Contacts of the helix formed by residues 662 - 684 (chain C) in PDB entry 1SL0
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 THR 662 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C VAL* 4.6 5.2 - - - -
660C CYS* 3.3 1.5 - - - +
661C ARG* 1.3 114.0 - - + +
663C GLU* 1.3 66.1 + - - +
664C GLU* 3.2 12.2 + - - +
665C ILE* 2.9 29.0 + - + +
666C ALA* 2.8 22.8 + - - +
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Residues in contact with GLU 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C VAL* 4.1 16.1 - - + +
662C THR* 1.3 72.4 - - - +
664C GLU* 1.3 56.9 + - - +
666C ALA* 3.1 11.3 - - - +
667C GLN* 2.9 26.5 + - - +
696C MET* 3.6 21.5 - - + +
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Residues in contact with GLU 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C THR* 3.0 10.5 - - - +
663C GLU* 1.3 75.3 - - - +
665C ILE* 1.3 67.4 + - + +
667C GLN* 3.0 16.1 + - - +
668C VAL* 3.2 15.8 + - - +
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Residues in contact with ILE 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C LEU* 4.0 30.1 - - + -
645C ASP* 3.5 43.5 - - + +
646C PHE* 4.6 2.9 - - + -
660C CYS* 4.2 4.5 - - + -
661C ARG* 3.8 19.1 - - - +
662C THR* 3.2 30.5 - - + +
664C GLU* 1.3 75.1 - - + +
666C ALA* 1.3 58.3 + - - +
668C VAL* 2.8 26.5 + - - +
669C VAL* 2.8 27.1 + - + +
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Residues in contact with ALA 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C VAL* 4.3 5.4 - - + -
472C ALA* 4.0 4.1 - - + +
660C CYS* 3.2 26.2 - - + +
662C THR 2.8 12.6 + - - +
663C GLU* 3.1 20.4 - - - +
665C ILE* 1.3 78.4 - - - +
667C GLN* 1.3 58.4 + - - +
669C VAL* 3.5 3.3 + - - +
670C ILE* 3.1 27.2 + - - +
696C MET* 3.9 22.7 - - + -
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Residues in contact with GLN 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C GLU 2.9 12.5 + - - +
664C GLU* 3.0 10.0 + - - +
666C ALA* 1.3 73.4 - - - +
668C VAL* 1.3 64.8 + - + +
670C ILE* 3.5 8.2 + - - +
671C GLU* 3.2 20.6 + - - +
696C MET* 3.6 16.8 - - + +
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Residues in contact with VAL 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C LEU* 4.2 8.3 - - + -
636C LYS* 5.8 4.9 - - + -
638C LEU* 4.3 13.5 - - + -
664C GLU 3.2 11.7 + - - +
665C ILE* 2.8 13.3 + - - +
667C GLN* 1.3 75.6 - - + +
669C VAL* 1.3 53.9 + - - +
671C GLU* 2.8 8.2 + - - +
672C THR* 2.4 53.5 + - - +
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Residues in contact with VAL 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ALA* 4.9 3.1 - - + -
629C THR* 4.9 5.4 - - + -
633C LEU* 3.3 40.8 - - + -
646C PHE* 5.0 2.2 - - + -
658C VAL* 3.9 28.3 - - + -
660C CYS* 3.4 24.9 - - - -
665C ILE* 2.8 27.3 + - + +
666C ALA 3.7 3.1 - - - +
668C VAL* 1.3 75.3 - - + +
670C ILE* 1.3 55.4 + - - +
672C THR* 3.5 0.3 - - - -
673C ALA* 2.6 39.5 + - + +
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Residues in contact with ILE 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ALA* 3.9 16.2 - - + -
473C GLY 5.5 0.7 - - - +
474C ILE* 5.3 6.1 - - + -
666C ALA 3.1 15.5 + - - +
667C GLN* 3.7 7.9 - - - +
668C VAL 3.2 0.4 - - - -
669C VAL* 1.3 77.2 - - - +
671C GLU* 1.3 59.4 + - - +
673C ALA* 3.8 7.7 - - - +
674C GLN* 3.7 14.4 + - - +
692C THR* 4.9 3.1 + - - -
694C GLY* 3.2 31.9 + - - +
695C LYS* 3.7 31.9 - - - +
696C MET* 3.9 23.6 - - + +
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Residues in contact with GLU 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C GLN 3.2 12.4 + - - +
668C VAL* 2.8 10.4 + - + +
670C ILE* 1.3 74.0 - - - +
672C THR* 1.3 62.3 + - - +
673C ALA 3.2 1.6 - - - -
674C GLN* 3.0 27.1 + - - +
675C GLU* 3.3 6.9 + - - +
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Residues in contact with THR 672 (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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629C THR* 3.6 20.2 - - + +
632C MET* 3.7 20.4 - - + -
633C LEU* 3.2 35.2 - - + +
636C LYS* 6.0 1.2 - - - +
668C VAL* 2.4 40.4 + - - +
669C VAL 3.5 2.0 - - - -
671C GLU* 1.3 69.6 - - - +
673C ALA* 1.3 65.1 + - - +
674C GLN 3.2 0.7 + - - -
675C GLU* 3.5 7.3 + - + +
676C ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 673 (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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474C ILE* 4.1 17.3 - - + -
625C TRP* 2.6 44.0 + - + -
629C THR* 3.8 22.0 - - + +
656C ILE* 5.2 1.6 - - + -
669C VAL* 2.6 21.6 + - + +
670C ILE 3.8 7.4 - - - +
672C THR* 1.3 75.0 - - - +
674C GLN* 1.3 62.7 + - - +
677C MET* 3.4 4.0 + - - +
692C THR* 4.2 4.0 + - - +
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Residues in contact with GLN 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C ILE 3.7 7.0 + - - +
671C GLU* 3.0 19.1 + - - +
673C ALA* 1.3 75.5 - - - +
675C GLU* 1.3 69.6 + - - +
677C MET* 3.0 14.4 + - - +
678C ARG* 3.0 19.6 + - + +
692C THR* 3.8 15.5 + - - +
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Residues in contact with GLU 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632C MET* 4.4 14.8 - - + -
671C GLU 3.3 6.8 + - - +
672C THR* 3.9 7.9 - - - +
674C GLN* 1.3 77.0 - - - +
676C ALA* 1.3 55.4 + - - +
678C ARG* 2.7 14.1 + - - +
679C TRP* 2.7 36.0 + - - +
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Residues in contact with ALA 676 (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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625C TRP* 3.8 5.2 - - + -
628C LYS* 4.0 4.3 - - + -
629C THR* 3.3 42.4 - - - +
632C MET* 3.7 17.1 - - - -
672C THR 3.2 12.8 + - - +
673C ALA 3.8 1.3 - - - +
675C GLU* 1.3 77.8 - - - +
677C MET* 1.3 58.2 + - - +
679C TRP* 3.0 7.2 - - - +
680C VAL* 2.8 33.4 + - - +
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Residues in contact with MET 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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476C ALA* 4.1 16.2 - - + -
479C LEU* 5.2 2.0 - - + -
621C ILE* 4.2 23.3 - - + +
625C TRP* 3.2 66.0 - - + +
673C ALA 3.4 2.6 + - - +
674C GLN* 3.0 9.9 + - - +
676C ALA* 1.3 74.8 - - - +
678C ARG* 1.3 68.4 + - + +
680C VAL* 3.0 18.3 + - - +
681C GLY* 3.1 9.0 + - - -
690C LEU* 4.0 19.7 - - + +
691C ASP* 4.0 20.6 - - - +
692C THR* 3.7 21.1 - - + -
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Residues in contact with ARG 678 (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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674C GLN* 3.0 17.8 + - + +
675C GLU* 2.7 17.2 + - - +
677C MET* 1.3 72.3 - - + +
679C TRP* 1.3 58.0 + - - +
681C GLY* 2.9 21.6 + - - -
682C ASP* 3.2 6.8 + - - +
689C LEU* 4.8 12.4 - - - +
690C LEU* 3.6 20.4 - - - +
691C ASP* 2.8 28.0 + - - -
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Residues in contact with TRP 679 (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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624C LEU* 3.5 24.2 - - + -
628C LYS* 3.8 41.9 - - + +
632C MET* 4.8 8.5 - - + -
675C GLU 2.7 15.2 + - - +
676C ALA* 3.0 15.5 - - - +
678C ARG* 1.3 67.8 - - - +
680C VAL* 1.3 76.5 + - + +
681C GLY 2.7 15.0 + - - -
682C ASP* 2.9 7.5 + - + +
683C HIS* 2.8 58.6 + + + +
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Residues in contact with VAL 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C ILE* 3.9 20.6 - - + +
624C LEU* 3.3 33.7 - - + +
625C TRP* 3.9 15.9 - - - -
628C LYS* 4.6 1.6 - - + -
676C ALA 2.8 20.6 + - - +
677C MET* 3.0 11.4 + - - +
679C TRP* 1.3 83.3 - - + +
681C GLY* 1.3 61.2 + - - +
683C HIS* 3.7 4.1 - - + +
684C TRP* 3.2 45.3 + - + +
686C PHE* 5.3 0.7 - - - +
690C LEU* 5.4 3.0 - - + +
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Residues in contact with GLY 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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677C MET 3.1 6.7 + - - -
678C ARG* 2.9 9.7 + - - -
679C TRP 2.7 3.0 + - - -
680C VAL* 1.3 76.2 - - - +
682C ASP* 1.3 65.2 + - - -
684C TRP 3.1 2.4 + - - -
685C ASN 3.0 3.3 + - - -
686C PHE* 3.0 41.0 + - - +
690C LEU* 4.8 12.3 - - - -
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Residues in contact with ASP 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C ARG 3.2 7.0 + - - +
679C TRP* 2.9 10.9 + - + +
681C GLY* 1.3 71.0 - - - +
683C HIS* 1.3 67.0 + - - +
685C ASN* 2.8 26.2 + - - +
686C PHE 5.1 0.2 - - - +
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Residues in contact with HIS 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C GLU* 2.9 24.4 + - - -
624C LEU* 4.9 4.4 - - + +
679C TRP* 2.8 55.7 + + + +
680C VAL* 3.7 9.4 - - - +
682C ASP* 1.3 79.6 + - - +
684C TRP* 1.3 93.9 + + - +
685C ASN* 3.7 5.5 + - - -
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Residues in contact with TRP 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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212C GLU* 3.0 39.8 + - + -
216C ILE* 5.7 2.5 - - + -
486C HIS* 4.6 3.6 - - - -
596C LEU* 3.3 50.2 + - + +
597C ASP* 4.1 14.1 - - + -
620C LEU* 3.7 22.7 - - + -
621C ILE* 3.9 10.8 - - + -
624C LEU* 3.5 42.2 - - + -
680C VAL* 3.2 24.5 + - + +
681C GLY 3.1 4.6 + - - +
683C HIS* 1.3 95.7 + + - +
685C ASN* 1.3 74.3 + - - +
686C PHE* 3.1 10.4 + + + -
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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