Contacts of the helix formed by residues 679 - 696 (chain C) in PDB entry 1U0O
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 679 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C GLU* 6.1 0.4 - - - -
653C ILE* 3.4 19.0 - - - +
654C GLY* 3.9 3.6 - - - -
655C PRO* 5.6 0.2 - - - -
677C LEU* 3.2 7.0 - - - +
678C SER* 1.3 82.8 + - - +
680C VAL* 1.3 64.8 + - - -
681C ASP* 3.3 3.8 - - - -
682C GLU* 3.5 15.8 + - - +
683C LEU 3.8 2.8 + - - -
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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
----------------------------------------------------------
525C LEU* 3.9 23.3 - - + -
529C GLU* 3.8 41.6 + - + +
532C VAL* 3.6 31.8 - - + +
533C LEU* 4.7 4.5 - - + +
653C ILE* 3.4 15.9 - - + +
679C GLY* 1.3 69.2 - - - -
681C ASP* 1.3 78.1 + - - +
683C LEU* 3.0 37.0 - - + +
684C GLU 3.8 0.3 + - - -
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Residues in contact with ASP 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL* 4.4 12.1 - - - +
679C GLY 3.3 1.2 - - - -
680C VAL* 1.3 85.9 - - - +
682C GLU* 1.3 65.0 + - - +
684C GLU* 2.9 26.5 + - - +
685C GLN* 4.1 3.7 + - - +
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Residues in contact with GLU 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C LEU 4.0 4.5 - - - +
677C LEU* 3.8 13.0 - - + -
678C SER* 2.4 56.0 + - - +
679C GLY 3.5 12.4 + - - +
680C VAL 3.2 0.4 - - - -
681C ASP* 1.3 77.4 - - - +
683C LEU* 1.3 62.5 + - - +
685C GLN* 2.9 42.9 - - - +
686C ARG* 2.9 35.8 + - - +
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Residues in contact with LEU 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL 4.6 1.1 - - - +
533C LEU* 4.1 24.0 - - + -
536C PHE* 3.7 47.1 - - + -
621C LEU* 4.6 2.2 - - + -
651C VAL* 4.2 6.7 - - + -
653C ILE* 3.1 39.0 - - + -
677C LEU* 3.4 11.8 - - + +
680C VAL* 3.0 41.4 + - + +
681C ASP 2.9 1.0 + - - -
682C GLU* 1.3 78.1 - - - +
684C GLU* 1.3 54.7 + - - +
686C ARG* 2.8 23.7 + - - +
687C ARG 3.4 8.8 + - - -
690C ILE* 5.2 1.3 - - + -
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Residues in contact with GLU 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL* 5.7 5.1 - - + +
536C PHE* 5.1 6.2 - - - +
680C VAL 3.8 1.7 + - - +
681C ASP* 2.9 17.3 + - - +
683C LEU* 1.3 78.3 - - - +
685C GLN* 1.3 57.9 + - + +
687C ARG* 2.8 36.7 + - - +
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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
----------------------------------------------------------
681C ASP 4.7 2.2 + - - +
682C GLU* 2.9 44.3 - - - +
684C GLU* 1.3 77.7 - - + +
686C ARG* 1.3 71.5 + - - +
687C ARG* 3.4 3.1 + - - -
688C ASP* 4.9 6.3 + - - +
689C GLU* 5.7 0.7 - - - +
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Residues in contact with ARG 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C PHE* 4.1 13.6 - - - +
676C LEU 3.6 7.5 + - - +
677C LEU* 2.9 45.2 - - + +
682C GLU* 2.9 42.6 + - - +
683C LEU* 2.8 11.9 + - - +
685C GLN* 1.3 84.6 - - - +
687C ARG* 1.3 69.0 + - - +
688C ASP 3.5 0.7 - - - -
689C GLU* 2.4 43.7 + - - +
690C ILE* 3.0 37.7 + - + +
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Residues in contact with ARG 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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535C ALA 4.9 0.2 + - - -
536C PHE* 3.7 40.1 + - + +
539C GLY* 3.6 39.2 + - - -
540C MET* 4.3 4.0 - - - -
543C ARG* 4.0 25.8 - - - +
683C LEU 3.4 4.2 + - - -
684C GLU* 2.8 41.7 + - - +
685C GLN 3.4 1.4 - - - -
686C ARG* 1.3 75.9 - - - +
688C ASP* 1.3 71.6 + - - +
689C GLU 2.8 1.4 + - - -
690C ILE 3.0 0.2 + - - -
691C VAL* 2.7 41.2 + - + +
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Residues in contact with ASP 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C PHE* 3.9 26.6 + - - +
543C ARG* 4.9 12.2 + - - +
685C GLN 4.9 5.0 + - - +
686C ARG 3.5 0.6 - - - -
687C ARG* 1.3 81.1 + - - +
689C GLU* 1.3 54.3 + - - +
691C VAL* 3.8 4.4 - - - +
692C SER* 2.3 38.0 + - - -
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Residues in contact with GLU 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C PHE* 4.0 20.7 - - + -
685C GLN 5.4 0.6 + - - +
686C ARG* 2.4 50.6 + - - +
687C ARG 2.8 3.4 + - - -
688C ASP* 1.3 73.4 - - - +
690C ILE* 1.3 69.6 + - - +
692C SER* 2.8 8.6 + - - -
693C TYR* 2.7 25.9 + - + +
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Residues in contact with ILE 690 (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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536C PHE* 3.9 18.8 - - + -
540C MET* 4.2 16.2 - - + -
619C LEU* 3.8 29.6 - - + -
649C ILE* 5.3 0.2 - - + -
651C VAL* 4.3 23.8 - - + -
675C PHE* 4.0 32.5 - - + -
677C LEU* 5.3 0.2 - - + -
683C LEU* 5.2 1.6 - - + -
686C ARG* 3.0 28.9 + - + +
687C ARG 3.0 7.2 + - - +
689C GLU* 1.3 76.0 - - - +
691C VAL* 1.3 67.4 + - - +
693C TYR* 3.4 6.4 - - + +
694C LEU* 2.8 28.2 + - + +
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Residues in contact with VAL 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C PHE* 3.6 26.2 - - + -
509C CYS* 4.9 4.9 - - + -
540C MET* 3.2 39.3 - - + +
543C ARG* 4.2 18.4 - - + +
544C LEU* 5.6 2.9 - - + -
687C ARG* 2.7 44.4 + - + +
688C ASP* 3.8 4.3 - - - +
690C ILE* 1.3 74.6 - - - +
692C SER* 1.3 62.9 + - - +
694C LEU* 3.2 11.5 + - + +
695C CYS* 3.0 19.6 + - - +
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Residues in contact with SER 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C PHE* 3.5 33.9 - - - -
688C ASP 2.3 26.7 + - - -
689C GLU* 2.8 12.1 + - - -
691C VAL* 1.3 76.2 - - - +
693C TYR* 1.3 63.5 + - - +
695C CYS* 3.1 5.8 + - - +
696C ASP* 2.6 28.5 + - - +
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Residues in contact with TYR 693 (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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649C ILE* 3.8 23.6 - - + -
671C GLU* 2.5 31.2 + - - -
673C LYS* 3.1 44.9 - - + +
675C PHE* 3.7 26.7 - + + -
689C GLU* 2.7 19.6 + - + +
690C ILE* 3.4 8.7 - - + +
692C SER* 1.3 75.2 - - - +
694C LEU* 1.3 56.5 + - + +
696C ASP* 3.1 11.9 + - + +
697C LEU* 2.7 48.3 - - + +
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Residues in contact with LEU 694 (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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509C CYS* 5.2 0.9 - - - -
513C LEU* 3.5 24.4 - - + +
515C LEU* 3.5 25.1 - - + -
540C MET* 3.4 31.9 - - + -
544C LEU* 4.8 7.4 - - + -
617C ILE* 3.2 33.0 - - + +
619C LEU* 4.1 15.7 - - + -
649C ILE* 4.3 8.7 - - + -
690C ILE* 2.8 17.2 + - + +
691C VAL* 3.4 11.0 - - + +
693C TYR* 1.3 82.8 - - + +
695C CYS* 1.3 63.5 + - + +
696C ASP 3.5 0.2 - - - -
697C LEU* 4.1 8.0 + - - +
698C ALA* 4.8 1.4 + - - +
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Residues in contact with CYS 695 (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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507C PHE* 4.3 7.0 - - + -
509C CYS* 2.0 56.1 - - + -
511C LYS* 3.0 39.9 + - - -
513C LEU* 5.3 0.7 - - - -
691C VAL 3.0 14.6 + - - +
692C SER* 3.7 9.4 - - - +
693C TYR 3.1 0.6 - - - -
694C LEU* 1.3 76.9 - - + +
696C ASP* 1.3 60.7 + - - +
697C LEU 3.1 9.1 + - - -
698C ALA* 3.4 10.8 + - - +
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Residues in contact with ASP 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C PHE* 5.3 2.8 - - - -
511C LYS* 4.5 6.9 + - - +
692C SER* 2.6 25.4 - - - +
693C TYR* 3.1 13.7 + - + +
695C CYS* 1.3 79.2 - - - +
697C LEU* 1.3 62.1 + - + +
698C ALA 3.5 1.1 - - - +
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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