Contacts of the helix formed by residues 609 - 625 (chain C) in PDB entry 5LS6
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 609 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.6 19.7 - - - -
607C ASN* 3.8 1.6 - - - -
608C GLU* 1.3 72.2 + - - -
610C GLU* 1.3 63.4 + - - -
612C GLU* 3.7 10.7 - - - +
613C VAL* 3.6 12.6 + - - +
652C LEU* 3.5 20.3 - - - +
655C ASN* 3.3 16.8 + - - -
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Residues in contact with GLU 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.6 9.3 - - - +
262A PRO 5.7 0.4 - - - +
276A GLN 5.2 1.0 - - - +
277A SER 3.5 20.6 - - - +
280A SER* 2.6 37.6 + - - -
281A PHE* 3.6 21.4 - - + -
606C VAL* 3.9 6.7 - - + -
607C ASN* 3.1 43.0 + - + +
609C GLY* 1.3 69.2 - - - -
611C LYS* 1.3 67.1 + - - +
613C VAL* 3.0 23.4 - - - +
614C MET* 3.2 17.9 + - + +
655C ASN* 3.8 8.7 - - - +
658C LEU* 4.4 2.4 - - - +
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Residues in contact with LYS 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ILE* 3.5 32.7 - - + +
601C GLU* 2.8 44.8 + - - +
603C PHE* 2.8 31.0 + - - -
604C SER* 5.2 0.2 - - - +
606C VAL* 3.6 27.2 + - + +
607C ASN 2.7 26.2 + - - +
608C GLU* 3.9 11.0 - - - +
610C GLU* 1.3 73.8 - - - +
612C GLU* 1.3 62.2 + - - +
614C MET* 3.5 2.7 + - - +
615C LYS* 3.1 30.9 + - + +
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Residues in contact with GLU 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C GLU 4.1 4.1 + - - +
609C GLY 3.7 16.6 + - - +
610C GLU 3.3 0.8 - - - -
611C LYS* 1.3 75.3 - - - +
613C VAL* 1.3 66.3 + - - +
615C LYS* 3.3 36.3 + - - +
616C LEU* 3.1 45.6 + - + +
650C LYS* 3.7 32.3 + - + +
652C LEU* 4.0 21.8 - - + -
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Residues in contact with VAL 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.1 13.9 - - + -
609C GLY 3.6 14.2 + - - +
610C GLU* 3.0 20.6 - - - +
612C GLU* 1.3 78.2 - - - +
614C MET* 1.3 60.6 + - - +
616C LEU* 3.3 13.3 + - + +
617C TRP* 3.0 21.5 + - - +
639C PHE* 4.4 9.1 - - + -
647C ILE* 5.2 2.9 - - + -
652C LEU* 4.4 9.9 - - + +
655C ASN* 3.7 22.0 - - + +
656C PHE* 4.1 31.2 - - + +
659C HIS* 4.5 12.6 - - + +
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Residues in contact with MET 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 3.5 39.9 - - - +
281A PHE* 4.0 14.4 - - + -
284A LEU* 4.2 17.9 - - + -
292A TYR* 3.6 55.2 - - + -
600C ILE* 4.4 11.9 - - + -
606C VAL* 4.5 12.3 - - + -
610C GLU* 3.2 23.3 + - + +
611C LYS* 3.7 8.1 - - - +
613C VAL* 1.3 72.7 - - - +
615C LYS* 1.3 59.1 + - - +
617C TRP* 3.1 2.8 + - - +
618C ASN* 2.8 38.9 + - - +
659C HIS* 5.9 0.2 - - - -
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Residues in contact with LYS 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C THR* 6.2 1.3 - - - -
597C ILE* 3.5 46.9 + - + +
600C ILE* 3.6 22.5 - - + +
601C GLU* 3.5 30.5 + - - +
608C GLU 5.9 1.0 + - - -
611C LYS* 3.1 23.3 + - - +
612C GLU* 3.3 41.7 + - - +
614C MET* 1.3 78.2 - - - +
616C LEU* 1.3 62.6 + - - +
618C ASN* 4.0 4.6 - - - +
619C LEU* 3.1 36.7 + - + +
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Residues in contact with LEU 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C GLU* 3.1 39.2 + - + +
613C VAL* 3.5 11.2 - - - +
614C MET 3.2 0.2 - - - -
615C LYS* 1.3 75.8 - - + +
617C TRP* 1.3 57.9 + - - +
619C LEU* 3.5 5.7 + - + -
620C HIS 3.0 21.1 + - - -
639C PHE* 3.6 15.0 - - + -
643C TYR* 3.5 37.3 - - + -
646C LYS* 4.7 27.4 - - + +
647C ILE* 4.1 24.0 - - + -
650C LYS* 5.5 2.9 - - + -
652C LEU* 4.1 12.8 - - + -
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Residues in contact with TRP 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PHE* 4.1 5.9 - - - -
290A PHE 3.0 26.3 + - - -
292A TYR* 3.7 23.3 - + + -
613C VAL 3.0 13.2 + - - +
614C MET 3.1 7.4 + - - +
616C LEU* 1.3 72.8 - - - +
618C ASN* 1.3 60.7 + - - +
620C HIS* 2.5 29.5 + - - +
621C VAL* 3.1 27.5 + - + +
632C MET* 3.9 8.7 - - - -
635C ALA* 3.9 24.7 - - + -
636C CYS* 4.2 9.4 - - - -
639C PHE* 3.6 56.0 - + + -
659C HIS* 3.3 34.1 - + + +
663C MET* 3.5 25.1 - - + -
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Residues in contact with ASN 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 3.2 17.7 - - - +
292A TYR* 2.5 59.7 + - - +
293A ASP 4.4 1.0 + - - -
294A CYS* 5.5 0.2 - - - +
295A PHE* 5.8 0.4 - - - -
596C THR* 3.2 30.2 - - + +
600C ILE* 5.0 1.9 - - + +
614C MET 2.8 19.2 + - - +
615C LYS* 4.0 4.9 - - - +
617C TRP* 1.3 73.7 - - - +
619C LEU* 1.3 55.8 + - + +
621C VAL* 3.6 9.0 - - - +
622C MET* 3.2 38.8 + - + +
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Residues in contact with LEU 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C ARG* 3.6 48.6 - - + +
596C THR* 5.6 2.7 - - - +
597C ILE* 4.4 24.9 - - + -
615C LYS* 3.1 28.3 + - + +
616C LEU* 3.6 11.2 - - + +
617C TRP 3.1 0.8 - - - -
618C ASN* 1.3 73.9 - - + +
620C HIS* 1.3 65.9 + - - +
622C MET* 3.8 7.5 - - - +
623C LYS* 3.0 25.3 + - - +
643C TYR* 3.9 18.0 + - + +
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Residues in contact with HIS 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU 3.0 13.0 + - - +
617C TRP* 2.5 22.4 + - - +
619C LEU* 1.3 71.2 - - - +
621C VAL* 1.3 57.9 + - + +
623C LYS* 3.2 3.1 + - - +
624C HIS* 2.8 69.3 + + - -
626C PHE* 3.8 22.2 - + - -
635C ALA 3.3 26.5 + - - -
638C LEU* 3.7 18.1 + - + +
639C PHE* 3.6 30.4 + + + +
642C ASN* 4.2 2.2 + - - -
643C TYR* 4.0 24.6 + + + -
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Residues in contact with VAL 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A CYS 4.8 2.5 - - - +
290A PHE* 3.7 20.6 - - + +
291A LYS* 3.9 23.5 - - + -
617C TRP* 3.1 44.4 + - + +
618C ASN* 3.6 12.8 - - - +
620C HIS* 1.3 73.5 - - - +
622C MET* 1.3 59.6 + - - +
624C HIS 3.8 0.2 - - - -
625C GLY* 2.8 31.0 + - - -
626C PHE* 3.8 33.8 + - + +
632C MET* 4.6 4.3 - - + -
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Residues in contact with MET 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LYS* 3.7 34.1 - - + +
295A PHE* 4.1 3.8 - - + -
587C LYS 5.2 2.4 - - - +
588C ASP* 3.9 30.1 - - - +
592C LEU* 3.7 34.5 - - + +
593C ARG* 4.7 9.6 - - + -
596C THR* 3.2 38.4 - - + +
618C ASN* 3.2 26.2 + - + +
619C LEU* 3.8 9.4 - - - +
621C VAL* 1.3 76.9 - - - +
623C LYS* 1.3 63.6 + - - +
625C GLY* 4.0 5.1 + - - -
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Residues in contact with LYS 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C LYS 5.7 1.0 - - - +
588C ASP* 4.5 8.9 + - - +
593C ARG* 4.9 16.0 - - - +
619C LEU 3.0 13.7 + - - +
620C HIS* 3.2 10.5 + - - +
622C MET* 1.3 77.8 - - - +
624C HIS* 1.3 79.9 + - + +
643C TYR* 4.2 17.9 - - + +
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Residues in contact with HIS 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A ASP* 5.5 2.9 - - - +
597A LYS* 4.5 9.2 + - - -
620C HIS* 2.8 54.3 + + - +
623C LYS* 1.3 100.8 - - + +
625C GLY* 1.3 64.0 + - - +
626C PHE* 3.5 27.9 - + + -
638C LEU* 3.7 26.3 - - + +
642C ASN* 3.9 13.6 + - - -
643C TYR* 5.3 0.9 - + - -
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Residues in contact with GLY 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 6.3 0.9 - - - -
597A LYS* 4.2 11.4 + - - -
621C VAL 2.8 19.9 + - - -
622C MET* 4.0 4.0 + - - -
623C LYS 3.7 1.8 - - - -
624C HIS* 1.3 75.8 - - - +
626C PHE* 1.3 61.4 + - - +
627C ILE* 3.6 13.8 + - - +
631C GLN* 4.8 1.6 + - - -
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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