Contacts of the helix formed by residues 570 - 581 (chain C) in PDB entry 6CIM
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 MET 570 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566C ALA 3.0 17.7 - - - +
567C LEU* 3.3 12.1 - - - +
569C ASP* 1.3 74.9 - - - +
571C GLU* 1.3 64.4 + - - +
572C GLU 3.1 3.4 - - - -
573C ASP* 2.8 29.2 + - + +
574C ILE* 3.0 17.6 + - + +
626C VAL* 4.0 22.9 - - + +
629C ILE* 3.9 20.0 - - - -
641C PHE* 3.4 37.0 - - + -
643C GLU* 5.5 0.2 - - - +
653C LYS* 5.6 5.6 - - - +
997C LYS* 3.6 27.1 - - + +
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Residues in contact with GLU 571 (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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567C LEU 3.0 10.2 + - - +
568C MET* 3.2 43.1 + - - +
569C ASP 3.3 0.4 - - - -
570C MET* 1.3 74.9 - - - +
572C GLU* 1.3 69.1 + - + +
574C ILE* 3.1 5.1 + - - +
575C LEU* 3.0 39.3 + - + +
691C MET* 4.0 22.3 - - + +
692C GLY* 3.4 30.0 + - - -
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Residues in contact with GLU 572 (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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569C ASP 4.6 4.2 + - - +
570C MET 3.1 1.2 - - - -
571C GLU* 1.3 82.7 - - + +
573C ASP* 1.3 63.5 + - - +
575C LEU* 3.4 6.5 + - + +
576C GLU* 2.9 31.9 + - - +
579C ARG* 4.8 1.6 + - - -
998C TYR* 4.2 26.3 - - + -
1001C LYS* 5.1 12.7 - - - +
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Residues in contact with ASP 573 (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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569C ASP 4.7 1.2 - - - +
570C MET* 2.8 28.1 + - + +
572C GLU* 1.3 77.1 - - - +
574C ILE* 1.3 60.5 + - - +
576C GLU* 3.9 7.0 - - - +
577C GLY* 2.9 25.5 + - - -
640C VAL 4.1 4.6 - - - +
641C PHE* 4.8 20.8 - - + +
997C LYS* 4.5 14.6 - - - +
1001C LYS* 2.6 41.9 + - - -
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Residues in contact with ILE 574 (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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567C LEU* 4.2 17.3 - - + +
570C MET* 3.0 20.3 + - + +
571C GLU 3.5 5.8 - - - +
573C ASP* 1.3 75.1 - - - +
575C LEU* 1.3 67.5 + - - +
577C GLY 3.1 0.3 + - - -
578C MET* 2.9 25.0 + - - +
591C PHE* 4.3 20.0 - - + -
629C ILE* 3.7 32.5 - - + -
640C VAL* 2.9 25.5 - - + +
641C PHE* 5.0 6.1 - - + -
691C MET* 3.9 30.1 - - + -
698C PHE* 4.8 8.3 - - + -
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Residues in contact with LEU 575 (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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571C GLU* 3.0 38.9 + - + +
572C GLU* 4.0 5.4 - - - +
574C ILE* 1.3 77.1 - - - +
576C GLU* 1.3 62.4 + - - +
578C MET* 3.2 14.8 + - - +
579C ARG* 3.0 43.7 + - - +
585C ASP* 3.8 11.9 - - + +
691C MET* 3.9 19.5 - - + -
692C GLY* 5.0 6.7 - - - -
696C ARG* 3.9 34.5 - - - +
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Residues in contact with GLU 576 (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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572C GLU 2.9 18.7 + - - +
573C ASP* 4.2 7.5 - - - +
575C LEU* 1.3 77.8 - - - +
577C GLY* 1.3 58.5 + - - +
579C ARG* 3.4 29.3 + - + +
580C SER* 2.9 28.2 + - - -
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Residues in contact with GLY 577 (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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573C ASP 2.9 14.3 + - - -
574C ILE 3.1 0.2 + - - -
576C GLU* 1.3 75.2 - - - +
578C MET* 1.3 64.7 + - - +
580C SER* 3.0 9.0 + - - -
581C GLN* 3.0 27.9 + - - +
640C VAL* 3.2 28.7 - - - -
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Residues in contact with MET 578 (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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574C ILE* 2.9 20.9 + - - +
575C LEU* 3.4 17.0 - - - +
577C GLY* 1.3 74.7 - - - +
579C ARG* 1.3 61.2 + - - +
581C GLN* 3.2 7.1 + - - -
583C LEU* 3.0 33.9 + - + +
584C ASP 3.1 31.2 - - - +
585C ASP* 3.8 13.2 - - - +
587C LEU* 3.6 34.8 - - + +
591C PHE* 4.0 16.4 - - + -
631C ILE* 3.7 14.1 - - + -
640C VAL* 3.5 24.6 - - + +
696C ARG* 4.2 5.2 - - - -
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Residues in contact with ARG 579 (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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572C GLU 4.8 1.4 + - - -
575C LEU* 3.0 22.7 + - - +
576C GLU* 3.6 40.8 - - + +
578C MET* 1.3 76.4 - - - +
580C SER* 1.3 57.5 + - - +
582C ASP* 2.9 22.3 + - - -
583C LEU 3.9 9.2 - - - +
585C ASP* 2.8 58.8 + - - +
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Residues in contact with SER 580 (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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576C GLU* 2.9 20.4 + - - -
577C GLY* 3.0 10.3 + - - -
579C ARG* 1.3 76.6 - - - +
581C GLN* 1.3 70.3 + - - +
582C ASP* 3.3 1.3 + - - +
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Residues in contact with GLN 581 (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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577C GLY 3.0 16.2 + - - +
578C MET* 3.2 6.0 + - - +
579C ARG 3.1 0.4 - - - -
580C SER* 1.3 88.5 + - - +
582C ASP* 1.3 65.2 + - - +
583C LEU* 3.0 20.6 - - + +
638C VAL* 3.1 29.2 - - + +
639C LYS* 3.5 25.9 + - - +
640C VAL* 5.1 1.6 - - + -
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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