Contacts of the helix formed by residues 597 - 617 (chain D) in PDB entry 3KXX
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 SER 597 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D SER* 1.3 77.1 - - - +
598D LYS* 1.3 64.7 + - - +
599D ASP 3.5 0.4 - - - -
600D LEU* 3.7 17.2 + - - +
601D VAL* 3.2 26.0 + - - +
761D THR* 4.8 13.2 - - - +
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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
----------------------------------------------------------
596D SER* 3.3 10.6 + - - +
597D SER* 1.3 78.9 - - - +
599D ASP* 1.3 55.4 + - - +
601D VAL* 3.1 7.6 + - - +
602D SER* 2.7 33.3 + - - -
757D ILE 3.5 1.2 + - - -
758D VAL* 2.5 51.9 + - + +
761D THR* 3.1 31.3 - - + +
762D SER* 3.1 34.3 - - - +
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Residues in contact with ASP 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595D LEU* 3.3 31.2 - - + +
596D SER* 2.6 50.1 + - - +
598D LYS* 1.3 76.9 - - - +
600D LEU* 1.3 74.5 + - - +
602D SER* 3.3 10.5 - - - -
603D CYS* 2.6 45.4 + - - -
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Residues in contact with LEU 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D LEU* 4.3 19.3 - - + -
595D LEU* 5.4 3.8 - - + -
596D SER 3.6 11.9 - - - +
597D SER* 3.7 17.0 - - - +
598D LYS 3.2 0.6 - - - -
599D ASP* 1.3 93.0 + - - +
601D VAL* 1.3 62.1 + - - +
603D CYS* 3.5 3.9 + - - +
604D ALA* 3.5 17.0 + - - +
693D ILE* 3.6 43.0 - - + +
694D PHE* 4.1 26.2 - - + -
696D LEU* 4.5 13.5 - - + -
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Residues in contact with VAL 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597D SER* 3.2 17.7 - - - +
598D LYS* 3.1 11.4 + - - +
600D LEU* 1.3 74.4 - - - +
602D SER* 1.3 65.4 + - - +
604D ALA* 3.6 6.5 + - - +
605D TYR 3.2 15.1 + - - -
694D PHE* 4.4 16.4 - - + -
729D LEU* 4.6 13.7 - - + -
754D LEU* 3.7 23.7 - - + +
757D ILE* 4.0 18.6 - - + +
758D VAL* 3.5 23.5 - - + +
761D THR* 5.0 9.6 - - - +
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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
----------------------------------------------------------
598D LYS* 2.7 17.8 + - - -
599D ASP* 2.9 14.6 + - - -
601D VAL* 1.3 76.4 - - - +
603D CYS* 1.3 54.4 + - - +
605D TYR* 3.1 10.9 + - - +
606D GLN* 2.8 53.6 + - - +
758D VAL* 4.5 14.9 - - - +
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Residues in contact with CYS 603 (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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569D LEU* 4.5 12.6 - - + -
572D TYR* 5.6 6.1 - - - -
573D LEU* 5.7 3.4 - - - -
595D LEU* 6.1 2.2 - - - -
599D ASP* 2.6 34.7 + - - +
600D LEU* 3.7 11.2 - - - +
601D VAL 3.3 0.2 - - - -
602D SER* 1.3 70.2 - - - +
604D ALA* 1.3 66.2 + - - +
606D GLN* 3.0 4.7 + - - +
607D VAL* 2.8 30.8 + - + +
637D MET* 4.0 37.0 - - - -
693D ILE* 4.4 15.0 - - + -
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Residues in contact with ALA 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D LEU 3.5 9.4 + - - +
601D VAL* 3.7 7.9 - - - +
603D CYS* 1.3 78.0 - - - +
605D TYR* 1.3 53.7 + - - +
607D VAL* 3.4 3.6 + - - -
608D ALA* 2.7 36.2 + - - +
686D PHE* 3.8 6.0 - - + -
690D LEU* 3.3 32.8 - - + -
693D ILE* 4.1 10.7 - - + +
694D PHE* 5.2 3.1 - - + -
754D LEU* 3.4 17.7 - - + +
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Residues in contact with TYR 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D VAL 3.2 11.6 + - - +
602D SER* 3.1 12.5 + - - +
603D CYS 3.1 0.6 - - - -
604D ALA* 1.3 76.6 - - - +
606D GLN* 1.3 63.8 + - + +
608D ALA* 3.1 1.2 + - - +
609D ARG* 2.6 64.7 + - + +
751D VAL* 3.5 40.8 - - + +
754D LEU* 3.3 10.1 - - + +
755D ASP* 4.0 29.2 + - + -
758D VAL* 3.7 24.9 - - + -
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Residues in contact with GLN 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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542D LYS* 5.0 5.2 - - - -
543D ASN* 2.8 38.7 + - - +
602D SER* 2.8 37.6 + - - +
603D CYS* 3.5 7.6 - - - +
605D TYR* 1.3 80.6 - - + +
607D VAL* 1.3 62.0 + - - +
609D ARG* 3.5 3.0 + - - +
610D GLY 3.1 15.1 + - - -
635D ASN 3.6 19.4 + - - -
636D VAL* 3.7 12.1 - - - +
637D MET* 3.5 34.0 + - + +
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Residues in contact with VAL 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ASN* 5.4 0.4 - - - -
569D LEU* 5.2 4.5 - - + -
603D CYS* 2.8 28.2 + - + +
604D ALA* 3.8 4.9 - - - +
606D GLN* 1.3 72.6 - - - +
608D ALA* 1.3 57.7 + - - +
610D GLY 3.6 0.2 + - - -
611D MET* 3.1 31.7 + - + +
624D LEU* 4.7 2.2 - - + -
629D VAL* 4.0 21.1 - - + -
637D MET* 4.0 20.6 - - + -
639D ILE* 3.9 21.3 - - + +
686D PHE* 4.3 6.5 - - + -
689D LEU* 3.5 31.9 - - + -
693D ILE* 5.2 1.1 - - + -
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Residues in contact with ALA 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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604D ALA 2.7 18.3 + - - +
605D TYR* 3.4 8.1 - - - +
607D VAL* 1.3 76.0 - - - +
609D ARG* 1.3 65.6 + - - +
610D GLY 3.1 0.2 - - - -
611D MET* 3.2 5.5 + - - +
612D GLU* 3.0 19.9 + - - +
686D PHE* 3.9 21.7 - - + -
747D PHE* 4.7 4.9 - - + -
750D LEU* 4.7 5.2 - - + +
751D VAL* 3.5 25.7 - - + +
754D LEU* 4.4 6.1 - - + -
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Residues in contact with ARG 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D HIS* 3.5 21.9 + - - +
542D LYS* 2.8 32.0 - - - +
543D ASN* 4.1 9.9 - - - +
605D TYR* 2.6 54.1 + - + +
606D GLN* 3.9 5.6 - - - +
608D ALA* 1.3 75.1 - - - +
610D GLY* 1.3 62.2 + - - +
612D GLU* 3.5 15.6 + - - +
613D TYR* 3.6 2.9 + - - +
751D VAL* 3.8 14.3 - - + +
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Residues in contact with GLY 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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541D HIS* 3.8 17.7 - - - -
543D ASN* 3.8 17.5 - - - +
544D ILE* 3.7 2.5 - - - +
606D GLN 3.1 11.4 + - - -
607D VAL 3.6 2.2 + - - -
609D ARG* 1.3 77.7 - - - +
611D MET* 1.3 62.8 + - - +
613D TYR* 3.0 15.6 + - - +
614D LEU* 3.1 19.8 - - - +
639D ILE* 4.4 2.9 - - - -
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Residues in contact with MET 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607D VAL* 3.1 24.0 + - + +
608D ALA* 3.2 4.9 + - - +
610D GLY* 1.3 73.0 - - - +
612D GLU* 1.3 65.6 + - - +
613D TYR 3.2 0.2 + - - -
614D LEU* 3.2 16.1 + - + +
615D ALA* 3.0 22.9 + - - +
619D CYS 6.0 0.9 - - - +
621D HIS* 4.2 18.4 - - + +
624D LEU* 3.9 23.8 - - + -
639D ILE* 3.8 19.9 - - + +
682D ASP* 3.6 34.3 - - + +
686D PHE* 5.1 0.9 - - + -
747D PHE* 3.6 39.7 - - + -
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Residues in contact with GLU 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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608D ALA 3.0 13.2 + - - +
609D ARG* 3.5 14.2 - - - +
610D GLY 3.2 0.2 - - - -
611D MET* 1.3 76.6 - - - +
613D TYR* 1.3 61.2 + - - +
615D ALA* 3.5 5.3 - - + +
616D SER* 3.4 20.1 + - - -
747D PHE* 4.0 11.0 - - + +
748D LYS* 3.9 34.2 - - + +
751D VAL* 3.0 34.2 - - + +
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Residues in contact with TYR 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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538D ILE* 3.1 29.2 + - + -
539D GLY* 3.8 1.7 - - - -
540D LYS 3.1 34.8 + - - -
541D HIS* 3.4 36.1 - + + +
544D ILE* 3.7 10.3 - - + -
609D ARG 3.6 1.8 + - - +
610D GLY 3.0 11.8 + - - +
612D GLU* 1.3 78.6 - - - +
614D LEU* 1.3 62.5 + - - +
616D SER* 2.7 26.1 + - - -
617D LYS* 3.0 43.9 + - - +
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Residues in contact with LEU 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D ILE* 4.1 13.5 - - + -
544D ILE* 3.2 26.9 - - + -
610D GLY 3.1 28.7 - - - +
611D MET* 3.2 18.1 + - + +
613D TYR* 1.3 75.6 - - - +
615D ALA* 1.3 68.1 + - - +
617D LYS* 2.8 18.3 + - - -
618D LYS 2.9 10.2 + - - -
619D CYS* 2.9 34.1 + - + +
620D ILE 5.5 0.2 - - - -
621D HIS* 4.2 23.1 - - + -
639D ILE* 5.0 2.2 - - + -
642D PHE* 3.7 27.8 - - + -
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Residues in contact with ALA 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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611D MET 3.0 13.4 + - - +
612D GLU* 3.5 15.5 - - + +
614D LEU* 1.3 74.6 - - - +
616D SER* 1.3 57.5 + - - +
618D LYS* 2.9 19.2 + - - +
619D CYS 4.2 0.6 + - - -
679D HIS* 3.4 38.7 + - + +
747D PHE* 4.4 15.9 - - + -
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Residues in contact with SER 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D GLU 3.4 10.0 + - - -
613D TYR* 2.7 31.2 + - - -
615D ALA* 1.3 78.6 - - - +
617D LYS* 1.3 58.3 + - - +
618D LYS* 3.0 15.7 + - - +
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Residues in contact with LYS 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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537D MET* 3.4 36.8 + - - +
538D ILE* 3.2 27.9 + - - +
539D GLY* 5.2 1.4 - - - -
613D TYR* 3.0 55.7 + - + +
614D LEU* 2.8 14.9 + - - +
616D SER* 1.3 77.5 + - - +
618D LYS* 1.3 72.6 + - - +
619D CYS* 3.4 5.2 + - + +
649D HIS* 5.8 0.2 + - - -
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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