Contacts of the helix formed by residues 601 - 618 (chain B) in PDB entry 3KN5
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 GLU 601 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B HIS* 3.5 50.4 + - + +
541B VAL* 3.6 23.6 - - + -
572B LYS* 4.5 4.5 - - - -
599B TYR* 3.1 32.9 + - + -
600B ASP* 1.3 72.7 + - - +
602B SER* 1.3 62.5 + - - +
603B CYS 3.2 0.6 + - - -
604B ASP 3.7 4.8 + - - +
605B LEU* 3.5 12.9 - - + +
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 3.0 25.3 + - - -
601B GLU* 1.3 76.1 - - - +
603B CYS* 1.3 59.7 + - - +
604B ASP 3.2 0.2 - - - -
605B LEU* 3.3 10.1 + - - +
606B TRP* 2.9 31.6 + - - +
675B ARG* 4.0 21.3 + - - -
677B LYS* 5.9 5.2 - - - -
722B PHE* 5.4 0.8 - - - -
726B LYS* 4.2 4.9 + - - -
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Residues in contact with CYS 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ARG* 4.8 20.2 - - + +
600B ASP* 3.4 37.5 - - - +
602B SER* 1.3 83.1 + - - +
604B ASP* 1.3 58.5 + - - +
606B TRP* 3.5 3.5 + - - +
607B SER* 2.7 35.8 + - - -
722B PHE* 4.0 25.2 - - + -
723B ASN* 6.1 1.3 - - - -
726B LYS* 3.9 17.5 - - - -
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Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 4.0 7.8 - - + +
535B MET* 4.8 2.6 - - - +
536B HIS* 3.1 33.9 + - + +
541B VAL* 3.8 5.0 - - - -
542B HIS* 3.0 22.6 + - - +
543B ARG* 2.9 31.2 + - - +
545B LEU* 3.6 22.8 - - + +
600B ASP 5.2 0.2 - - - -
601B GLU 3.7 2.2 + - - +
602B SER 3.2 0.6 - - - -
603B CYS* 1.3 74.9 - - - +
605B LEU* 1.3 66.2 + - - +
607B SER* 3.3 6.4 + - - -
608B LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 4.6 2.0 - - + -
536B HIS* 4.1 9.4 - - + +
601B GLU* 3.5 16.4 - - + +
602B SER* 3.3 10.8 + - - +
604B ASP* 1.3 74.0 - - - +
606B TRP* 1.3 65.9 + - - +
608B LEU* 3.2 10.0 + - + +
609B GLY 3.2 16.8 + - - -
667B LEU* 3.7 19.2 - - + +
675B ARG* 4.5 6.7 - - - +
676B LEU 3.5 24.7 - - - +
677B LYS* 3.6 26.0 - - + -
678B MET* 3.5 30.3 - - + +
681B LEU* 4.2 17.7 - - + -
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Residues in contact with TRP 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B SER 2.9 17.2 + - - +
603B CYS 3.6 4.0 - - - +
605B LEU* 1.3 75.3 - - - +
607B SER* 1.3 71.7 + - - +
609B GLY 3.2 2.3 + - - -
610B VAL* 3.1 46.0 + - + +
622B PHE* 3.6 30.4 - + - -
641B ILE* 3.8 17.0 + - + +
667B LEU 3.9 17.2 + - - +
668B LEU* 3.5 25.3 + - + +
670B VAL* 5.7 5.3 - - + +
675B ARG* 4.5 7.1 - - - +
718B THR* 4.1 17.5 - - + -
719B PHE* 4.1 18.2 - + - -
722B PHE* 3.5 65.7 - + + -
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Residues in contact with SER 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ARG 5.7 2.8 - - - -
545B LEU* 4.1 27.1 + - - +
603B CYS 2.7 22.6 + - - -
604B ASP* 3.5 10.4 + - - -
606B TRP* 1.3 85.9 - - - +
608B LEU* 1.3 58.3 + - - +
610B VAL* 3.2 3.7 + - - +
611B ILE* 3.0 33.9 + - - +
719B PHE* 3.8 24.1 - - - -
722B PHE* 5.4 1.2 - - - -
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B MET* 4.3 13.1 - - - +
528B LEU* 4.1 29.2 - - + -
529B VAL* 4.2 18.6 - - + -
532B VAL* 4.0 36.1 - - + -
545B LEU* 5.0 6.1 - - + -
604B ASP 3.0 21.0 + - - +
605B LEU* 3.2 15.7 + - + +
607B SER* 1.3 76.8 - - - +
609B GLY* 1.3 57.1 + - - +
611B ILE* 3.3 10.3 + - + +
612B LEU* 2.9 29.5 + - - +
667B LEU* 3.9 9.4 - - + -
678B MET* 4.9 0.4 - - + -
681B LEU* 4.3 13.5 - - + -
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Residues in contact with GLY 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B LEU 3.2 8.5 + - - -
606B TRP 3.2 2.4 + - - -
608B LEU* 1.3 78.2 - - - +
610B VAL* 1.3 57.7 + - - +
612B LEU* 3.3 4.6 + - - +
613B TYR* 2.9 29.6 + - - +
664B ILE* 4.3 5.7 - - - +
667B LEU* 3.3 29.7 - - - +
668B LEU* 3.8 14.1 - - - +
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Residues in contact with VAL 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TRP* 3.1 53.0 + - + +
607B SER 3.5 7.0 - - - +
609B GLY* 1.3 75.1 - - - +
611B ILE* 1.3 63.7 + - - +
613B TYR* 3.4 7.8 + - - +
614B THR* 3.2 24.7 + - - +
620B VAL* 5.7 1.1 - - + -
621B PRO* 4.1 18.3 - - + +
622B PHE* 4.5 5.6 - - + -
668B LEU* 3.6 9.6 - - + +
715B VAL* 5.2 5.6 - - + -
718B THR* 5.1 5.4 - - + -
719B PHE* 3.8 26.2 - - + -
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Residues in contact with ILE 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B LEU* 4.1 25.8 - - + -
507B PHE* 4.1 8.6 - - + -
525B MET* 4.4 4.9 - - + -
528B LEU* 4.4 4.0 - - + -
545B LEU* 3.2 30.7 - - + +
546B LYS 4.8 0.2 - - - -
547B PRO* 4.7 12.6 - - + -
550B LEU* 4.1 20.0 - - + -
607B SER* 3.0 26.4 + - - +
608B LEU* 3.7 13.2 - - + +
610B VAL* 1.3 73.7 - - - +
612B LEU* 1.3 60.7 + - - +
614B THR* 3.7 1.7 + - - -
615B MET* 2.9 41.7 + - + +
719B PHE* 4.6 8.7 - - + -
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B ALA* 5.1 0.9 - - + -
525B MET* 4.0 25.1 - - + +
608B LEU 2.9 17.8 + - - +
609B GLY* 3.6 5.8 - - - +
611B ILE* 1.3 74.1 - - - +
613B TYR* 1.3 65.8 + - - +
615B MET* 3.1 9.4 + - + -
616B LEU* 2.9 50.2 + - + +
660B ALA 4.6 2.5 - - - +
663B LEU* 3.8 31.0 - - + -
664B ILE* 3.6 24.9 - - + +
667B LEU* 5.2 3.4 - - + -
686B TRP* 4.0 18.8 - - + -
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Residues in contact with TYR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLY 2.9 14.3 + - - +
610B VAL* 3.4 10.5 - - - +
612B LEU* 1.3 78.0 - - - +
614B THR* 1.3 61.4 + - - +
616B LEU 3.3 0.3 + - - -
617B SER* 2.8 27.4 + - - -
619B GLN* 3.1 35.3 + - + +
620B VAL 3.8 4.1 + - - -
621B PRO* 3.5 41.6 - - + +
622B PHE 5.3 0.2 + - - -
646B PHE* 4.6 8.5 - + + -
647B SER 2.8 29.5 + - - -
648B PHE* 4.1 6.3 - + - -
653B TRP* 3.5 33.9 + + - -
664B ILE* 3.9 27.5 - - + +
668B LEU* 4.3 4.5 - - + -
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Residues in contact with THR 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B PHE* 3.8 27.7 - - + -
610B VAL* 3.2 16.3 + - - +
611B ILE* 4.3 0.6 - - - -
613B TYR* 1.3 74.4 - - - +
615B MET* 1.3 65.0 + - - +
617B SER* 3.9 0.4 - - - -
618B GLY* 2.7 32.4 + - - -
619B GLN 3.1 33.9 + - - +
620B VAL* 4.2 1.2 - - - -
621B PRO* 4.0 7.3 - - - +
700B THR* 4.2 1.2 + - - -
704B LEU* 4.9 1.1 - - + -
711B VAL* 4.2 20.2 - - + -
715B VAL* 4.4 10.4 - - + +
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Residues in contact with MET 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B LEU* 4.3 6.7 - - + -
507B PHE* 3.8 21.5 - - + -
510B ILE* 4.1 10.3 - - + -
516B PHE* 3.3 33.4 - - - -
521B ALA* 4.0 18.6 - - - +
524B ILE* 3.7 29.4 - - + -
525B MET* 3.1 35.7 - - + -
528B LEU* 4.6 0.4 - - + -
611B ILE* 2.9 28.6 + - + +
612B LEU* 3.3 11.0 - - + +
614B THR* 1.3 78.0 - - - +
616B LEU* 1.3 58.8 + - + +
700B THR* 3.0 24.4 + - - +
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Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B GLU* 4.8 4.0 - - + -
521B ALA* 3.7 30.1 - - + -
612B LEU* 2.9 37.1 + - + +
613B TYR 4.0 3.4 - - - +
614B THR 3.1 0.2 - - - -
615B MET* 1.3 76.3 - - - +
617B SER* 1.3 59.1 + - - +
652B ALA 4.4 2.6 - - - +
653B TRP* 4.0 11.4 - - + -
656B VAL* 4.0 18.7 - - + +
660B ALA* 3.5 31.6 - - + -
664B ILE* 4.3 10.3 - - + -
686B TRP* 4.4 9.2 - - + -
698B LEU* 3.7 37.9 - - + +
699B MET 5.0 1.6 + - - -
700B THR* 4.2 3.1 - - - +
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Residues in contact with SER 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B TYR 2.8 17.0 + - - -
616B LEU* 1.3 77.2 - - - +
618B GLY* 1.3 59.5 + - - +
619B GLN* 2.9 30.1 + - - +
652B ALA* 4.0 10.8 - - - +
653B TRP* 3.3 39.0 - - - -
699B MET* 4.4 1.4 - - - +
700B THR* 3.9 9.2 + - - +
703B ILE* 3.0 26.7 - - - +
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Residues in contact with GLY 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B THR* 2.7 27.7 + - - -
617B SER* 1.3 72.5 - - - +
619B GLN* 1.3 60.0 + - - +
700B THR* 3.7 14.9 - - - -
703B ILE* 3.7 16.3 - - - +
704B LEU* 4.0 16.2 - - - +
711B VAL* 3.6 21.0 - - - +
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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
------------------------------------------------------------
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