
600D ALA* 1.3 78.8 - - - +
602D SER* 1.3 64.9 + - - +
604D MET* 3.2 19.0 + - + +
605D LEU* 3.0 25.2 + - + +
624D ILE* 4.2 21.1 - - + -
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Residues in contact with SER 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D PRO* 4.6 18.7 - - - +
501D VAL* 5.0 17.5 - - - +
502D PRO* 5.8 0.9 - - - -
598D LYS* 3.0 14.7 + - - -
599D LYS* 3.4 14.6 - - - -
600D ALA 3.1 0.2 - - - -
601D ILE* 1.3 81.1 - - - +
603D LYS* 1.3 63.7 + - - +
605D LEU* 3.2 8.6 + - - +
606D ASN* 3.0 20.4 + - - +
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Residues in contact with LYS 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591D ILE* 4.8 14.6 - - + -
594D GLN* 4.8 12.6 - - - +
599D LYS* 3.0 16.9 + - + +
600D ALA* 3.4 19.5 - - - +
602D SER* 1.3 73.2 - - - +
604D MET* 1.3 65.7 + - - +
606D ASN* 3.9 10.8 - - + +
607D THR* 2.9 33.2 + - + +
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Residues in contact with MET 604 (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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510D LEU* 5.8 1.6 - - + -
579D LEU* 5.3 2.9 - - + -
583D VAL* 5.6 0.7 - - - -
587D LEU* 4.7 9.8 - - + +
591D ILE* 3.9 23.3 - - + +
592D VAL* 3.5 30.5 - - + -
596D LEU* 3.7 27.6 - - + -
600D ALA 2.9 12.5 + - - +
601D ILE* 3.2 18.2 - - + +
602D SER 3.1 0.2 - - - -
603D LYS* 1.3 75.2 - - - +
605D LEU* 1.3 63.8 + - - +
607D THR* 2.7 23.8 + - - -
608D CYS* 2.9 10.5 + - + +
620D PHE* 3.8 34.1 - - + -
624D ILE* 4.3 11.2 - - + -
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Residues in contact with LEU 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D PRO* 5.2 10.5 - - + -
500D ILE* 3.9 30.3 - - + +
501D VAL* 5.0 0.9 - - - -
502D PRO* 4.1 19.3 - - + -
601D ILE* 3.0 14.6 + - + +
602D SER* 3.7 7.6 - - - +
604D MET* 1.3 79.6 - - + +
606D ASN* 1.3 63.7 + - - +
608D CYS* 3.2 6.4 + - + +
609D TYR* 2.9 23.9 + - - +
617D THR* 4.7 18.9 - - + +
620D PHE* 3.8 31.0 - - + -
621D ALA* 4.8 15.7 - - + -
624D ILE* 4.8 6.1 - - + -
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Residues in contact with ASN 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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491D LEU* 5.7 1.2 - - - +
496D GLY 5.2 3.6 + - - +
497D GLU* 5.5 3.0 - - - +
498D PRO* 4.1 28.4 - - + +
602D SER 3.0 14.4 + - - +
603D LYS* 3.6 14.2 - - - +
604D MET 3.1 0.2 - - - -
605D LEU* 1.3 76.2 - - - +
607D THR* 1.3 64.8 + - + +
609D TYR* 3.1 8.2 + - - +
610D ARG* 2.9 46.9 + - - +
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Residues in contact with THR 607 (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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587D LEU* 4.4 11.3 - - - +
591D ILE* 4.6 10.9 - - + +
603D LYS* 2.9 23.6 + - + +
604D MET* 2.7 22.7 + - - -
606D ASN* 1.3 76.7 - - + +
608D CYS* 1.3 63.7 + - - +
610D ARG* 3.1 7.4 + - - +
611D ILE* 2.9 41.7 + - + +
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Residues in contact with CYS 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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584D PRO* 4.6 13.7 - - - -
587D LEU* 4.5 28.5 - - + -
604D MET 2.9 9.1 + - - +
605D LEU* 3.4 14.6 - - + +
606D ASN 3.2 0.2 - - - -
607D THR* 1.3 83.7 + - - +
609D TYR* 1.3 57.4 + - - +
611D ILE* 5.1 1.3 - - - -
612D LEU* 2.9 31.8 + - - +
616D PRO* 4.7 4.9 - - - -
617D THR* 3.3 31.5 + - + +
620D PHE* 4.8 11.9 - - + -
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Residues in contact with TYR 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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490D ILE* 3.4 32.4 - - + +
491D LEU* 3.9 20.0 - - + +
605D LEU 2.9 12.9 + - - +
606D ASN* 3.6 9.0 - - - +
608D CYS* 1.3 77.7 - - - +
610D ARG* 1.3 93.1 + - - +
611D ILE 3.3 0.5 + - - -
613D GLY* 3.0 40.4 + - - +
614D LEU* 3.7 16.1 - - + +
617D THR* 3.5 13.7 + - + +
901D ARG* 6.1 0.2 - - - -
904D ALA 5.4 0.5 + - - -
905D ARG* 4.9 2.5 - - - -
906D GLY* 4.3 21.3 + - - -
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Residues in contact with ARG 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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491D LEU* 4.3 9.1 - - - +
496D GLY* 4.3 19.2 + - - -
606D ASN* 2.9 34.6 + - - +
607D THR* 3.1 10.5 + - - +
609D TYR* 1.3 111.8 - - - +
611D ILE* 1.3 66.5 + - + +
613D GLY 5.2 0.2 - - - -
840D LEU* 5.7 4.4 - - - +
866D GLU* 2.9 37.9 + - - +
901D ARG* 4.1 29.5 - - - +
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Residues in contact with ILE 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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557D LYS* 3.7 35.3 + - + -
586D GLY 5.0 5.8 - - - +
587D LEU* 5.9 4.5 - - + -
588D PRO* 5.6 10.5 - - + -
607D THR* 2.9 30.6 + - - +
608D CYS* 5.1 0.2 - - - -
610D ARG* 1.3 89.4 - - + +
612D LEU* 1.3 79.1 + - + +
613D GLY 3.7 2.2 + - - -
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Residues in contact with LEU 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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557D LYS* 5.2 6.5 - - + +
563D LEU* 6.5 0.7 - - + -
584D PRO* 4.7 11.9 - - + -
585D LYS* 4.9 3.8 - - + +
586D GLY* 3.9 39.3 - - - +
587D LEU* 4.6 8.1 - - + -
608D CYS* 2.9 16.5 + - - +
611D ILE* 1.3 104.9 - - + +
613D GLY* 1.3 62.9 + - - +
616D PRO* 3.2 42.5 - - + +
617D THR* 5.0 0.6 + - - -
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Residues in contact with GLY 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 TYR* 3.0 35.6 + - - +
610D ARG 5.2 0.2 - - - -
611D ILE 3.7 1.8 - - - -
612D LEU* 1.3 77.3 - - - +
614D LEU* 1.3 60.5 + - - -
617D THR* 3.8 6.0 + - - -
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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