Contacts of the helix formed by residues 617 - 630 (chain C) in PDB entry 7ATU
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 LEU 617 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577C PRO* 5.5 6.7 - - + -
606C THR* 3.7 7.0 - - - +
607C LEU* 6.1 2.0 - - + +
610C HIS* 3.8 31.6 + - + +
615C LEU 3.8 1.2 + - - -
616C PRO* 1.3 72.7 - - - +
618C GLY* 1.3 65.1 + - - +
621C LEU* 3.3 38.6 - - + +
622C GLU* 5.2 5.2 - - + +
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Residues in contact with GLY 618 (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 THR* 5.4 1.8 - - - -
616C PRO* 3.2 11.5 - - - +
617C LEU* 1.3 83.6 - - - +
619C PRO* 1.3 78.1 - - - +
620C GLN 3.3 1.9 + - - -
622C GLU* 3.3 17.5 + - - +
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Residues in contact with PRO 619 (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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618C GLY* 1.3 83.5 - - - +
620C GLN* 1.3 59.8 + - + +
622C GLU* 3.4 5.2 + - + +
623C GLN* 2.8 29.6 + - - +
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Residues in contact with GLN 620 (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 TRP* 4.5 19.1 - - + +
618C GLY 3.3 0.8 - - - -
619C PRO* 1.3 80.4 - - + +
621C LEU* 1.3 69.4 + - + +
623C GLN* 3.0 8.1 + - - +
624C LEU* 2.9 30.4 + - - +
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Residues in contact with LEU 621 (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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578C SER* 3.2 35.9 - - - +
582C ILE* 3.8 7.9 - - + -
603C TRP* 3.8 41.5 - - + +
606C THR* 3.5 28.3 - - + +
607C LEU* 4.4 7.6 - - + +
617C LEU* 3.3 32.3 - - + +
618C GLY 3.7 0.6 + - - -
620C GLN* 1.3 79.6 - - + +
622C GLU* 1.3 58.0 + - - +
624C LEU* 3.4 6.4 + - + +
625C ASP* 2.9 29.6 + - - +
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Residues in contact with GLU 622 (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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617C LEU* 5.1 5.9 - - + +
618C GLY 3.3 17.3 + - - +
619C PRO* 3.7 4.7 - - + +
620C GLN 3.3 0.4 - - - -
621C LEU* 1.3 78.4 - - - +
623C GLN* 1.3 57.6 + - - +
625C ASP* 3.5 6.9 - - - +
626C ARG* 2.8 32.1 + - - +
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Residues in contact with GLN 623 (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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619C PRO 2.8 14.9 + - - +
620C GLN* 3.0 12.5 + - - +
622C GLU* 1.3 72.2 - - - +
624C LEU* 1.3 59.6 + - - +
625C ASP 2.9 9.6 + - - -
626C ARG* 3.3 3.1 + - - +
627C GLY* 3.0 22.3 + - - -
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Residues in contact with LEU 624 (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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578C SER* 5.7 2.9 - - - -
581C PRO* 3.4 25.2 - - + +
582C ILE* 5.7 4.9 - - + +
585C ARG* 6.3 4.0 - - + -
603C TRP* 5.6 17.3 - - + -
620C GLN 2.9 17.9 + - - +
621C LEU* 3.7 7.4 - - + +
623C GLN* 1.3 72.3 - - - +
625C ASP* 1.3 55.5 + - - +
627C GLY* 5.0 0.7 - - - +
628C PHE* 3.5 15.6 + - - +
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Residues in contact with ASP 625 (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 PRO* 3.6 15.1 - - + +
578C SER* 2.8 30.9 + - - +
581C PRO* 3.9 10.6 - - - +
621C LEU 2.9 16.8 + - - +
622C GLU* 3.5 9.0 - - - +
623C GLN 2.9 2.0 + - - -
624C LEU* 1.3 77.2 - - - +
626C ARG* 1.3 66.1 + - - +
627C GLY 3.3 0.7 - - - -
628C PHE* 3.5 1.4 + - - +
629C TRP* 3.0 40.6 + - - -
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Residues in contact with ARG 626 (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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622C GLU 2.8 20.1 + - - +
623C GLN* 4.2 3.1 - - - +
625C ASP* 1.3 72.6 + - - +
627C GLY* 1.3 62.5 + - - +
629C TRP* 3.2 6.6 + - - +
630C GLU* 3.0 24.4 + - - +
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Residues in contact with GLY 627 (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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623C GLN 3.0 15.5 + - - -
624C LEU* 4.8 0.7 - - - -
626C ARG* 1.3 77.0 - - - +
628C PHE* 1.3 61.2 + - - +
630C GLU* 3.7 10.9 - - - +
631C THR* 3.1 18.2 + - - -
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Residues in contact with PHE 628 (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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563C VAL* 4.3 6.7 - - + -
567C LEU* 5.8 3.1 - - + -
580C PHE* 4.2 21.8 - + - -
581C PRO* 3.8 25.8 - - + -
584C VAL* 3.8 28.3 - - + -
624C LEU 3.5 20.9 + - - +
625C ASP 3.5 5.6 + - - +
626C ARG 3.2 0.8 - - - -
627C GLY* 1.3 78.2 - - - +
629C TRP* 1.3 106.5 + + - +
631C THR* 3.1 20.2 - - - -
632C TYR* 3.2 48.2 - + + -
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Residues in contact with TRP 629 (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* 5.7 9.6 - - + -
580C PHE* 6.2 1.6 - + - -
581C PRO* 5.3 2.5 - - + +
625C ASP* 3.0 42.4 + - - -
626C ARG* 3.2 7.8 + - - +
628C PHE* 1.3 102.0 - + - +
630C GLU* 1.3 53.8 + - - +
631C THR 2.5 18.2 + - - -
632C TYR* 3.1 35.1 + - + +
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Residues in contact with GLU 630 (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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626C ARG 3.0 16.3 + - - +
627C GLY* 3.7 7.8 - - - +
628C PHE 3.4 0.2 - - - -
629C TRP* 1.3 72.3 - - - +
631C THR* 1.3 66.8 + - - +
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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