Contacts of the helix formed by residues 670 - 685 (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 SER 670 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A ARG* 4.2 10.1 - - - +
633C ASN* 3.3 11.3 + - - +
664C HIS* 3.9 0.4 - - - -
668C LEU 4.4 0.2 - - - -
669C ILE* 1.3 75.7 - - - +
671C ILE* 1.3 58.7 + - - +
672C MET* 3.6 16.2 + - - +
673C SER* 3.0 41.6 + - - -
674C ILE* 3.5 5.5 - - - +
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Residues in contact with ILE 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 4.8 1.4 - - - +
312A GLU* 5.3 9.9 - - + +
446A THR* 3.3 25.8 - - - +
447A TYR* 3.3 53.2 + - + +
664C HIS* 3.5 21.7 + - + +
670C SER* 1.3 72.2 - - - +
672C MET* 1.3 63.6 + - + +
673C SER 3.1 4.9 + - - -
674C ILE* 3.1 22.3 + - + -
675C ASP* 3.7 4.0 + - - +
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Residues in contact with MET 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C SER* 3.1 13.8 - - - +
671C ILE* 1.3 84.1 - - + +
673C SER* 1.3 56.0 + - - +
675C ASP* 4.5 3.6 - - - +
676C LYS* 3.3 26.4 + - - +
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Residues in contact with SER 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C ASN* 2.7 36.6 + - - +
636C CYS* 5.3 6.5 - - - -
637C MET* 6.0 3.2 - - - +
660C LEU* 5.1 0.6 - - - +
669C ILE* 4.4 11.4 - - - -
670C SER* 3.0 15.1 + - - -
672C MET* 1.3 75.8 - - - +
674C ILE* 1.3 61.9 + - - +
675C ASP 3.3 1.8 - - - -
676C LYS* 3.8 7.1 - - - +
677C ALA* 2.9 33.5 + - - +
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Residues in contact with ILE 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A THR* 6.2 1.6 - - + -
447A TYR* 3.6 22.2 - - + +
457A LEU* 4.0 16.6 - - + +
657C MET* 5.0 7.0 - - + -
660C LEU* 3.9 31.3 - - + +
661C VAL* 5.1 8.1 - - + -
664C HIS* 3.4 42.6 - - + -
669C ILE* 3.6 17.7 - - + -
670C SER 3.5 11.2 - - - +
671C ILE* 3.1 10.0 + - + -
673C SER* 1.3 75.6 - - - +
675C ASP* 1.3 61.2 + - - +
678C VAL* 3.4 25.7 + - + +
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Residues in contact with ASP 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A TYR* 3.8 11.8 + - + +
453A ALA* 5.9 0.2 - - - -
456A ARG* 3.3 33.9 + - - +
457A LEU* 3.1 26.4 - - + +
671C ILE 3.7 6.7 + - - +
672C MET* 5.0 3.4 - - - +
673C SER 3.3 0.2 - - - -
674C ILE* 1.3 81.5 - - - +
676C LYS* 1.3 57.4 + - - +
678C VAL* 3.7 2.5 + - - +
679C THR* 2.8 38.2 + - - -
682C ARG* 5.7 0.9 + - - -
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Residues in contact with LYS 676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C MET* 4.0 31.9 - - + +
672C MET 3.3 21.7 + - - +
673C SER* 3.5 6.8 + - - +
674C ILE 3.4 0.2 - - - -
675C ASP* 1.3 80.4 - - - +
677C ALA* 1.3 58.7 + - - +
679C THR* 3.7 9.4 - - + +
680C LYS* 3.4 35.2 + - + +
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Residues in contact with ALA 677 (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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636C CYS* 4.7 16.2 - - + +
637C MET* 5.5 4.0 - - + +
640C VAL* 4.1 10.9 - - + +
656C PHE* 4.4 9.2 - - + -
660C LEU* 4.1 24.2 - - + -
673C SER* 2.9 19.1 + - - +
676C LYS* 1.3 74.7 - - - +
678C VAL* 1.3 60.4 + - - +
679C THR 3.2 1.6 - - - -
680C LYS* 3.3 8.2 + - - +
681C LEU* 3.1 25.6 + - - +
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Residues in contact with VAL 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU* 5.6 5.6 - - + -
656C PHE* 4.3 7.4 - - + -
657C MET* 3.7 35.4 - - + -
660C LEU* 3.6 20.6 - - + -
674C ILE* 3.4 19.4 + - + +
675C ASP* 4.3 3.4 - - - +
677C ALA* 1.3 72.5 - - - +
679C THR* 1.3 64.3 + - - +
681C LEU* 3.9 9.4 - - + -
682C ARG* 3.3 60.7 + - + +
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Residues in contact with THR 679 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 3.3 27.4 + - - +
675C ASP* 2.8 27.7 + - - -
676C LYS* 3.7 12.7 - - + +
678C VAL* 1.3 76.2 - - - +
680C LYS* 1.3 60.3 + - + +
681C LEU 3.2 0.3 + - - -
682C ARG* 3.3 3.8 + - - +
683C GLU* 2.9 43.3 + - + +
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Residues in contact with LYS 680 (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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637C MET* 4.6 9.4 - - + +
640C VAL* 4.0 19.5 - - + -
641C GLU* 3.8 36.4 - - - +
676C LYS* 3.4 27.7 + - + +
677C ALA* 3.3 8.3 + - - +
679C THR* 1.3 79.5 - - + +
681C LEU* 1.3 58.9 + - - +
683C GLU* 4.0 16.5 - - - +
684C MET* 3.0 40.7 + - + +
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Residues in contact with LEU 681 (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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640C VAL* 4.6 11.4 - - + +
644C GLY* 3.6 36.8 - - - +
647C ILE* 4.0 13.5 - - + -
648C ILE* 3.8 5.5 - - + +
653C CYS* 3.6 38.8 - - + +
656C PHE* 3.9 23.1 - - + -
657C MET* 6.1 0.7 - - + -
677C ALA 3.1 15.8 + - - +
678C VAL* 4.1 11.0 - - + +
679C THR 3.2 0.6 - - - -
680C LYS* 1.3 76.3 - - - +
682C ARG* 1.3 67.9 + - + +
684C MET* 3.6 15.1 - - - +
685C GLN* 3.5 15.7 - - - +
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Residues in contact with ARG 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 2.8 30.9 + - - +
457A LEU* 3.0 26.1 + - - +
458A ILE 4.4 1.6 + - - -
459A GLY* 3.9 15.6 - - - -
653C CYS* 6.4 0.4 - - + -
657C MET* 4.6 5.0 - - - +
675C ASP* 5.7 0.8 + - - -
678C VAL* 3.3 41.1 + - + +
679C THR* 4.2 2.6 - - - +
681C LEU* 1.3 80.6 - - + +
683C GLU* 1.3 63.6 + - - +
684C MET 3.3 0.7 - - - -
685C GLN* 3.5 37.0 + - - +
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Residues in contact with GLU 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C THR* 2.9 31.5 + - + +
680C LYS* 4.1 16.2 - - - +
681C LEU 3.4 0.2 - - - -
682C ARG* 1.3 78.8 - - - +
684C MET* 1.3 58.3 + - + +
685C GLN 3.5 1.8 - - - -
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Residues in contact with MET 684 (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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640C VAL 4.0 24.2 - - - +
641C GLU* 5.1 5.4 - - - -
644C GLY* 4.5 15.5 - - - +
645C GLN* 4.6 18.2 + - - +
648C ILE* 4.3 9.9 - - + -
680C LYS* 3.0 36.5 + - + +
681C LEU* 3.6 14.8 - - - +
683C GLU* 1.3 78.1 - - + +
685C GLN* 1.3 64.3 + - - +
268E LYS* 4.8 7.8 + - - -
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Residues in contact with GLN 685 (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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648C ILE* 3.6 35.8 - - + +
653C CYS* 4.6 11.3 - - - -
681C LEU* 3.5 13.6 - - - +
682C ARG* 3.5 40.8 + - - +
683C GLU 4.9 1.8 - - - -
684C MET* 1.3 83.1 - - - +
268E LYS* 4.7 17.4 + - - -
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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