Contacts of the helix formed by residues 607 - 617 (chain C) in PDB entry 6UZA
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 PHE 607 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450C PHE* 4.7 4.3 - - - -
454C LEU* 3.9 29.8 - - + -
457C LEU* 4.9 6.1 - - + -
458C VAL* 5.0 3.1 - - + -
603C VAL* 3.2 34.1 - - + -
604C VAL 3.4 5.3 + - - +
605C LEU 3.2 1.2 - - - -
606C SER* 1.3 80.2 + - - +
608C SER* 1.3 53.9 + - - +
609C ARG 3.2 4.0 - - - -
610C ILE* 3.3 33.1 - - + +
1003C S9Y 3.5 13.8 - - + +
1005C Y01 3.8 31.0 - - + -
643D MET* 4.6 5.8 - - + -
646D VAL* 4.1 12.8 - - + -
647D ALA* 3.7 35.9 - - + -
650D ILE* 4.3 19.1 - - + -
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Residues in contact with SER 608 (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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526C TRP* 3.4 32.7 + - - -
529C LEU* 3.4 27.2 - - - +
533C MET* 5.7 0.3 - - - +
604C VAL 4.5 0.4 + - - -
605C LEU* 2.5 23.8 + - - -
606C SER 3.2 0.4 - - - -
607C PHE* 1.3 75.3 - - - +
609C ARG* 1.3 59.5 + - - +
610C ILE 3.2 5.9 + - - -
611C ALA* 3.7 5.6 + - - +
1003C S9Y 4.1 30.0 - - - +
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Residues in contact with ARG 609 (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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450C PHE* 3.7 34.7 - - + +
453C PHE* 6.3 1.3 - - - -
505C MET* 3.5 38.2 + - - +
509C GLU* 4.3 5.1 + - - -
526C TRP* 5.8 0.2 - - - +
530C ASP* 2.6 44.2 + - - +
533C MET* 3.7 23.1 - - + +
606C SER* 3.7 2.9 + - - +
607C PHE 3.2 2.0 - - - -
608C SER* 1.3 77.8 + - - +
610C ILE* 1.3 63.2 + - - +
611C ALA 3.1 2.0 - - - -
612C TYR* 3.5 28.5 + - + +
613C ILE* 4.3 2.1 + - - +
762C VAL* 5.6 4.0 - - - +
1002C R0G 3.5 50.6 + - + +
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Residues in contact with ILE 610 (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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450C PHE* 3.7 20.9 - - + -
454C LEU* 4.8 3.4 - - + -
607C PHE* 3.3 35.9 - - + +
608C SER 3.2 1.0 - - - -
609C ARG* 1.3 75.1 - - - +
611C ALA* 1.3 55.8 + - - +
612C TYR 3.1 5.6 - - - -
613C ILE* 3.3 13.7 + - + -
614C LEU* 2.9 46.6 + - + +
1003C S9Y 4.7 6.3 - - + -
1005C Y01 3.7 33.2 - - + -
643D MET* 3.7 36.6 - - + -
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Residues in contact with ALA 611 (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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526C TRP* 3.7 30.5 - - + +
608C SER 3.7 5.8 + - - +
609C ARG 3.1 0.2 - - - -
610C ILE* 1.3 79.0 - - - +
612C TYR* 1.3 54.8 + - - +
613C ILE 3.5 0.2 - - - -
614C LEU* 4.4 0.2 - - - -
615C PRO* 3.3 19.0 - - - +
624C GLN* 3.3 25.4 + - - +
1003C S9Y 3.4 39.8 - - + +
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Residues in contact with TYR 612 (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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443C PHE* 4.6 2.1 - - - -
526C TRP* 3.5 43.8 + + - +
527C ASN* 3.8 14.9 + - - -
530C ASP* 3.8 18.0 + - - -
609C ARG* 3.5 18.3 + - + +
610C ILE 3.1 1.0 - - - -
611C ALA* 1.3 79.6 - - - +
613C ILE* 1.3 59.1 + - - +
749C LEU* 3.3 23.6 - - - +
753C TYR* 4.9 4.5 + - - -
1002C R0G 3.7 69.1 + + + -
1003C S9Y 3.7 26.2 - - - -
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Residues in contact with ILE 613 (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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443C PHE* 3.8 33.0 - - + -
447C ALA* 4.2 13.7 - - + -
450C PHE* 4.5 13.7 - - + -
609C ARG 4.6 0.7 - - - +
610C ILE* 3.6 23.1 - - + +
612C TYR* 1.3 78.9 - - - +
614C LEU* 1.3 65.4 + - - +
615C PRO* 3.6 1.8 - - - -
616C ALA* 3.7 10.7 + - - +
1002C R0G 3.6 33.0 - - + -
1005C Y01 3.9 56.7 - - + +
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Residues in contact with LEU 614 (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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610C ILE* 2.9 27.2 + - + +
613C ILE* 1.3 73.6 - - - +
615C PRO* 1.3 57.1 - - - +
616C ALA 3.1 9.4 + - - -
617C ASN* 3.4 14.6 + - + +
620C PHE* 3.8 34.1 - - + +
621C GLY* 3.8 10.3 + - - -
624C GLN* 3.2 27.6 - - + +
1003C S9Y 5.0 13.2 - - + +
1005C Y01 4.2 18.2 - - + -
640D ILE* 4.8 13.2 - - + -
643D MET* 4.0 28.3 - - + -
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Residues in contact with PRO 615 (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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611C ALA 3.3 16.6 - - - +
612C TYR 4.3 0.9 - - - -
613C ILE 3.8 2.5 - - - -
614C LEU* 1.3 85.2 - - - +
616C ALA* 1.3 57.4 + - - -
617C ASN 3.2 2.8 + - - -
621C GLY* 4.0 16.4 - - - +
624C GLN* 3.3 23.6 - - - +
625C ILE* 6.1 2.9 - - + -
742C TRP* 3.9 9.6 + - + -
745C ALA* 4.9 20.6 - - + +
746C ARG* 3.6 22.2 - - - +
749C LEU* 3.7 22.2 - - + -
1003C S9Y 4.7 8.3 - - - -
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Residues in contact with ALA 616 (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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391C TRP* 5.4 0.4 - - + -
443C PHE* 3.7 29.2 - - + -
613C ILE 3.7 5.1 + - - +
614C LEU 3.1 1.4 - - - -
615C PRO* 1.3 77.8 - - - +
617C ASN* 1.3 58.5 + - - +
746C ARG* 4.2 15.7 + - + -
749C LEU* 3.7 26.6 - - + +
1005C Y01 3.7 37.0 - - + +
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Residues in contact with ASN 617 (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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403C MET* 4.8 17.4 - - - +
613C ILE 4.8 0.2 + - - -
614C LEU 3.4 11.6 + - - +
615C PRO 3.2 0.8 - - - -
616C ALA* 1.3 80.2 - - - +
618C GLU* 1.3 70.6 + - - +
619C SER* 3.3 12.4 + - - +
620C PHE* 3.3 35.0 - - + +
621C GLY* 3.5 10.4 + - - -
742C TRP* 3.3 21.1 + - - -
746C ARG* 5.5 0.4 - - - -
1005C Y01 3.2 37.0 - - + +
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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
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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