Contacts of the helix formed by residues 609 - 625 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G ASN* 3.2 23.1 - - - -
607I ASN* 3.6 2.9 - - - -
608I GLU* 1.3 73.7 + - - +
610I GLU* 1.3 58.9 + - - +
611I LYS 4.0 1.8 - - - +
612I GLU* 4.0 10.6 - - - +
613I VAL* 3.8 8.5 + - - +
652I LEU* 3.7 15.3 - - - +
655I ASN* 2.9 24.9 + - - -
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Residues in contact with GLU 610 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G THR* 4.4 14.4 + - - +
262G PRO 4.4 3.8 - - - +
264G ILE* 5.8 1.9 - - - +
277G SER 4.2 11.7 - - - +
280G SER* 2.7 35.2 + - - -
281G PHE* 3.8 21.5 - - + -
606I VAL* 3.9 9.4 - - + -
607I ASN* 3.2 43.2 + - + +
609I GLY* 1.3 71.2 - - - +
611I LYS* 1.3 58.3 + - - +
612I GLU 3.5 0.4 - - - -
613I VAL* 3.1 11.1 - - - +
614I MET* 3.0 34.8 + - + +
655I ASN* 3.8 13.2 - - - +
658I LEU* 4.9 2.8 - - - +
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Residues in contact with LYS 611 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600I ILE* 3.7 34.1 - - + +
601I GLU* 3.7 27.3 + - - +
603I PHE 3.1 28.2 + - - -
606I VAL* 3.3 36.3 + - + +
607I ASN 3.3 11.3 + - - +
608I GLU* 3.7 12.5 - - - +
610I GLU* 1.3 77.0 - - - +
612I GLU* 1.3 52.2 + - - +
614I MET* 2.9 6.0 + - - +
615I LYS* 2.7 46.4 + - - +
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Residues in contact with GLU 612 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601I GLU* 5.3 0.3 - - - +
608I GLU 4.2 2.4 + - - +
609I GLY 4.0 14.5 - - - +
610I GLU 3.5 0.2 - - - -
611I LYS* 1.3 78.3 - - - +
613I VAL* 1.3 57.4 + - - +
615I LYS* 3.4 34.6 + - - +
616I LEU* 3.1 46.2 + - + +
650I LYS* 4.2 29.2 + - + +
652I LEU* 3.8 24.2 - - + -
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Residues in contact with VAL 613 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE* 4.1 15.0 - - + -
292G TYR* 5.1 0.8 - - - -
609I GLY 3.8 2.9 + - - +
610I GLU* 3.1 29.1 - - - +
612I GLU* 1.3 77.8 - - - +
614I MET* 1.3 57.8 + - - +
616I LEU* 3.8 6.7 - - + +
617I TRP* 3.1 27.0 + - - +
639I PHE* 4.4 13.4 - - + -
647I ILE* 5.7 2.9 - - + -
652I LEU* 4.3 11.6 - - + +
655I ASN* 3.7 24.5 - - + -
656I PHE* 3.9 31.0 - - + +
659I HIS* 4.3 12.7 - - + -
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Residues in contact with MET 614 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G SER* 3.8 42.4 - - - +
281G PHE* 4.2 8.1 - - + +
284G LEU* 3.8 29.8 - - + -
292G TYR* 3.5 42.2 - - + -
600I ILE* 4.2 16.6 - - + -
603I PHE* 6.3 0.4 - - - -
606I VAL* 4.6 8.3 - - + -
610I GLU* 3.0 22.4 + - + +
611I LYS* 2.9 10.5 + - - +
613I VAL* 1.3 76.1 - - + +
615I LYS* 1.3 58.9 + - - +
617I TRP* 3.3 3.1 + - - +
618I ASN* 2.8 34.7 + - - +
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Residues in contact with LYS 615 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596I THR* 5.2 1.6 - - - -
597I ILE* 3.5 53.2 - - + +
600I ILE* 3.6 23.1 - - + +
601I GLU* 3.6 28.6 + - - +
608I GLU 5.3 1.4 + - - -
611I LYS* 2.7 23.7 + - - +
612I GLU* 3.4 48.1 + - - +
614I MET* 1.3 71.7 - - - +
616I LEU* 1.3 57.3 + - + +
618I ASN* 3.3 6.4 + - - +
619I LEU* 2.9 39.4 + - + +
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Residues in contact with LEU 616 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612I GLU* 3.1 37.6 + - + +
613I VAL* 3.8 4.9 - - - +
615I LYS* 1.3 73.8 - - + +
617I TRP* 1.3 68.8 + - - +
619I LEU* 3.4 10.8 + - + +
620I HIS* 3.0 21.7 + - - +
639I PHE* 3.6 18.4 - - + -
643I TYR* 3.4 36.8 - - + +
646I LYS* 4.5 17.7 - - + +
647I ILE* 3.8 33.9 - - + +
650I LYS* 6.6 0.4 - - + -
652I LEU* 5.1 7.2 - - + -
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Residues in contact with TRP 617 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285G PHE* 4.2 5.4 - + - -
290G PHE* 2.8 29.4 + - - +
292G TYR* 3.8 26.0 - + + -
613I VAL 3.1 12.9 + - - +
614I MET 3.5 7.0 - - - +
616I LEU* 1.3 76.9 - - - +
618I ASN* 1.3 58.4 + - - +
620I HIS* 2.8 29.9 + - - +
621I VAL* 3.0 30.1 + - + +
632I MET* 4.0 9.9 - - + -
635I ALA* 4.1 17.9 - - + -
636I CYS* 3.9 23.3 - - - -
639I PHE* 3.6 42.9 - + + -
659I HIS* 3.2 30.7 - + + +
663I MET* 3.8 18.6 - - + -
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Residues in contact with ASN 618 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G LYS* 3.4 14.4 - - - +
292G TYR* 2.6 60.1 + - - +
293G ASP 4.3 3.0 + - - -
295G PHE* 5.2 1.4 - - - -
596I THR* 3.1 33.0 - - + +
600I ILE* 4.4 0.8 - - - +
614I MET 2.8 18.1 + - - +
615I LYS 3.7 3.4 - - - +
617I TRP* 1.3 73.6 - - - +
619I LEU* 1.3 60.4 + - - +
621I VAL* 3.6 7.6 - - - +
622I MET* 3.2 36.2 + - + +
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Residues in contact with LEU 619 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588I ASP* 4.9 1.2 - - - +
593I ARG* 3.5 57.9 - - + +
596I THR* 5.4 2.9 - - - -
597I ILE* 3.8 26.9 - - + -
615I LYS* 2.9 29.1 + - + +
616I LEU* 3.8 10.8 - - + +
618I ASN* 1.3 78.7 - - + +
620I HIS* 1.3 58.7 + - - +
622I MET* 3.4 7.1 + - - +
623I LYS* 2.9 28.8 + - - +
643I TYR* 3.8 16.2 - - + +
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Residues in contact with HIS 620 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616I LEU 3.0 12.8 + - - +
617I TRP* 2.8 18.9 + - - +
619I LEU* 1.3 77.6 - - - +
621I VAL* 1.3 59.5 + - - +
623I LYS* 3.3 3.5 + - - +
624I HIS* 3.0 62.3 + + - +
626I PHE* 4.2 12.5 - + - -
635I ALA 3.2 28.4 + - - -
638I LEU* 3.7 13.0 + - + +
639I PHE* 3.3 36.8 + + + +
642I ASN* 4.5 3.9 + - - -
643I TYR* 3.6 27.7 + + + -
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Residues in contact with VAL 621 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G CYS 5.2 0.4 - - - +
290G PHE* 3.8 14.4 - - + +
291G LYS* 3.6 35.7 - - + -
617I TRP* 3.0 46.5 + - + +
618I ASN* 3.6 15.5 - - - +
620I HIS* 1.3 73.5 - - - +
622I MET* 1.3 59.6 + - - +
625I GLY* 2.8 33.1 + - - -
626I PHE* 3.6 31.5 + - + +
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Residues in contact with MET 622 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291G LYS* 4.0 26.5 - - + +
295G PHE* 4.0 13.7 - - + -
587I LYS 5.4 1.0 - - - +
588I ASP* 3.4 29.1 - - - +
592I LEU* 3.7 21.5 - - + -
593I ARG* 4.3 19.3 - - + -
596I THR* 3.1 27.4 - - - +
618I ASN* 3.2 35.8 + - + +
619I LEU* 3.6 6.5 - - - +
621I VAL* 1.3 78.2 - - - +
623I LYS* 1.3 61.8 + - - +
624I HIS 4.5 0.2 - - - -
625I GLY* 3.9 6.8 + - - -
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Residues in contact with LYS 623 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588I ASP* 3.9 9.0 + - - +
593I ARG* 5.1 11.2 - - - +
619I LEU 2.9 14.3 + - - +
620I HIS* 3.4 11.7 - - - +
621I VAL 3.2 0.2 - - - -
622I MET* 1.3 78.1 - - - +
624I HIS* 1.3 79.7 + - + +
642I ASN* 4.4 10.3 - - - +
643I TYR* 4.5 18.8 - - + +
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Residues in contact with HIS 624 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G LYS* 4.6 9.7 + - - -
620I HIS* 3.0 46.1 + + - -
622I MET 4.5 0.2 - - - -
623I LYS* 1.3 99.6 - - + +
625I GLY* 1.3 65.4 + - - +
626I PHE* 3.3 30.9 - + + -
638I LEU* 3.9 23.8 - - + +
642I ASN* 3.9 11.7 + - - -
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Residues in contact with GLY 625 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G LYS* 4.6 7.8 + - - -
621I VAL 2.8 19.3 + - - -
622I MET* 3.9 5.7 + - - -
623I LYS 3.7 1.4 - - - -
624I HIS* 1.3 76.2 - - - +
626I PHE* 1.3 64.5 + - - +
627I ILE* 3.6 14.7 + - - +
631I GLN* 4.3 3.6 + - - -
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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
------------------------------------------------------------
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