Contacts of the helix formed by residues 652 - 666 (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 LEU 652 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASN* 5.2 2.0 - - - +
265A ASP* 3.4 7.6 - - + -
609C GLY* 3.5 33.9 - - - +
612C GLU* 4.0 24.9 - - + -
613C VAL* 4.4 9.2 - - + +
616C LEU* 4.1 17.5 - - + -
647C ILE* 3.4 20.8 + - + +
650C LYS* 3.6 31.0 - - + +
651C ASN* 1.3 84.9 - - - +
653C CYS* 1.3 59.8 + - - +
654C ARG 3.2 3.1 - - - -
655C ASN* 3.1 9.1 + - + +
656C PHE* 2.9 29.3 + - - +
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Residues in contact with CYS 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 3.3 3.9 + - - +
647C ILE* 4.0 8.4 - - - +
648C ILE* 4.0 35.7 - - - -
651C ASN* 5.2 4.7 + - - +
652C LEU* 1.3 76.8 - - - +
654C ARG* 1.3 59.5 + - + +
656C PHE* 3.6 7.7 - - - +
657C MET* 3.3 32.1 + - + +
681C LEU* 3.6 27.0 - - + +
682C ARG* 6.4 0.2 - - + -
685C GLN* 4.6 10.8 - - - +
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Residues in contact with ARG 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.5 36.9 + - + -
265A ASP* 2.9 38.8 + - - +
266A GLY 4.8 0.8 - - - +
435A ALA* 4.2 14.5 - - - +
436A GLU* 6.2 1.6 - - - +
439A MET* 4.6 12.5 - - + +
460A THR* 5.9 5.3 - - - +
651C ASN* 4.1 14.3 + - - +
653C CYS* 1.3 77.9 - - + +
655C ASN* 1.3 59.8 + - - +
656C PHE 3.3 0.2 - - - -
657C MET* 3.5 13.1 + - + +
658C LEU* 3.0 29.7 + - - +
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Residues in contact with ASN 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.1 28.6 - - - +
264A ILE* 4.2 9.4 + - - +
265A ASP* 2.8 17.5 + - - +
281A PHE* 3.6 6.0 - - + -
607C ASN* 3.7 2.5 + - - +
609C GLY* 3.3 22.7 + - - +
610C GLU* 3.6 14.8 - - - +
613C VAL* 3.7 20.6 - - + +
652C LEU* 3.1 8.3 + - - +
654C ARG* 1.3 71.6 - - - +
656C PHE* 1.3 56.5 + - - +
658C LEU* 3.3 24.6 + - - +
659C HIS* 2.8 32.9 + - - +
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Residues in contact with PHE 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C VAL* 4.1 13.4 - - + +
636C CYS* 5.1 2.7 - - - -
639C PHE* 3.6 38.6 - + + -
640C VAL* 3.3 29.2 - - + -
647C ILE* 4.2 12.6 - - + -
652C LEU 2.9 15.9 + - - +
653C CYS* 3.6 8.3 - - - +
655C ASN* 1.3 75.5 - - - +
657C MET* 1.3 60.9 + - - +
659C HIS* 3.3 9.3 + + + +
660C LEU* 2.9 59.4 + - + +
677C ALA* 4.4 7.6 - - + -
678C VAL* 4.3 8.5 - - + -
681C LEU* 3.9 24.5 - - + -
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Residues in contact with MET 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A MET* 3.4 33.9 - - + +
443A LEU* 5.0 1.1 - - + -
457A LEU* 4.1 31.4 - - - +
653C CYS* 3.3 20.0 + - + +
654C ARG* 3.6 13.9 - - + +
655C ASN 3.3 0.4 - - - -
656C PHE* 1.3 76.2 - - - +
658C LEU* 1.3 66.3 - - - +
660C LEU* 2.8 23.4 + - + +
661C VAL* 2.9 18.1 + - + +
674C ILE* 5.0 9.2 - - + -
678C VAL* 3.7 40.4 - - + -
681C LEU* 6.1 0.9 - - + -
682C ARG* 4.6 4.7 - - - +
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Residues in contact with LEU 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.6 30.5 - - + -
277A SER* 3.3 25.1 - - - +
278A LEU* 3.3 19.3 - - + +
281A PHE* 3.8 16.6 - - + -
439A MET* 4.6 8.3 - - - -
442A VAL* 3.9 33.0 - - + -
610C GLU* 4.4 2.2 - - - +
654C ARG 3.0 18.3 + - - +
655C ASN* 3.4 25.1 - - - +
657C MET* 1.3 75.9 - - - +
659C HIS* 1.3 55.1 + - - +
661C VAL* 3.3 4.2 + - - +
662C SER* 2.9 24.6 + - - -
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Residues in contact with HIS 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.8 18.7 - - + -
292A TYR* 2.6 28.6 + + - -
613C VAL* 4.5 8.7 - - + +
617C TRP* 3.3 57.1 - + + +
636C CYS* 4.7 1.4 - - - -
639C PHE* 5.3 0.9 - + - -
655C ASN 2.8 17.4 + - - +
656C PHE* 3.3 22.7 - + - +
657C MET 3.1 0.2 - - - -
658C LEU* 1.3 70.8 - - - +
660C LEU* 1.3 72.4 + - + +
662C SER* 3.1 2.9 + - - -
663C MET* 2.8 54.6 + - + +
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Residues in contact with LEU 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636C CYS* 3.7 29.6 - - + -
656C PHE* 2.9 54.7 + - + +
657C MET* 2.8 14.9 + - - +
659C HIS* 1.3 74.0 - - + +
661C VAL* 1.3 57.3 + - - +
663C MET* 4.3 0.7 - - - -
664C HIS* 2.8 27.0 + - - +
669C ILE* 3.2 17.3 - - + +
673C SER 5.1 0.4 - - - +
674C ILE* 3.9 29.4 - - + +
677C ALA* 4.1 13.0 - - + -
678C VAL* 3.6 22.7 - - + -
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Residues in contact with VAL 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.2 30.7 - - - +
278A LEU* 3.7 13.9 - - + -
439A MET* 4.9 2.5 - - + -
442A VAL* 3.9 22.9 - - + -
443A LEU* 4.5 12.1 - - + -
446A THR* 4.2 20.6 - - + -
657C MET* 2.9 20.4 + - + +
658C LEU 3.5 7.0 - - - +
660C LEU* 1.3 74.5 - - + +
662C SER* 1.3 53.7 + - - +
664C HIS* 3.1 7.4 + - - +
665C ASP* 2.7 40.9 + - - +
674C ILE* 5.1 7.0 - - + -
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Residues in contact with SER 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.4 1.1 - - - +
281A PHE* 3.7 32.8 + - - +
282A HIS* 3.8 17.8 + - - -
285A PHE* 4.5 3.1 - - - +
292A TYR* 4.4 5.9 + - - -
658C LEU 2.9 12.0 + - - -
659C HIS* 3.1 9.2 + - - -
661C VAL* 1.3 74.0 - - - +
663C MET* 1.3 57.7 + - - +
665C ASP* 2.9 18.2 + - - +
666C PHE* 2.9 40.5 + - - -
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Residues in contact with MET 663 (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* 3.3 36.1 - - + -
292A TYR* 4.8 1.3 - - - +
617C TRP* 3.5 18.4 - - + -
632C MET* 3.5 36.1 - - + -
636C CYS* 4.5 9.0 - - - -
659C HIS* 2.8 48.6 + - + +
660C LEU* 3.6 4.9 - - - +
662C SER* 1.3 73.0 - - - +
664C HIS* 1.3 60.4 - - - +
666C PHE* 3.5 6.4 + - - +
667C ASN 3.5 3.6 + - - -
668C LEU* 3.2 36.0 + - + +
669C ILE* 3.7 15.7 + - + -
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Residues in contact with HIS 664 (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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308A ARG* 3.0 71.4 + - + +
446A THR* 2.6 37.5 + - + +
660C LEU 2.8 17.9 + - - +
661C VAL* 3.3 11.0 - - - +
663C MET* 1.3 71.0 - - - +
665C ASP* 1.3 66.1 + - - +
667C ASN 3.1 5.4 + - - -
669C ILE* 3.2 19.8 - - - +
671C ILE* 3.5 23.5 - - + +
674C ILE* 3.4 27.1 - - + -
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Residues in contact with ASP 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 2.8 36.4 + - - -
278A LEU* 3.8 0.5 - - - +
282A HIS* 3.2 26.5 + - + -
305A THR 3.2 6.2 - - - +
306A TYR* 3.4 27.2 - - + +
307A LYS 3.8 3.6 - - - +
308A ARG* 4.0 9.7 - - - +
446A THR* 3.9 9.5 + - - -
661C VAL* 2.7 24.3 + - - +
662C SER 2.9 8.8 + - - +
664C HIS* 1.3 69.2 + - - +
666C PHE* 1.3 58.3 + - - +
667C ASN* 3.0 23.7 + - - +
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Residues in contact with PHE 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A HIS* 3.5 31.9 - - - -
285A PHE* 3.5 43.3 - + + -
287A ARG* 3.9 22.2 + - + -
301A ALA* 4.3 4.7 - - + -
305A THR* 3.5 43.7 + - + +
306A TYR* 3.8 19.7 - + + -
662C SER* 2.9 43.9 + - - +
663C MET 3.9 5.8 - - - +
664C HIS 3.3 0.6 - - - -
665C ASP* 1.3 73.9 - - - +
667C ASN* 1.3 67.2 + - - +
668C LEU* 3.2 23.0 - - + +
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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