Contacts of the helix formed by residues 609 - 625 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D ASN* 3.1 26.0 - - - -
607F ASN* 3.9 0.4 - - - -
608F GLU* 1.3 67.9 + - - +
610F GLU* 1.3 62.7 + - - -
611F LYS 3.3 0.9 + - - +
612F GLU* 3.3 15.7 + - - +
613F VAL* 3.5 12.3 + - - +
652F LEU* 3.8 14.7 - - - +
655F ASN* 3.5 14.2 + - - -
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Residues in contact with GLU 610 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR* 4.3 13.8 + - - +
262D PRO 4.8 0.9 - - - +
264D ILE* 5.3 2.1 - - - +
277D SER 3.6 15.3 - - - +
280D SER* 2.7 34.4 + - - -
281D PHE* 3.6 28.3 - - + -
606F VAL* 4.3 6.7 - - + -
607F ASN* 3.1 41.8 + - + +
609F GLY* 1.3 70.9 - - - -
611F LYS* 1.3 65.1 + - - +
613F VAL* 3.2 21.1 - - - +
614F MET* 3.2 20.1 - - + +
655F ASN* 3.8 8.6 - - - +
658F LEU* 4.0 6.2 - - - +
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Residues in contact with LYS 611 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600F ILE* 3.7 27.9 - - + +
601F GLU* 3.0 39.8 + - - +
603F PHE 2.8 30.9 + - - -
606F VAL* 3.8 28.6 + - + +
607F ASN 2.8 20.0 + - - +
608F GLU* 3.5 14.6 - - - +
609F GLY 3.1 0.6 - - - -
610F GLU* 1.3 77.4 - - - +
612F GLU* 1.3 57.9 + - - +
614F MET* 2.9 22.3 + - - +
615F LYS* 3.0 19.5 + - - +
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Residues in contact with GLU 612 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F GLU* 4.6 0.5 - - - +
608F GLU 4.7 3.4 - - - +
609F GLY 3.3 12.9 + - - +
611F LYS* 1.3 75.3 - - - +
613F VAL* 1.3 64.6 + - - +
615F LYS* 3.0 40.4 + - - +
616F LEU* 3.0 45.5 + - + +
619F LEU* 5.9 1.0 - - - +
650F LYS* 3.3 45.0 + - + +
652F LEU* 4.2 11.4 - - + -
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Residues in contact with VAL 613 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D PHE* 4.2 12.8 - - + -
609F GLY 3.5 12.9 + - - +
610F GLU* 3.2 24.7 - - - +
612F GLU* 1.3 76.7 - - - +
614F MET* 1.3 56.5 + - - +
616F LEU* 3.3 9.4 + - - +
617F TRP* 2.9 28.2 + - + +
639F PHE* 4.3 15.8 - - + -
647F ILE* 5.3 3.8 - - + -
652F LEU* 4.3 11.4 - - + +
655F ASN* 4.0 17.5 - - + +
656F PHE* 4.3 24.7 - - + +
659F HIS* 4.5 14.1 - - + +
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Residues in contact with MET 614 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D SER* 3.2 40.6 - - - +
281D PHE* 4.2 11.9 - - + -
284D LEU* 4.0 14.1 - - + -
292D TYR* 3.5 56.3 - - + -
600F ILE* 4.5 12.8 - - + -
603F PHE* 6.5 0.2 - - - -
606F VAL* 4.6 9.9 - - + -
610F GLU* 3.2 21.3 - - + +
611F LYS* 2.9 11.7 + - - +
613F VAL* 1.3 73.8 - - - +
615F LYS* 1.3 57.6 + - - +
617F TRP* 3.1 3.6 + - - +
618F ASN* 2.7 40.1 + - - +
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Residues in contact with LYS 615 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596F THR* 5.4 1.6 - - - -
597F ILE* 3.6 44.8 - - + +
600F ILE* 3.5 23.3 - - + -
601F GLU* 2.7 35.1 + - + +
608F GLU 5.5 0.6 + - - -
611F LYS* 3.0 20.1 + - - +
612F GLU* 3.0 47.4 + - - +
613F VAL 3.4 0.2 - - - -
614F MET* 1.3 75.3 - - - +
616F LEU* 1.3 52.8 + - + +
618F ASN* 3.3 6.2 + - - +
619F LEU* 2.8 49.6 + - + +
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Residues in contact with LEU 616 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612F GLU* 3.0 45.4 + - + +
613F VAL* 3.7 6.7 - - - +
615F LYS* 1.3 72.9 - - - +
617F TRP* 1.3 60.0 + - - +
619F LEU* 3.3 14.9 + - + +
620F HIS* 2.8 28.8 + - - +
639F PHE* 3.5 10.4 - - + -
643F TYR* 3.4 35.7 - - + -
646F LYS* 4.4 20.2 - - + +
647F ILE* 4.4 24.2 - - + +
650F LYS* 4.9 8.1 - - + +
652F LEU* 4.5 7.0 - - + -
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Residues in contact with TRP 617 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D PHE* 3.9 4.9 - - - -
290D PHE 2.9 26.6 + - - -
292D TYR* 3.5 24.5 - + + -
613F VAL* 2.9 14.4 + - + +
614F MET 3.5 7.6 - - - +
616F LEU* 1.3 74.1 - - - +
618F ASN* 1.3 59.6 + - - +
620F HIS* 2.8 28.7 + - - +
621F VAL* 2.8 24.4 + - + +
632F MET* 3.9 11.9 - - - -
635F ALA* 3.5 34.8 - - + -
636F CYS* 3.9 17.7 - - - -
639F PHE* 3.4 39.3 - + + -
659F HIS* 3.3 33.3 - + + +
663F MET* 3.7 20.2 - - + -
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Residues in contact with ASN 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LYS* 3.5 13.4 - - - +
292D TYR* 2.9 52.4 + - - +
293D ASP 5.2 0.8 + - - -
295D PHE* 6.1 0.2 - - - -
596F THR* 3.2 27.8 - - + +
600F ILE* 4.3 4.2 - - - +
614F MET 2.7 23.1 + - - +
615F LYS 3.5 4.3 - - - +
617F TRP* 1.3 72.6 - - - +
619F LEU* 1.3 56.7 + - + +
621F VAL* 3.2 10.5 - - - +
622F MET* 3.0 46.0 + - + +
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Residues in contact with LEU 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593F ARG* 3.3 49.0 - - + +
596F THR* 5.9 2.2 - - + -
597F ILE* 4.3 28.3 - - + -
612F GLU* 5.9 1.1 - - - +
615F LYS* 2.8 36.4 + - + +
616F LEU* 3.5 16.8 - - + +
618F ASN* 1.3 74.3 - - + +
620F HIS* 1.3 56.2 + - - +
622F MET* 4.0 8.2 - - + +
623F LYS* 3.2 27.2 + - - +
643F TYR* 3.8 15.4 + - + +
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Residues in contact with HIS 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616F LEU 2.8 12.0 + - - +
617F TRP* 2.8 22.3 + - + +
619F LEU* 1.3 69.6 - - - +
621F VAL* 1.3 65.1 + - - +
623F LYS* 3.4 2.3 + - + +
624F HIS* 3.2 60.8 + + - -
626F PHE* 3.9 19.2 - + - -
635F ALA 3.1 27.7 + - - -
638F LEU* 3.5 17.8 + - + +
639F PHE* 3.5 32.1 + + + +
642F ASN* 4.2 1.7 + - - -
643F TYR* 3.7 24.9 + + + -
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Residues in contact with VAL 621 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D CYS 5.1 0.9 - - - +
290D PHE* 3.9 15.0 - - + +
291D LYS* 3.4 38.6 - - + -
617F TRP* 2.8 50.6 + - + +
618F ASN* 3.2 14.6 - - - +
620F HIS* 1.3 73.0 - - + +
622F MET* 1.3 58.8 + - - +
624F HIS 3.4 0.2 + - - -
625F GLY* 2.7 36.4 + - - -
626F PHE* 3.6 29.0 + - + +
632F MET* 4.8 0.7 - - + -
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Residues in contact with MET 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LYS* 4.1 23.8 - - + +
295D PHE* 4.7 3.6 - - + -
587F LYS 5.3 1.4 - - - +
588F ASP* 3.6 28.1 - - - +
592F LEU* 3.6 28.7 - - + -
593F ARG* 4.2 20.2 - - + -
596F THR* 3.1 39.5 - - + +
618F ASN* 3.0 33.9 + - + +
619F LEU* 4.0 7.4 - - + +
621F VAL* 1.3 76.1 - - - +
623F LYS* 1.3 67.5 + - - +
625F GLY* 4.0 5.9 + - - -
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Residues in contact with LYS 623 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587F LYS 5.7 0.7 - - - +
588F ASP* 3.9 11.6 + - - +
593F ARG* 4.7 18.0 - - - +
619F LEU 3.2 16.0 + - - +
620F HIS 3.6 5.8 - - - +
621F VAL 3.3 0.4 - - - -
622F MET* 1.3 81.7 - - - +
624F HIS* 1.3 76.3 + - + +
642F ASN* 5.6 1.8 - - - +
643F TYR* 4.2 20.2 - - + +
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Residues in contact with HIS 624 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595D ASP* 4.7 12.1 - - - +
597D LYS* 4.7 8.3 + - - -
620F HIS* 3.2 50.9 + + - -
623F LYS* 1.3 93.1 - - + +
625F GLY* 1.3 65.7 + - - +
626F PHE* 3.7 26.2 - + + -
638F LEU* 3.7 19.8 - - + +
642F ASN* 3.8 13.5 + - - -
322G PRO* 4.9 14.8 - - + -
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Residues in contact with GLY 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597D LYS* 4.4 10.8 + - - -
621F VAL 2.7 19.4 + - - -
622F MET 4.0 4.0 + - - -
623F LYS 3.6 1.4 - - - -
624F HIS* 1.3 77.2 - - - +
626F PHE* 1.3 63.4 + - - +
627F ILE* 3.7 12.3 + - - +
631F GLN* 4.7 3.3 + - - +
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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