Contacts of the helix formed by residues 613 - 623 (chain B) in PDB entry 3O8C
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 HIS 613 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B VAL* 3.6 33.5 + - + +
570B ARG* 6.0 2.4 - - - +
571B ALA* 4.5 13.9 + - + +
597B PRO* 3.9 23.2 - - + +
610B THR 5.1 0.8 + - - -
611B LEU 3.5 1.2 - - - -
612B THR* 1.3 82.5 + - - +
614B PRO* 1.3 85.2 - - + +
615B ILE* 3.1 38.3 + - + +
616B THR* 3.2 15.3 + - - +
617B LYS* 3.0 24.9 + - - +
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Residues in contact with PRO 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B THR 3.9 4.3 - - - +
613B HIS* 1.3 109.3 - - + +
615B ILE* 1.3 55.4 + - + +
617B LYS* 3.3 10.1 + - + +
618B TYR* 2.7 33.1 + - - +
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Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLY 3.7 20.4 - - - +
539B LEU* 3.8 27.1 - - + -
540B THR* 5.3 3.1 - - - +
563B TYR* 4.0 19.1 - - + +
567B VAL* 4.2 4.7 - - + -
599B LEU* 3.8 19.1 - - + -
613B HIS* 3.1 26.1 + - + +
614B PRO* 1.3 78.6 - - + +
616B THR* 1.3 54.4 + - - +
618B TYR* 3.1 9.8 + - + +
619B ILE* 2.8 39.6 + - + +
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Residues in contact with THR 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 4.3 5.8 - - + -
443B THR* 4.3 0.8 - - + +
597B PRO 4.0 3.5 + - - -
598B LEU 2.7 29.3 + - - +
599B LEU* 3.5 16.7 - - - +
610B THR 4.7 0.5 + - - -
611B LEU* 3.9 32.5 - - + +
613B HIS* 3.2 20.7 + - - +
615B ILE* 1.3 77.3 - - - +
617B LYS* 1.3 57.5 + - - +
619B ILE* 3.3 4.5 + - - +
620B MET* 2.8 48.0 + - + +
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Residues in contact with LYS 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A THR* 3.9 27.1 - - - +
611B LEU 3.9 16.2 - - - +
612B THR* 3.6 25.8 + - - +
613B HIS 3.0 14.0 + - - +
614B PRO* 3.6 11.2 - - + +
616B THR* 1.3 77.1 - - - +
618B TYR* 1.3 61.4 + - - +
620B MET* 3.5 13.2 + - - +
621B ALA* 3.0 22.3 + - - +
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Residues in contact with TYR 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B SER* 2.6 33.7 + - - -
535B VAL* 4.0 4.0 - - - -
537B THR* 4.2 8.1 - - - +
538B GLY* 3.3 33.7 + - - -
614B PRO 2.7 17.0 + - - +
615B ILE* 3.1 15.2 + - + +
617B LYS* 1.3 74.2 - - - +
619B ILE* 1.3 72.9 + - + +
621B ALA* 3.0 11.8 + - + +
622B CYS* 3.0 37.1 + - - -
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Residues in contact with ILE 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B THR* 3.5 27.6 - - + -
444B PHE* 4.1 16.6 - - + -
535B VAL* 4.4 20.6 - - + -
539B LEU* 4.2 9.2 - - + -
599B LEU* 3.8 15.9 - - + +
600B TYR* 3.8 30.3 - - + -
615B ILE* 2.8 33.6 + - + +
616B THR 3.9 1.1 - - - +
618B TYR* 1.3 83.3 - - + +
620B MET* 1.3 64.1 + - - +
622B CYS* 3.0 15.4 + - - +
623B MET* 3.3 12.3 + - - +
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Residues in contact with MET 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A VAL* 5.8 8.7 - - + +
610A THR* 6.4 0.2 - - - -
611A LEU* 3.6 34.5 - - + +
161B ARG* 6.1 0.2 - - - -
442B PRO* 3.7 20.9 - - + +
443B THR* 3.6 20.2 - - + +
611B LEU* 4.8 9.2 - - - +
616B THR* 2.8 41.4 + - - +
617B LYS* 3.7 11.7 - - - +
619B ILE* 1.3 72.6 - - - +
621B ALA* 1.3 62.9 + - - +
623B MET* 3.2 22.2 + - - +
624B SER* 4.1 4.9 + - - -
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Residues in contact with ALA 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B LYS 3.0 13.8 + - - +
618B TYR* 3.0 15.9 + - + +
620B MET* 1.3 73.2 - - - +
622B CYS* 1.3 64.6 + - - +
623B MET 3.1 1.8 - - - -
624B SER* 3.1 21.8 + - - -
625B ALA 4.5 0.7 + - - -
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Residues in contact with CYS 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B PHE* 3.5 11.6 - - + -
534B SER* 3.4 32.9 + - - +
535B VAL* 4.0 16.2 - - + -
618B TYR* 3.0 50.0 + - - -
619B ILE* 3.0 12.1 + - - +
621B ALA* 1.3 76.3 - - - +
623B MET* 1.3 61.6 + - - +
624B SER 3.1 1.5 + - - -
625B ALA* 3.3 22.1 + - - +
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Residues in contact with MET 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG* 3.9 19.2 + - + +
438B PHE* 3.7 38.1 - - + -
440B LEU* 3.8 20.2 - - + +
442B PRO 4.5 1.3 - - - +
443B THR* 3.4 46.2 - - - +
444B PHE* 4.2 5.2 - - + -
531B PHE* 3.6 25.1 - - + -
619B ILE* 3.3 16.1 + - - +
620B MET* 3.3 13.7 - - - +
621B ALA 3.1 1.0 - - - -
622B CYS* 1.3 76.9 - - - +
624B SER* 1.3 58.4 + - - +
625B ALA 3.2 7.7 + - - +
627B LEU* 4.4 11.6 - - + +
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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