Contacts of the helix formed by residues 601 - 612 (chain C) in PDB entry 2DB3
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 ILE 601 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566C MET* 3.7 30.7 - - + -
567C PRO* 3.6 25.1 - - + +
568C SER 3.8 10.3 - - - +
569C LYS 3.6 4.7 - - - +
570C ILE* 3.5 47.1 - - + +
573C TYR* 4.9 0.9 - - + -
593C PHE* 4.4 4.3 - - + -
598C ASP* 3.0 24.9 + - + +
600C ALA* 1.3 77.3 - - + +
602C ALA* 1.3 60.8 + - - +
603C ALA 3.4 1.8 - - - -
604C ASP* 3.4 9.0 + - + +
605C LEU* 2.9 26.3 + - + +
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Residues in contact with ALA 602 (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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593C PHE* 4.0 17.0 - - + -
598C ASP 3.7 0.8 + - - -
599C ARG* 3.3 38.3 + - - +
600C ALA 3.5 0.2 - - - -
601C ILE* 1.3 75.6 - - - +
603C ALA* 1.3 68.7 + - - +
605C LEU* 3.1 7.0 + - - +
606C VAL* 2.8 29.0 + - - +
620C LEU* 3.7 17.9 - - + +
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Residues in contact with ALA 603 (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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599C ARG 4.7 1.8 + - - -
600C ALA 4.9 3.9 + - - +
601C ILE 3.4 0.4 - - - -
602C ALA* 1.3 78.8 - - - +
604C ASP* 1.3 65.4 + - - +
606C VAL* 3.2 9.2 + - - +
607C LYS* 3.2 37.2 + - - +
620C LEU 5.6 0.4 - - - -
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Residues in contact with ASP 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ILE* 3.8 37.7 + - + +
600C ALA 5.0 5.6 + - - +
601C ILE* 3.4 12.9 + - + +
602C ALA 3.3 0.4 - - - -
603C ALA* 1.3 80.5 - - - +
605C LEU* 1.3 62.9 + - - +
607C LYS* 3.2 27.5 + - - +
608C ILE* 3.0 25.6 + - + +
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Residues in contact with LEU 605 (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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469C ILE* 4.2 18.2 - - + -
566C MET* 3.6 23.3 - - + -
570C ILE* 3.7 9.3 - - + +
573C TYR* 3.7 43.7 - - + +
593C PHE* 4.4 5.4 - - + -
601C ILE 2.9 19.0 + - - +
602C ALA* 3.1 5.6 + - - +
604C ASP* 1.3 74.3 - - - +
606C VAL* 1.3 65.8 + - - +
608C ILE* 3.3 1.6 + - + -
609C LEU* 2.9 38.6 + - + +
620C LEU* 4.0 32.3 - - + -
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Residues in contact with VAL 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C ALA 2.8 23.8 + - - +
603C ALA* 3.2 10.1 + - - +
605C LEU* 1.3 75.7 - - - +
607C LYS* 1.3 58.9 + - + +
609C LEU* 3.1 11.1 + - - +
610C GLU* 2.9 56.4 + - + +
616C VAL* 4.2 8.3 - - + -
620C LEU* 4.0 30.5 - - + +
621C ARG* 3.8 24.5 - - + +
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Residues in contact with LYS 607 (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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603C ALA* 3.2 23.6 + - - +
604C ASP* 3.5 25.7 + - - +
606C VAL* 1.3 81.6 - - + +
608C ILE* 1.3 60.6 + - + +
610C GLU* 3.4 10.8 + - - +
611C GLY* 2.8 27.0 + - - -
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Residues in contact with ILE 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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459C GLY 4.0 17.7 - - - +
460C GLY* 5.0 2.2 - - - -
461C ALA* 3.7 24.1 + - + +
467C GLN* 3.9 6.3 - - - +
570C ILE* 3.8 28.5 - - + -
573C TYR* 3.9 23.3 - - + -
574C VAL* 3.7 19.1 - - + -
604C ASP* 3.0 15.3 + - + +
605C LEU* 3.9 4.9 - - + +
607C LYS* 1.3 79.9 - - + +
609C LEU* 1.3 62.3 + - - +
611C GLY* 3.3 2.2 + - - +
612C SER* 2.8 28.1 + - - -
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Residues in contact with LEU 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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467C GLN* 3.5 38.8 - - + +
469C ILE* 4.1 18.4 - - + -
573C TYR* 4.2 4.9 - - - +
605C LEU* 2.9 26.6 + - + +
606C VAL* 3.5 5.4 - - - +
608C ILE* 1.3 77.8 - - - +
610C GLU* 1.3 60.4 + - - +
612C SER* 3.2 10.1 + - - -
614C GLN* 2.9 40.7 + - + -
615C THR 4.2 13.0 - - - +
616C VAL* 4.2 11.4 - - + -
617C PRO* 4.3 3.6 - - + -
620C LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 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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606C VAL* 2.9 30.3 + - - +
607C LYS* 3.9 8.8 - - - +
609C LEU* 1.3 75.6 - - - +
611C GLY* 1.3 62.3 + - - +
612C SER 3.4 0.5 + - - -
613C GLY* 3.5 9.4 + - - -
614C GLN 4.5 4.7 - - - +
616C VAL* 3.6 15.6 - - + +
621C ARG* 2.7 29.6 + - - -
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Residues in contact with GLY 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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457C ILE* 4.1 24.4 - - - +
460C GLY* 6.5 0.7 - - - -
461C ALA 5.4 2.0 - - - +
607C LYS 2.8 17.0 + - - -
608C ILE* 3.3 2.9 + - - -
609C LEU 3.2 0.2 - - - -
610C GLU* 1.3 79.2 - - - +
612C SER* 1.3 56.6 + - - +
613C GLY 3.5 0.4 - - - -
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Residues in contact with SER 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ALA* 3.7 26.8 - - - +
463C SER* 3.5 27.0 - - - -
467C GLN* 3.0 28.1 + - - -
608C ILE 2.8 21.9 + - - -
609C LEU 3.2 3.9 + - - -
611C GLY* 1.3 76.5 - - - +
613C GLY* 1.3 57.1 + - - +
614C GLN* 2.9 20.2 + - - +
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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