Contacts of the helix formed by residues 680 - 689 (chain C) in PDB entry 1SO2
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 PRO 680 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673C LYS* 4.1 22.0 - - + +
676C ASN* 4.8 3.6 - - - +
678C ASN 3.2 10.9 - - - +
679C PHE* 1.3 88.7 - - + +
681C ILE* 1.3 65.4 + - - +
682C PHE 3.2 2.9 - - - -
683C GLU* 3.0 45.3 + - + +
684C LEU* 3.4 8.7 + - - +
947C LEU* 4.8 8.1 - - + -
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Residues in contact with ILE 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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679C PHE* 2.4 49.5 + - + +
680C PRO* 1.3 72.1 - - - +
682C PHE* 1.3 90.4 + - + +
684C LEU* 3.3 4.0 - - - +
685C VAL* 3.1 24.9 + - - +
695C ILE* 4.5 9.9 - - + -
740C ILE* 3.6 36.3 - - + +
743C THR* 4.2 11.0 - - + -
744C ASP* 3.9 29.2 - - + +
947C LEU* 4.5 5.5 - - + +
951C TRP* 4.3 6.7 - - + +
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Residues in contact with PHE 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PRO 3.1 1.6 + - - -
681C ILE* 1.3 88.3 - - + +
683C GLU* 1.3 66.8 + - + +
685C VAL* 3.3 11.8 + - + +
686C GLU* 3.0 23.4 + - - +
740C ILE* 4.3 24.5 - - + -
946C ASP 5.7 0.2 - - - -
947C LEU* 4.0 17.3 - - + -
950C LYS* 3.5 53.8 - - + -
951C TRP* 3.5 38.4 - + - -
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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
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680C PRO* 3.0 39.3 + - + +
682C PHE* 1.3 77.7 - - + +
684C LEU* 1.3 55.2 + - - +
686C GLU* 3.0 7.5 + - - +
687C LYS* 2.8 36.9 + - - +
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Residues in contact with LEU 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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670C LEU* 5.0 19.3 - - + -
673C LYS* 5.4 15.9 - - + +
679C PHE* 3.5 37.2 - - + -
680C PRO 3.4 3.5 + - - +
681C ILE 3.3 8.5 - - - +
683C GLU* 1.3 80.2 - - - +
685C VAL* 1.3 62.0 + - - +
687C LYS* 3.3 10.8 + - + +
688C MET* 3.1 45.6 + - + +
695C ILE* 3.7 28.7 - - + -
699C VAL* 4.3 13.2 - - + -
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Residues in contact with VAL 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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681C ILE 3.1 16.8 - - - +
682C PHE* 3.4 15.7 - - + +
683C GLU 3.1 0.2 - - - -
684C LEU* 1.3 77.9 - - - +
686C GLU* 1.3 63.5 + - - +
688C MET* 3.2 14.1 + - - +
689C GLY* 3.6 7.6 + - - +
692C SER* 3.8 22.6 - - - +
695C ILE* 3.7 23.6 - - + -
740C ILE* 4.3 31.6 - - + -
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Residues in contact with GLU 686 (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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682C PHE 3.0 14.0 + - - +
683C GLU* 3.0 7.4 + - - +
685C VAL* 1.3 78.2 - - - +
687C LYS* 1.3 63.5 + - - +
688C MET 3.4 0.3 + - - -
689C GLY* 3.4 11.5 + - - +
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Residues in contact with LYS 687 (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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669C SER* 4.4 6.7 + - - -
673C LYS* 3.3 29.1 - - - +
683C GLU 2.8 16.4 + - - +
684C LEU* 3.8 10.8 - - + +
686C GLU* 1.3 78.6 - - - +
688C MET* 1.3 61.0 + - + +
689C GLY 3.3 0.4 + - - -
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Residues in contact with MET 688 (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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684C LEU* 3.1 34.0 + - + +
685C VAL* 3.7 6.3 - - - +
686C GLU 3.2 0.6 - - - -
687C LYS* 1.3 79.1 - - + +
689C GLY* 1.3 63.9 + - - +
690C GLU 3.2 0.9 + - - -
691C LYS* 3.0 51.4 + - + +
692C SER* 3.8 11.4 - - - +
694C ARG* 3.8 20.4 - - + +
695C ILE* 4.0 29.8 - - - -
698C GLN* 4.3 14.8 - - + -
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Residues in contact with GLY 689 (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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685C VAL 3.6 4.2 + - - +
686C GLU* 3.4 11.8 + - - -
687C LYS 3.3 3.6 - - - -
688C MET* 1.3 75.9 - - - +
690C GLU* 1.3 59.8 + - - -
691C LYS 3.1 0.6 + - - -
692C SER* 3.0 24.8 + - - -
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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
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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